https://wiki.hackuarium.ch/api.php?action=feedcontributions&feedformat=atom&user=SachikoHackuarium - User contributions [en]2026-04-16T22:13:00ZUser contributionsMediaWiki 1.35.3https://wiki.hackuarium.ch/index.php?title=Pushing_the_P1&diff=8723Pushing the P12017-03-25T10:10:43Z<p>Sachiko: /* Safety */</p>
<hr />
<div>=Introduction=<br />
Having a laboratory and instruments is one thing, possessing the tools to do actual biology research is another thing. For close to two years now, the Hackuarium community has built a space, where people can work on projects related to biology among other fields. The ambition of the international DIY biology scene is to bring to the people the tools to perform and work on the whole range of biological applications, as qualitatively and cheaper than what the industrial or academic institutions do. To achieve such level, the Hackuarium lab has to be upgraded to a higher level of competency. One aspect is the P1 biosafety level where genetic manipulation opens the door to a vast range of research topic and engineering opportunities. This scientifically enriching, yet delicate step, is now in motion but in order to start practicing several items involving legal, technical and community topics have to be settled. Indeed, our laboratory practices and transparency as a citizen lab have to be absolutely irreproachable. The challenges we face are described in this document.<br><br><br />
We will prepare for the P1 work assuming it will start out in bacteria, and then depending on future demands, we imagine adding other organisms.<br><br><br />
[[File:Map 33.png|600px|thumb|center|The future lab configuration]]<br />
= Abreviations =<br />
Biological safety level 1 lab (P1), biosafety officer (BSO), standard operating procedure (SOP),<br />
<br />
=Timeline=<br />
Here is the basic timeline we will try to keep in order to make the project move on. It is obviously a "best case scenario" approximation.<br />
[[File:P1_timeline.PNG|1000px|thumb|center|Proposed timeline for the project]]<br><br><br />
The schedule could not be held due to renovations in the building<br />
<br />
=Critical Points=<br />
'''What we need to sort out before we start:'''<br />
<br />
'''Announce the first activities''' <br><br />
::YES, Luc has a form<br />
'''Will the enclosure be satisfactory?'''<br />
::YES, but it may be a good idea to inform the Canton <br />
'''Do we need a bio safety officer? Does this person need a specific training?'''<br />
::Legally yes! I think it is good if 2-3 people get this training, either at EPFL, or in Bern.<br />
'''Risk assessment'''<br />
::*The biological risk assessment will be made through the form each member as to fill when he creates a new genetically modified strain to ensure no pathological or harmful gene is inserted in the micro-organism. <br />
::*Chemically, any inflammable liquid will be stored in the solvent cabinet. The acids and bases will be separated in two "geographically" remote cabinets. The bottles will be stored close to ground level in a resistant container able to contain the full volume of the bottles it contains to avoid spillage. <br />
'''Waste elimination'''<br />
:: -> OK (see below)<br />
<br />
Federal Coordination Centre for Biotechnology (where you have to notify level 1 activities with GMOs):<br><br />
http://www.bafu.admin.ch/biotechnologie/01744/01745/index.html?lang=en<br><br />
<br />
BSO-Curriculum (courses for biosafety officers):<br><br />
http://www.bafu.admin.ch/biotechnologie/01744/02964/index.html?lang=en<br><br />
<br />
Cantonal authority (Vaud, contact persons)<br><br />
-Isabelle Dessaux (isabelle.dessaux@vd.ch )<br><br />
-Olivier Gianina (olivier.gianina@vd.ch )<br><br />
<br />
'''Our (very helpful) contact is:'''<br><br />
<br />
Manuela Ocaña<br><br />
Collaboratrice scientifique, PhD<br><br />
<br />
Département fédéral de l'intérieur DFI<br><br />
Office fédéral de la santé publique OFSP<br><br />
Unité de direction Santé publique<br><br />
<br />
Schwarzenburgstrasse 157, 3003 Berne<br><br />
Tél. +41 58 462 63 66<br><br />
Fax +41 58 462 62 33<br><br />
manuela.ocana@bag.admin.ch<br><br />
www.bag.admin.ch<br><br />
<br />
'''Her initial email was as follow:'''<br><br />
<br />
Bonjour,<br><br />
<br />
L’office fédéral de la santé publique (OFSP) est, en collaboration avec l’office fédéral de l’environnement (OFEV), responsable pour les aspects de sécurité biologique en Suisse. L'ordonnance sur l'utilisation des organismes en milieu confiné (ordonnance sur l’utilisation confinée, OUC ; RS 814.912) règle l'utilisation d'organismes génétiquement modifiés, pathogènes ou exotiques en milieu confiné (par ex. laboratoires de recherche, de diagnostic ou d’enseignement et développement). Cette ordonnance a pour but de protéger l’être humain, les animaux et l'environnement des menaces et atteintes possibles résultant de l’utilisation en milieu confiné de tels organismes. Les instituts, les entreprises et les organisations qui utilisent des organismes génétiquement modifiés, pathogènes ou exotiques en milieu confiné sont ainsi tenus de notifier leur activité (classes 1 et 2) ou de demander une autorisation (classes 3 et 4).<br><br />
<br />
Nous avons pris connaissance, avec grand intérêt, des informations concernant les activités et prestations proposées par votre laboratoire « Hackuarium », qui pourraient par ailleurs tomber dans le champ d’application de l’OUC. En effet, et selon le type de matériel utilisé (par ex. organismes génétiquement modifiés ou pathogènes) ainsi que la nature et l’ampleur de vos activités, ces dernières pourraient être soumises au devoir de notifier selon l’OUC. Mais avant d’entreprendre des démarches qui pourraient s’avérer finalement inutiles, je vous propose de consulter d’abord les informations disponibles sur le site du [http://www.bafu.admin.ch/biotechnologie/01744/01745/index.html?lang=fr Bureau de Biotechnologie de la Confédération] puis de reprendre contact avec nos services afin de clarifier au mieux votre situation.<br><br />
<br />
N’hésitez à me contacter en tout temps si vous avez des questions ou besoin d’informations supplémentaires.<br />
<br />
<br><br />
<br />
=Pivot Points=<br />
Here we develop and tackle down the most critical points of this project. The idea is to estimate if our space can accommodate such an infrastructure and if our community has the shoulders to carry the necessary responsibilities. The points have to be assessed keeping in mind the first standardized lab procedure that will be globally used by the lab (see generalized procedure). <br />
<br />
==Lab room and material==<br />
Here we discuss the size features and needed characteristics of the room we are going to use for the lab. We also describe a material list we would need to equip the lab to the minimum. <br />
<br />
===Room features===<br />
<br />
===Material===<br />
<br />
All the details for the material we would need is on the following doc: <br />
https://docs.google.com/spreadsheets/d/1tBvxEk4UVtvzfeW_-yR9yNbrLmC1V9IDjAPit37TzAg/edit#gid=1606970814<br />
<br />
==Waste eliminations==<br />
Here we describe who can and accepts to eliminate our wastes at what cost and try to estimate the frequency of elimination.<br />
We base the frequency on a per project base. How many liters of cultures are produced per production? How many biowaste bag can be filled in a week? etc...<br />
===Procedure===<br />
Based on: http://www.cusstr.ch/repository/138.pdf<br />
*'''Les souches non pathogènes et non modifiées génétiquement ne nécessitent pas d’inactivation.''' Les déchets liquides peuvent être éliminés dans l’évier pour autant qu’il n’y ait pas d’autres contaminants p.ex. chimiques ou radioactifs. Les déchets solides doivent être éliminés avec les déchets incinérables, avec les mêmes restrictions que les liquides.<br />
*'''Tout matériel de laboratoire contaminé par un OGM de classe 1 doit être inactivé''' avant élimination pour une '''filière de déchet normal'''. Un marquage clair des sacs à déchets biologiques doit être effectué afin de pouvoir identifier aisément les déchets autoclavés de ceux qui ne l’ont pas encore été. Par exemple, le sac auroclavé sera transféré dans un autre sac de couleur différente ne laissant plus apparaître le sigle biohazard et le contenu.<br />
*Les objets tranchants ou coupants doivent être éliminés comme déchets spéciaux.<br />
''' In english in a sentence '''<br />
Bio-waste bags have to be clearly distinguishable from other waste bags for example with the bio-hazard sign on them. Once inactivated (i.e. autoclaved) you have to package the waste in a way that it neither doesn't look nor doesn't smell disgusting or dangerous. Then you can discard it as household waste. If this is not possible, it needs to be discarded as special waste, how it is done at EPFL (white bag with red stripes).<br />
<br />
===Service providers===<br />
Since the bags of solid wastes can be eliminated through the classical way and the autoclaved liquids can be poured to the toilets the cost can be estimated negligible.<br><br />
No need for special waste removal<br><br />
<br />
==Calculated base costs==<br />
*Here we estimate the cost of starting the whole setup. <br />
*We take a standardized method which is documented lower (protocol) based only on biology with e.coli.<br />
*The costs are detailed on the doc below and is calculated on the academic standards.<br />
*The goal then is to find hacks and shortcuts to largely cut the costs and make it affordable.<br />
https://docs.google.com/spreadsheets/d/1tBvxEk4UVtvzfeW_-yR9yNbrLmC1V9IDjAPit37TzAg/edit#gid=0<br />
<br />
==Softwares and Databases==<br />
Here we discuss the gene editing softwares to design plasmids, primers and gene building blocks. A total transparency has to be implemented in order for people to follow our activities. What kind of database will we use to store the ordered primers sequences? Same for the plasmids? <br />
<br />
===Softwares===<br />
*[http://www.geneious.com Geneious] powerful but the file format is not opensource or genebank<br />
*[http://www.snapgene.com/products/snapgene_viewer/ Snapgene] never tried, anyone ?<br />
<br />
===Database===<br />
<br />
==Providers==<br />
Here we discuss the possible service providers, their costs and if they are ready to deal with us. We canot create plasmids without primers or genes and therefore need providers. We cannot confirm the authenticity of our work without a verified plasmid sequence and therefore need sequencing services.<br />
<br />
===Microbes===<br />
We have only the right to work with organisms classified as BSL1 according to Swiss Law.<br />
<br />
The first step is to check if the microbe you want to work is BSL1, go to https://www.bafu.admin.ch/bafu/fr/home/themes/biotechnologie/publications-etudes/publications/classification-des-organismes.html<br />
to find the official Swiss classification.<br />
<br />
The second step is to borrow the microbe from someone that already used it before. All BSL1 manipulations are announced to the government that makes the database freely accessible here: http://www.ecogen.ch/ecogen/Forms/Register/RegisterSearch.aspx go and find a researcher. Talking with someone that has experience on that specific microbe will be useful also to get some tips and tricks on growing conditions, etc..<br />
<br />
If nobody worked with the microbe before. It is possible to purchase a culture.<br />
One well recognised repository is ATCC: https://www.lgcstandards-atcc.org/?geo_country=ch Note: the ATCC BSL classification is American. It may differ from the Swiss one. Check the Swiss one before!<br />
<br />
===Primers===<br />
* [http://www.microsynth.ch/ Microsynth] : ~ 10.-/30 bp primer<br />
<br />
===Sequencing===<br />
*[http://www.gatc-biotech.com/fr/lp/sequencage-nextgen.html?gclid=CKzRrtTbm80CFdiZGwodBycOaA GATC]<br />
<br />
===Genes===<br />
<br />
==Legal==<br />
Hackpad first exploration document : https://hackpad.com/Wanna-go-P1--I8F1GOCYTR9 (Most of the necessary infos can be found here)<br><br />
As said previously our laboratory practices have to be irreproachable. We carry the "hacker" label and therefore, for the public opinion and the built of trust, cannot fuck around. We need to study in depth several aspects of the legislation governing genetic manipulation. <br />
===WHO===<br />
The very good lab safety manual right [http://www.who.int/csr/resources/publications/biosafety/WHO_CDS_CSR_LYO_2004_11/en/ here]<br><br />
Go through it if you have the time or are curious, safety in the lab is everybody's job.<br><br />
<br />
===Swiss legislation===<br />
On Feb 3 2016, we got some pointers from the Vice Dean of the School of Biology of UniL who passed us information from Audvion.ch (Ingénieur de sécurité MSST)<br />
<blockquote><br />
From:<br />
Objet: AVP réponse biosécurité Re: Laboratoires P1<br />
Date: 3 février 2016 13:58:56 UTC+1<br />
<br />
Pour toutes les questions de sécurité biologique (biosécurité) les règles de base sont données dans deux ordonnances doit :<br />
*OUC Ordonnance sur l'utilisation des organismes en milieu confiné https://www.admin.ch/opc/fr/classified-compilation/20100803/index.html<br />
*OPTM Ordonnance sur la protection des travailleurs contre les risques liés aux microorganismes https://www.admin.ch/opc/fr/classified-compilation/19994946/index.html<br />
<br />
Vous pouvez aussi consulter<br />
*Le site de la CUSSTR (Commission universitaire pour la santé et la sécurité au travail romande) http://cusstr.ch/fr/doc/technique/detail/?idcat=14<br />
*Un petit aide mémoire de la SUVA sur le sujet (missing link)<br />
*Vous référer au coordinateur de biosécurité BSO de votre département<br />
</blockquote><br />
<br />
On Feb 25 2016, we got some more pointers from the Office fédéral de la santé publique OFSP<br />
<blockquote><br />
L’office fédéral de la santé publique (OFSP) est, en collaboration avec l’office fédéral de l’environnement (OFEV), responsable pour les aspects de sécurité biologique en Suisse. L'ordonnance sur l'utilisation des organismes en milieu confiné (ordonnance sur l’utilisation confinée, OUC ; RS 814.912) règle l'utilisation d'organismes génétiquement modifiés, pathogènes ou exotiques en milieu confiné (par ex. laboratoires de recherche, de diagnostic ou d’enseignement et développement). Cette ordonnance a pour but de protéger l’être humain, les animaux et l'environnement des menaces et atteintes possibles résultant de l’utilisation en milieu confiné de tels organismes. Les instituts, les entreprises et les organisations qui utilisent des organismes génétiquement modifiés, pathogènes ou exotiques en milieu confiné sont ainsi tenus de notifier leur activité (classes 1 et 2) ou de demander une autorisation (classes 3 et 4).<br />
<br />
Nous avons pris connaissance, avec grand intérêt, des informations concernant les activités et prestations proposées par votre laboratoire « Hackuarium », qui pourraient par ailleurs tomber dans le champ d’application de l’OUC. En effet, et selon le type de matériel utilisé (par ex. organismes génétiquement modifiés ou pathogènes) ainsi que la nature et l’ampleur de vos activités, ces dernières pourraient être soumises au devoir de notifier selon l’OUC. Mais avant d’entreprendre des démarches qui pourraient s’avérer finalement inutiles, je vous propose de consulter d’abord les informations disponibles sur le site du Bureau de Biotechnologie de la Confédération (http://www.bafu.admin.ch/biotechnologie/01744/01745/index.html?lang=fr ) puis de reprendre contact avec nos services afin de clarifier au mieux votre situation.<br />
</blockquote><br />
<br />
===BioSafety Officier (BSO)===<br />
Courses : http://www.bafu.admin.ch/biotechnologie/01744/02964/index.html?lang=f<br />
Infos:<br />
BSO, niveau de sécurité 1 (BSL1_2016)<br><br />
Date: 9 septembre 2016 (1 jour)<br><br />
Lieu: Université de Berne<br><br />
Inscription d'ici au 30 juin 2016 à: registration@curriculum-biosafety.ch<br><br />
Coûts: 550 francs par personne<br><br />
Langue: anglais<br><br />
<br />
===Annonce confédération===<br />
Through the [http://www.bafu.admin.ch/biotechnologie/01744/03225/index.html?lang=fr BAFU portail]<br />
<br />
===Norms===<br />
<br><br><br />
<br />
=Generalized procedure=<br />
These procedure will be implemented in the lab as first benchmark in order to have a work basis. <br><br />
The "project request" procedure will be a way to ensure complete transparency and applicability. It will have to be filled before any project can start by any member willing to perform GMO activities. <br><br />
<br />
They are optimized for cost & material efficiency. <br />
==Maximal Culture Size==<br />
Technically the space does not allow us yet to use flasks over a volume of 500ml (incubator volume). A culture grows well at a fifth of the total volume (oxigenation requisit) which theoretically makes it 100ml culture. Safety wise, using a rather small enclosed space, spills have to stay managable. To avoid bacterial spread outside of the enclosure a maximal volume of populated medium of 200ml per flask is allowed. A maximal volume of 1L in total, populated or sterile medium, is allowed.<br />
<br />
==Spill management==<br />
Droping a vial containing liquid is common. In a lab if not prpoerly handled a spill can have more dramatic effects than droping your milk at home. Here we depict the SOP for the 4 types of spills that happen with their respective anti-spill kits; acidic, basic, contaminated and neutral spills.<br />
<br />
*1. Alert your collaborators<br />
*2. Unplug and turn-off all proximate electric equipment. <br />
*3. Follow the procedure describing your situaion:<br />
:: <br />
'''Acidic spill'''<br />
<br />
==Project Request==<br />
Develop a document/wiki page as template where people will have to explain the GMO they want to produce. <br><br />
As an idea it could be a form or a wiki page that '''anybody''' could see structured as the following<br />
*Goal:<br />
:: - What is the purpose of the GMO / protein you want to create OR: What question should it help you answer<br />
::: ex: - Sense endocrine disruptors / Produce methane / Produce dyes<br />
*How does it help reach your goal<br />
::: ex: - This enzyme is known to biochemically produce red dye (add source)<br />
::: ex: - The combination of protein A,B&C could produce a sensor...<br />
*Plasmid<br />
:: - Tell which plasmid you will use (for archive purpose)<br />
:: - Give the code of the cassette you will use<br />
:: - Give the peptide translation of such cassette<br />
*Template<br />
:: - If you want to use several building blocks for you proteins, give details on the templates<br />
*Primers<br />
:: - Give the primers you are going to use to realise your clones<br />
<br />
== Storage and Nomenclature ==<br />
A recurrent behavior, often observed in institutionalized spaces, where the followup on ones item naming and storage procedure is inexistant, is the massive loss of time to find a special item belonging to a past member. Here we describe a strict naming procedure for items that is, we think, unambiguous and still logical.<br />
=== Users ===<br />
Oppositely to the Hackuarium's "P0" lab where users can come and experiment in the greatest of liberties the P1, as previously stated, will be restricted to card holders having followed an initiatory course. Each user will be registered in a database and will chose a three letter OR digit code to identify items made by himself. Example:<br />
* John Doe : joh<br />
* Martin Luther King : mlk<br />
* George Junior : gj2 <br />
This three letter acronym is practical as it is short enough to be stuck on small tubes with a descriptor i.e: joh_p7 (John Doe Plasmid 7)<br />
=== Descriptors ===<br />
In the process of producing for example a protein from scratch (from synthetic DNA) only a few items have to be stored and conserved for further use. These items often in the forms of solutions rarely exceed volumes of 200ul. Therefore the whole process of protein engineering and plasmid creation can hold in 1.5ml tubes stored in 96well cardboard freezer boxes. We list what we extimate should be conserved for further uses by other collaborators and give them a single letter code.<br />
* project/task/job : j<br />
* DNA segments : d<br />
* primers/amorces : a<br />
* plasmids : p<br />
* proteins/constructs : c<br />
* bacteria/strain : b <br />
These six items are the valuable items to be stored. The project (j) item might seem counter intuitive but makes sense in the whole nomenclature system. Let's give some examples with the hypothetical John Doe project 41 (i.e joh_j41).<br />
*He might do a plasmid (joh_j41_p1) that sadly he failed so he produced four more for sequencing (joh_j41_p2, joh_j41_p3, joh_j41_p4, joh_j41_p5).<br />
*The plasmid was a construction of a vector (joh_j41_dV) and two inserts (joh_j41_dI1, joh_j41_dI2)<br />
*The latter were made with six primers (joh_j41_a1, joh_j41_a2, joh_j41_a3, joh_j41_a4, joh_j41_a5, joh_j41_a6)<br />
*He finally made it and expressed his protein (joh_j41_c1) (Usually you only make a protein from a plasmid so if you re-express, as a 3rd batch, it later on: joh_j41_c3)<br />
The nomenclature might appear cumbersome at some point but it should make more sense once the final ''project draft'' is presented. <br />
<br />
=== Storage ===<br />
When you're in the working process, the following behavior is observed: You open the freezer, look for the box containing the items of interest (generally you have a primer box, a plasmid box, etc.), open the box and in those 96 tubes you want to find them by looking at the top of them. The "morphology" of a 1.5ml tube gives you only two options: You can write on the top only limited information. Forget about markers they will fade away unless you add transparent tape on top (which is boring). Or you can add stickers on the side of the tube that can contain more details on the content. So the following storage procedure will be observed:<br><br />
*Boxes will only contain a single type of items such as primers, plasmids or proteins. <br><br />
*Each item of whatever sort will have a unique 4 letter/digit hex code preceded by the type of item. That's roughly 65500 possibilities. This code is preceded by the adequate descriptor. Example: joh_j41_p1 (the plasmid N°1 of John's project 41) was given '''by the system''' the code p019A this is 5 letters which perfectly fit on a 1.5ml tube top if printed on a sticker. Again this looks cumbersome know but will make more sense later since the system gives and stores all the info for you.<br />
<br />
=== Job page === <br />
We presented previously the request form. This form generates for you a wiki project page or whatever online lab-book that we still have to find. The final idea is that on the server the access to these code and data is easily accessible from a terminal in the P1 lab. <br />
Here is an hypothetical [[hypo_proj | '''project job page''']] and how it should look like in the end '''after the form has been filled'''.<br><br />
When somebody works and experimentally gets the product design then he can directly fill the page or the online lab-book that should transfer the data.<br />
A final page, with experimental data filled in should look [[hypo_proj_pract | '''like this''']] <br><br />
If a page is filled with such details, reproducibility and experimental follow-up is much easier. The important point is having a strong automation of the main points so as to avoid time loss of creating manually those files (took me more than 30 min making a complete one by hand, it should not take more than 10 and should be done while doing the experiment). <br><br />
[http://wiki.hackuarium.ch/w/Form:GMO_Project » Project request form with above points is now here].<br />
<br />
==Bacterial==<br />
All of these components have to be open source.<br><br />
'''Strain''': e.coli<br><br />
'''Plasmid''': <br><br />
'''Resistance''': Ampicilin<br><br />
<br />
===DNA Amplification / Cloning===<br />
*Good old openTaq<br />
*DNA fragment purification by gel extraction. (cheap, easy, no need of DPNI enzymes)<br />
*Ligation through modified Gibson (lysed bacterial supernatant + enzymatic complementation (Exonuclease mostly), To investigate further see the [[Media:SLiCE.PDF | SLiCE]] method)<br />
*Transformation in chemo competent cells by heat shock (way cheaper than electro-competent cells)<br />
*Usual LB-agar plating with ampicilin selection<br />
*How do we purify the DNA from the cultures ? (yeah of course we can use qiagen minipreps but it's expensive...) There is an easy spermidine DNA prep that works all the times and costs nothing.<br />
<br />
===Primers production===<br />
Can we inspire ourselves from the cheap DIY peptide synthetiser and turn it to a primer systhetiser ? <br />
Source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4045704/#!po=52.8409<br />
<br />
===Cultures===<br />
*e.coli chemo competent cells will be stored in a -80°C fridge. <br />
*Transformation will be made by heat shock as described in ("doc name here"). <br />
*Classical LB-Amp plating with static overnight 37°C incubation. <br />
*Liquid cultures can be either made as:<br />
::*LB-Amp followed by IPTG induction.<br />
::(-) IPTG is expensive<br />
::(-) Monitoring of optical density requires time + UV-spectro <br />
::(-) Large volumes (1L medium in 5L flasks) for decent yields + large capacity incubator cooling to 16°C = more waste<br />
::(-) Have to centrifuge in 500ml flasks = more post-culture work.<br />
::(+) yields are often good, procedure is bulletproof<br><br />
<br />
::*Modified auto-inducible Terrific-Broth (TB-of-doom)<br />
::(-) more complex medium preparation (can still be made as large stock)<br />
::(+/-) yields are good but proteins might be hard to extract<br />
::(+) No UV monitoring ("by eye check"), after growth expression can be made at room temp.<br />
::(+) small 100ml cultures in 500ml flasks<br />
::(+) all post-culture fork can be made in 2x50 ml flasks (convenient)<br><br />
<br />
=== Protein purification===<br />
*Purification can be made by single His tag purification<br />
::*We have more than 200ml of Ni-NTA resin<br />
::*The resin can be recycled easily<br />
::*Quite simple procedure (requires 3 buffers)<br />
::(-) Single His-tag purif will not yield absolutely pure proteins<br />
<br />
<br />
*Concentration<br />
::problem remains to be solved<br />
<br />
*Storage will be done at -20°C in 40% glycerol<br />
<br />
==Yeast==<br />
Yeast specialists please provide a protocol applicable here, keep in mind cost & material optimization.<br />
<br />
=OP Greenhouse Effect=<br />
Building the P1 in a green house... I can already smell ideas fresh as spring flourishing in there...<br />
<br />
==Idea==<br />
This clever and original idea was brought to us by our master of "let's just do it it's gonna work anyways" Gustavo, congratulation to him!<br><br />
Therefore we can buy a greenhouse for a reasonable price and set it up as a P1. The size will be indeed smaller but will be enough to accomodate the transformation, growth, cell lysis and waste storage until elimination.<br><br />
Several greenhouses models are presented with a rationale on which one to pick. <br><br />
The end of the document is supplemented with tasks and points to investigate <br><br />
<br />
==Greenhouses==<br />
We indeed aim for the best size/price ratio.<br><br />
*Serre Delia, Hornbach, 11m2, 1399.- [https://www.hornbach.ch/shop/Serre-Delia-6-Allin-256x434-cm-aluminium/5624313/article.html link]<br />
:: Initial idea<br />
:: (-) Expensive<br />
:: (+) Higher at the wall/roof junction (1m40) than the others. Still 1m40 is not very high. <br><br />
*Serre Vida XL, 12.25m2, VidaXL, 399.- [https://fr.vidaxl.ch/p/40193/serre-1225-m-alu-polycarbonate link]<br />
:: (+)Free delivery<br />
:: (+)Cheap<br />
:: (-)Low at the wall/roof junction (95cm). BUT! For the price we can get 2 and add the two walls on top of the other giving 1.9m!. <br><br />
<br />
==Building Plan==<br />
OBSOLETE: will be built where the storage is drawn<br />
[[File:GH_lab.png|500px|thumb|center|Greenhouse on top]] <br><br />
We can build the greenhouse in the corner there for the following reasons:<br />
*1. We can fix it to two walls<br />
*2. Add benches in front for people working outside to see what is inside (+ safety)<br />
*3. The benches can also ensure things are not going to be leaning against the walls<br />
<br />
==Tasks==<br />
===General===<br />
*1. Members validate the idea or propose other ideas until Wed. (DONE)<br />
*2. Ordering and building all together on the 2nd of Oct. (MATERIAL RECEIVED)<br />
*3. Building zone cleaned (DONE)<br />
<br />
===Material & Orders===<br />
*1. Rearrange lab space (DONE)<br />
*2. Think about a list of vital chems and consumables that are needed and could be stored in the P1 for easier access.<br />
:: look at: https://docs.google.com/spreadsheets/d/1tBvxEk4UVtvzfeW_-yR9yNbrLmC1V9IDjAPit37TzAg/edit#gid=0 and select the vital items.<br />
*3. Get labcoats of various sizes, get hooks for those<br />
*4. Get a set of safety goggles<br />
*5. Find fridge + -20 freezer<br />
*6. Order desinfectant dispenser<br />
*7. Get 3x6 multiplugs<br />
*8. Card access system ( can use yann's raspi3)<br />
*9. Get sturdy, closable bin for solid biowaste<br />
*10. Bin for classic wastes<br />
*11. Sam, get a hell stock of printable stickers (we're gonna label the shit out of everything)<br />
*12. Organize one cupboard with:<br />
:: pcr purif kits<br />
:: miniprep kits<br />
:: gel purif kits<br />
:: 50, 12 & 1.5 ml plastic tubes<br />
:: 1, 200 & 1000ul tips<br />
:: his tag purification buffers<br />
*13. On the sterile hood, find a plexiglass that we can fix on and that will cover 2/3 of the front pannel (i.e. Will make a separation betwwen the user and the working environement<br />
*13. Order a pipetor on SMIPLES / ricardo for serological pipettes<br />
:: https://www.fr.ricardo.ch/acheter/bureau-et-commerces/autres-metiers/laboratoires/pipette-17/v/an820658344/<br />
*14. We have two benches with the glass tops: one is not held with screws, fix it, buy long enough screws (obi)<br />
*15. Clean a set of micropipettes<br />
<br />
===Safety===<br />
*1. Announce our first activity on the confederation website (Yann)<br />
*2. Design the safety standard operating procedures (SOP) such as:<br />
:: MSDS for common chemicals<br />
:: What to do if a spillage of contaminated liquid occurs (how to clean it).<br />
:: What to do if you get injured working with bacteria.<br />
:: How to eliminate wastes, liquid and solid.<br />
:: Standard lab behavior (blouse, glasses, gloves)<br />
:: Where to store: acids, bases, solvents -> Rules for using each of them (how bases and acids have to be separated separately)<br />
:: A very good example : http://ehs.berkeley.edu/standard-operating-procedures<br />
*3. Print the following decals<br />
:: Biohazard 2x<br />
:: Authorized personnel only<br />
:: "Wash your hands when done" <br />
:: "Max X users inside" (X to be defined)<br />
*4. Find an easy an accessible way to put blouses and glasses (gloves can be stored and boxes left above the bench)<br />
*5. Make instrument procedures (print and put in a folder)<br />
*6. Questions? There is a service in the DIYBio community for [http://ask.diybio.org/ Ask a Biosafety Professional]<br />
<br />
===Ideas & Concerns===<br />
*As the name says it's a greenhouse, how do we make sure it doesn't become super warm ? Can we make a cheap air cycling system ?<br />
<br />
==Lab Setup==<br />
An idea: Can be discussed<br />
[[File:GH P1.PNG|300px|thumb|center|the essential in 12m2]]</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Main_Page&diff=8438Main Page2017-02-10T08:34:39Z<p>Sachiko: /* Upcoming Hackuarium Events */</p>
<hr />
<div>Welcome to the wiki of [http://www.hackuarium.ch/ Hackuarium] community.<br />
<br />
At Hackuarium, we want to bring biology (and biologists) to the world, and the real world back to biology. Our laboratory is an excuse to meet and discuss, build and develop ideas in a neutral, open, noncompetitive and not-for-profit environment.<br />
<br />
<div><br />
''[[Hackuarium | Cliquez ici pour accéder à la version française de ce wiki.]]'' <br />
</div><br />
<br />
This page was launched during our [[1st Ever Hackuarium Wiki Sprint]] that took place on 7 December 2014. As you might notice quickly, it is a work-in-progress.<br />
<br />
Scroll down and find out what this is all about!<br />
<br />
__TOC__<br />
<br />
<br><br />
<br />
=DIY Bio=<br />
<br />
==What is DIYbio?==<br />
<br />
DIYbio (Do-It-Yourself biology) is a movement that wants to free the practice of biological research and innovation from the institutional and industrial laboratories. Pursued both by amateurs and professional biologists, DIYbio is developing low-cost and low-tech solutions to problems identified by the community.<br />
<br />
The movement is characterised by an extremely diverse set of practices and participants. Some call themselves 'biohackers', in reference to the hacker culture.<br />
<br />
[http://DIYbio.org DIYbio.org] and [http://DIYbio.eu DIYbio.eu] are the portals of the international and european communities, respectively.<br />
<br />
For more information, visit the [http://www.wikipedia.org Wikipedia] page dedicated to [https://en.wikipedia.org/wiki/DIYbio DIYbio].<br />
<br><br />
<br />
=Hackuarium=<br />
<br />
Hackuarium is a not-for-profit association aiming at democratizing science through public engagement.<br />
<br><br />
<br />
Our laboratory in Renens (Switzerland) is open to anyone sharing the values of the association and who is dedicated to follow the [http://diybio.org/codes/draft-diybio-code-of-ethics-from-european-congress/ DIYbio Europe ethical guidelines].<br />
<br />
Our projects are initiated and carried out by scientists as well as non-scientists from a variety of background. They are passionate about tinkering with biology in particular, and technology in general. Some are engineers, architects, designers, IT and computer scientists or retired professionals, but others have no scientific education. They are mostly citizens interested in open and participatory research and innovation, outside the contrains of traditional institutions.<br />
<br />
Hackuarium members want to investigate new ways of carrying out interdisciplinary research and innovation, by making their results accessible (low-cost), simple and easily reproducible (low-tech) and by promoting an open source philosophy.<br />
<br />
Hackuarium is proudly using infrastructures provided by [http://www.univercite.ch UniverCité], an unconventional innovation hub opened in May 2014. Our equipment is mostly upcycled material from institutions and industries from western Switzerland.<br />
<br />
=Who we are=<br />
<br />
Renens is a hopping hub - and our members reflect the diversity that is in and around Lausanne/Renens.<br />
<br><br />
[[People | Check us out]], and find out what makes Hackuarium a good mix.<br />
<br><br />
<br />
==Committee==<br />
<br />
The current [[Board|committee]] is composed of the following people:<br />
<br />
* President & Treasurer: [[User:luchenry | Luc Henry]]<br />
* Secretary: [[User:mmastern | Michal Masternak]]<br />
* Lab Manager: [[User:hekkcess | Yann Pierson]]<br />
* Information technology & Infrastructure: [[User:Sam | Sam Sulaimanov]]<br />
* Art and Design coordinator: [[User:Vlorenzo | Vanessa Lorenzo]]<br />
* Talent scout and evangelist: [[User:Randogp | Gianpaolo Rando]]<br />
* Events and coordinator: [[User:Alpittet | Anne-Laure Pittet]]<br />
* Member: Ana Roldan<br />
<br />
The Agenda of the last board meeting can be found [[20161128_Board_meeting | here]].<br><br><br />
<br />
==Members and Membership==<br />
<br />
Hackuarium operates on a membership basis at this current time.<br />
<br />
The monthly membership fee is 20 CHF. It gives 24/7 access to the lab.<br />
<br />
Please ask a member of the board if you want to join as a member.<br />
<br />
All events are open to anyone, including non-members.<br />
<br />
==Friends of Hackuarium==<br />
<br />
Spaces:<br />
::<li>[http://www.univercite.ch UniverCité]<br />
::<li>[http://lapaillasse.org La Paillasse, Paris]<br />
::<li>[https://lapaillassaone.wordpress.com Paillasse Saône, Lyon]<br />
<br />
Projects:<br />
::<li>[[Exodes_Urbains | Exodes Urbains]]<br />
::<li>[http://echopen.org/index.php?title=Main_Page EchOpen]<br />
::<li>[http://octanis.org Octanis]<br />
<br />
==Where we are==<br />
Hackuarium is one of the association active at UniverCité, an innovation space under construction since May 2014 in the IRL building in Renens. We have documented our working environment as it has evolved.<br><br />
As of December 2015, UniverCité regroups a laboratory, a workshop and co-working space.<br><br />
<br><br />
<br />
=Events=<br />
<br />
<br><br />
<big>'''[[Open_Hackuarium | OpenHackuarium]]: Every Wednesday, 19:00-22:00'''</big><br />
<br />
Our lab and space are open to the public. Please come and have a chat! And if you have any questions [mailto:hello@hackuarium.ch get in touch!]<br />
<br />
==Upcoming Hackuarium Events==<br />
<br><br />
:<li>'''2017.02.08''' Wednesday 19:30-21:30: [[Openhackuarium_vol._136 | General Assembly]]<br />
:<li>'''2017.02.01''' Wednesday 19:30-20:30: [[20170201_Board_meeting | Board meeting]]<br />
<br>or follow our [https://calendar.google.com/calendar/embed?src=mgvq9goephpmna0kb7rj9ipei8%40group.calendar.google.com&ctz=Europe/Zurich google calendar]<br><br />
<br />
==Other Upcoming Events at [http://www.univercite.ch UniverCité]==<br />
<br><br />
<br />
:<li>'''2016.12.09-11''' Friday-Sunday 9:30-18:30: [http://openscienceschool.org/about/co-lab-epfl/ Co-Lab Biomaterial] at EPFL & Hackuarium, apply [https://docs.google.com/forms/d/e/1FAIpQLSeRIYETBMSqWHywvLlHOgTURqD1xWU-WoihwODMF-cyG0JaXg/viewform?entry.45591608&entry.1546709342&entry.850914894&entry.1164969935&entry.1675893756 here] before November 30th!<br />
:<li>'''2016.11.25-27''' Friday-Sunday 9:30-18:30: [[Science_Hackathon_#SHUC2016 | Science Hackathon 2016]] The first ever Science Hackathon at UniverCité: let's hack research!<br />
<br />
==Other Upcoming Events==<br />
<br><br />
<br />
:<li>'''2017.02.11-12''' Friday-Saturday: The [https://food.opendata.ch Food Hackdays] by [https://fr.opendata.ch the OpenData.ch association]<br />
<br />
==Past Hackuarium Events==<br />
<br><br />
You can find the complete list of our '''past events''' [[past events | here]].<br />
<br />
<br><br />
<br />
=Projects=<br />
<br />
Here, you will find the projects going on in the Hackuarium.<br />
<br />
== Active Projects ==<br />
<br />
* [[Hacktion | Hacktion challenges]]<br />
* [[Pushing_the_P1 | The P1 project]]<br />
* [[BeerDeCoded]]<br />
* [[Living Instruments]]<br />
* [[Protein purification systems]]<br />
* [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Micro to Macro Water Pollution]] - with [http://www.hammerdirt.ch/ Hammerdirt] and [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Spectro-pointer]]<br />
* [[Darty_Monkeys]]<br />
* [[Octanis]] - with more information about their Rover / Balloon [http://octanis.org/rover here]<br />
* [[Grow%26Mix_Bioink]]<br />
* [[unmapping]]<br />
* [[AGiR! for genomic integrity]]<br />
* [[Moss Menageries with AGiR!]]<br />
* [[Open_Source_Bioreactor | Open Source Bioreactor]]<br />
* [[Bioreactor | Steady state bioreactor]]<br />
* [[Workshop_Bioprinter| Workshop Bioprinter]]<br />
<br />
== Archived Projects ==<br />
<br />
* [[Open-Food-DNA |Open-Food-DNA]]<br />
* [[Bience | Bience (Beer and Science!)]]<br />
* [[Mycelium Structures]]<br />
* [[Live Type]]<br />
* [[Projects:LivingLab Design|LivingLab Design]]<br />
* [[Projects:bioluminescence|Bioluminescence]]<br />
* [[Projects:Quantitative Anthropology|Quantitative Anthropology]]<br />
* [[Projects:Impression 3D|Impression 3D]]<br />
* [[Projects:Dépollution des stands de tirs Suisses]]<br />
* [[Incubateur bon marché]]<br />
* [[Space Seed]]<br />
* [[Reception d'images satellites]]<br />
* [[Edible wall]]<br />
* [[ZéBU CH]]<br />
* [[Compost Bacteria]]<br />
<br />
<br><br><br />
<br />
= Practical Informations =<br />
<br />
Following this [[ Media:Univercite map2-01.png | link]] you will find a general plan of Hackuarium.<br><br />
Following this [[ Media:Map 2-01.png | link]], you will find the plan of Hackuarium with the position of equipment.<br />
<br />
== [[Life_Main | Rules at Hackuarium]] ==<br />
[[Life_Main | This page ]] describe the code of conduct for Hackuarium members.<br />
<br />
<br />
==[[Create an Event! | Create an Event!]]== <br />
<br />
Wiki express for EVENT organisation: <br />
<br><br />
*Want to organise an event with particulars/companies/universities/your grandpapa and mama???? <br />
Talk to Juliette Davenne juliette@univercite.ch for checking if the space is free <br />
AND<br />
Talk to the community, to spread the word (not for permission) —> slack UC Events (best) and/or board board@hackuarium.ch<br />
<br><br />
Go for it!<br />
<br><br />
*Is it a WORKSHOP?? All the previousTalk ALSO to Marie Lou marielou.ravet@gmail.com for the workshop scheduling, she is doing the "dirty job" of scheduling everything nicely and communicate it to the whole community at UC. <br />
*Is there a SIMILAR workshop ALREADY planned? If yes, negotiate dates and: Do you target the SAME people? If yes, negotiate. If not, no problem. Maybe interesting to see what others do. <br />
*Go for it! and spread the love for tech, science, art and design. <br />
<br><br />
<br />
== [[Protocols | Protocols]] ==<br />
All the protocols that we use at Hackuarium can be found [[ BioP_Main | here ]]<br />
They are detailed and structured so that the main focus is on applications. The idea is to give crucial information on how to apply the most common techniques of the Biology toolbox. The protocols are structured as follow:<br />
::<li> A scheme describing each <br />
::<li> A brief description of the protocol and its use<br />
::<li> A description of the different ways of carrying out the protocol. Ideally there should be a description of a commercial kit and a DIY kit.<br />
::<li> A description of the safety issues and best practice<br />
::<li> Information specific to Hackuarium and where to find the components, tools and reagents.<br />
<br />
== [[Instru_Main | Instruments available]] ==<br />
[[Instru_Main | This page ]] describes all the instruments available at Hackuarium (work in progress..), their location and how to use them.<br />
<br />
== Up-to-date list of instruments we still need ==<br />
This [https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing on-line document] contains all the instruments, tools and consumables we are looking for. Our standard donation contract (French) [[Contrat_de_donation]]. If your organisation happen to discard a piece of equipment we are (or may be) looking for, [mailto:hello@hackuarium.ch contact us]!<br />
<br />
== [[Where we shop | Where we shop]] ==<br />
===Wetware===<br />
Consumables can be purchased from [http://www.huberlab.ch Huber Lab].<br />
<br />
Swiss-based [http://www.smiples.ch Smiples] has a very extensive listing of second hand laboratory and technical items. These can be bought from their online shop or from [https://www.ricardo.ch/online-shop/smiples/?SellerNickName=Smiples Ricardo].<br />
<br />
===Hardware===<br />
Options for electronic parts<br />
* [http://www.ebay.com Ebay] (international)<br />
* [http://www.aliexpress.com AliExpress] (China)<br />
* [https://www.adafruit.com Adafruit] (UK)<br />
* [http://www.seeedstudio.com/depot/ Seeedstudio] (China)<br />
* [http://www.tmart.com/ Tmart] (Hong Kong)<br />
* [https://www.pi-shop.ch/ Rasberry pi shop] (Switzerland)<br />
* [http://www.distrelec.ch/ Distrilec] (Switzerland)<br />
<br />
==How to built a new project page on our Wiki==<br />
<br />
If you want to start or edit a project page on Hackuarium's wiki, please follow these [[Editing the wiki | instructions]].<br />
<br><br />
<br />
==Library and ReadingList ==<br />
<br />
=== The DIY biology / Biohacking movement ===<br />
<li>[http://delfanti.org/biohackers/ Biohackers. The politics of open science] by Alessandro Delfanti (2013) London: Pluto Press.<br />
::[http://delfanti.org/wp-content/uploads/2013/05/Science-2014-Golinelli-521.pdf A review] by [[User:luchenry | Luc Henry]]<br />
<li>[http://link.springer.com/article/10.1186/s40504-016-0039-1 DIY-Bio – economic, epistemological and ethical implications and ambivalences] by Jozef Keulartz and Henk van den Belt (2016) Life Sciences, Society and Policy<br />
<li>[http://www.biobasedworldnews.com/biohacking-everything-you-need-to-know-about-diy-biology Biohacking] everything you need to know about diy biology, (Accessed 05.2016)<br><br />
<li>[http://www.prnewswire.com/news-releases/genspace-nyc-receives-350000-in-support-from-the-simons-foundation-300237457.html Genspace gets funding], PRNewswire, (Accessed 05.2016)<br><br />
<li>[http://www.nature.com/news/governance-learn-from-diy-biologists-1.19507 Learn from DIY biologists], Todd Kuiken, Nature, (Accessed 05.2016)<br><br />
<br />
=== Open Hardware ===<br />
<li>[http://www.nature.com/news/open-hardware-pioneers-push-for-low-cost-lab-kit-1.19518 Open-hardware, pioneers push for low-cost lab kit]Elizabeth Gibney, Nature, (Accessed 05.2016)<br><br />
<li>[http://www.appropedia.org/Open-source_Lab#Examples Appropedia] a source of DIY instruments builds, Dr. Joshua Pearce, (Accessed 05.2016)<br><br />
<li>[http://www.ohwr.org/projects/fr_pcb_mm The PCB milling machine], Open Hardware Repository, (Accessed 05.2016)<br><br />
:: [https://pt.wikiversity.org/wiki/Pesquisa:Ferramentas_livres:Work_group_for_development_of_the_hyperobject_workbench More]<br />
<li>http://www.creativeapplications.net/processing/sensortape-3d-aware-dense-sensor-network-on-a-tape/, Sensory network on a roll of tape, Filip Visnjic, (Accessed 05.2016)<br><br />
<li>[http://oceanoptics.com/product/redeye-oxygen-sensing-patches/ RedEye Oxygen Sensing Patches], Ocean Optics, (Accessed 05.2016) <br><br />
<br><br />
<br />
=== Art ===<br />
<li> [http://www.booooooom.com/2016/04/04/mattia-menchetti-gives-wasps-coloured-paper-to-create-rainbow-nests/#more-78906 Rainbow wasp nests], Mattia Menchetti, (Accessed 05.2016)<br><br />
<li> [http://thecreatorsproject.vice.com/blog/dirty-beats-hear-music-generated-from-bacteria Dirty beats] making music with bacteria, Interspecifics(Accessed 05.2016)<br><br />
::[http://www.interspecifics.cc/-/ More1], [http://www.ncbi.nlm.nih.gov/pubmed/21239171, More2], [http://www.ncbi.nlm.nih.gov/pubmed/12501293, More3]<br><br />
<br><br />
<br />
=== Ideas/Concepts/Science ===<br />
<li>[http://ideas.ted.com/a-newly-drawn-tree-of-life-reminds-us-to-question-what-we-know/ The new tree of life] TED (Accessed 05.2016)<br><br />
<li>[https://medium.com/now-of-work/the-workplace-of-the-future-work-of-today-16c58df1fa29#.zhbu0c57f Rethinking work], Yann Heurtaux, (Accessed 05.2016)<br><br />
<li>[https://www.kickstarter.com/projects/910418035/plastic-bottle-cutter That plastic bottle cutter], Pavel & Ian, (Accessed 05.2016)<br><br />
<br><br />
<br />
=== Open Source ===<br />
<li>[https://blogs.openaire.eu/?p=882 Results held hostage], Francesco Mondada, (Accessed 05.2016)<br><br />
<br><br />
<br />
== Media and Press ==<br />
<br />
* 2016.09.27 - Hackuarium is mentioned in a paper by Celia Luterbacher on citizen science: [http://www.swissinfo.ch/eng/democratisation_citizen-science--not-a-scientist--not-a-problem/42437940 Citizen science: Not a scientist? Not a problem]<br />
<br />
*2016.09.18 - [[User:Luchenry | Luc Henry]], co-founder of Hackuarium, is interviewed in this podcast on citizen science: [http://www.swissinfo.ch/eng/podcast_science-for-non-scientists/42438132 Science for non-scientists]<br />
<br />
*<br />
<br />
== Wanted ==<br />
Do you want to contribute to making Hackuarium a diverse and lively community? Check out our wanted lists:<br />
::<li>Skills<br />
::<li>Ideas<br />
::<li>[https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing Equipment]<br />
::<li>Consumables<br />
<br />
<br><br></div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Main_Page&diff=8437Main Page2017-02-10T08:34:18Z<p>Sachiko: /* Upcoming Hackuarium Events */</p>
<hr />
<div>Welcome to the wiki of [http://www.hackuarium.ch/ Hackuarium] community.<br />
<br />
At Hackuarium, we want to bring biology (and biologists) to the world, and the real world back to biology. Our laboratory is an excuse to meet and discuss, build and develop ideas in a neutral, open, noncompetitive and not-for-profit environment.<br />
<br />
<div><br />
''[[Hackuarium | Cliquez ici pour accéder à la version française de ce wiki.]]'' <br />
</div><br />
<br />
This page was launched during our [[1st Ever Hackuarium Wiki Sprint]] that took place on 7 December 2014. As you might notice quickly, it is a work-in-progress.<br />
<br />
Scroll down and find out what this is all about!<br />
<br />
__TOC__<br />
<br />
<br><br />
<br />
=DIY Bio=<br />
<br />
==What is DIYbio?==<br />
<br />
DIYbio (Do-It-Yourself biology) is a movement that wants to free the practice of biological research and innovation from the institutional and industrial laboratories. Pursued both by amateurs and professional biologists, DIYbio is developing low-cost and low-tech solutions to problems identified by the community.<br />
<br />
The movement is characterised by an extremely diverse set of practices and participants. Some call themselves 'biohackers', in reference to the hacker culture.<br />
<br />
[http://DIYbio.org DIYbio.org] and [http://DIYbio.eu DIYbio.eu] are the portals of the international and european communities, respectively.<br />
<br />
For more information, visit the [http://www.wikipedia.org Wikipedia] page dedicated to [https://en.wikipedia.org/wiki/DIYbio DIYbio].<br />
<br><br />
<br />
=Hackuarium=<br />
<br />
Hackuarium is a not-for-profit association aiming at democratizing science through public engagement.<br />
<br><br />
<br />
Our laboratory in Renens (Switzerland) is open to anyone sharing the values of the association and who is dedicated to follow the [http://diybio.org/codes/draft-diybio-code-of-ethics-from-european-congress/ DIYbio Europe ethical guidelines].<br />
<br />
Our projects are initiated and carried out by scientists as well as non-scientists from a variety of background. They are passionate about tinkering with biology in particular, and technology in general. Some are engineers, architects, designers, IT and computer scientists or retired professionals, but others have no scientific education. They are mostly citizens interested in open and participatory research and innovation, outside the contrains of traditional institutions.<br />
<br />
Hackuarium members want to investigate new ways of carrying out interdisciplinary research and innovation, by making their results accessible (low-cost), simple and easily reproducible (low-tech) and by promoting an open source philosophy.<br />
<br />
Hackuarium is proudly using infrastructures provided by [http://www.univercite.ch UniverCité], an unconventional innovation hub opened in May 2014. Our equipment is mostly upcycled material from institutions and industries from western Switzerland.<br />
<br />
=Who we are=<br />
<br />
Renens is a hopping hub - and our members reflect the diversity that is in and around Lausanne/Renens.<br />
<br><br />
[[People | Check us out]], and find out what makes Hackuarium a good mix.<br />
<br><br />
<br />
==Committee==<br />
<br />
The current [[Board|committee]] is composed of the following people:<br />
<br />
* President & Treasurer: [[User:luchenry | Luc Henry]]<br />
* Secretary: [[User:mmastern | Michal Masternak]]<br />
* Lab Manager: [[User:hekkcess | Yann Pierson]]<br />
* Information technology & Infrastructure: [[User:Sam | Sam Sulaimanov]]<br />
* Art and Design coordinator: [[User:Vlorenzo | Vanessa Lorenzo]]<br />
* Talent scout and evangelist: [[User:Randogp | Gianpaolo Rando]]<br />
* Events and coordinator: [[User:Alpittet | Anne-Laure Pittet]]<br />
* Member: Ana Roldan<br />
<br />
The Agenda of the last board meeting can be found [[20161128_Board_meeting | here]].<br><br><br />
<br />
==Members and Membership==<br />
<br />
Hackuarium operates on a membership basis at this current time.<br />
<br />
The monthly membership fee is 20 CHF. It gives 24/7 access to the lab.<br />
<br />
Please ask a member of the board if you want to join as a member.<br />
<br />
All events are open to anyone, including non-members.<br />
<br />
==Friends of Hackuarium==<br />
<br />
Spaces:<br />
::<li>[http://www.univercite.ch UniverCité]<br />
::<li>[http://lapaillasse.org La Paillasse, Paris]<br />
::<li>[https://lapaillassaone.wordpress.com Paillasse Saône, Lyon]<br />
<br />
Projects:<br />
::<li>[[Exodes_Urbains | Exodes Urbains]]<br />
::<li>[http://echopen.org/index.php?title=Main_Page EchOpen]<br />
::<li>[http://octanis.org Octanis]<br />
<br />
==Where we are==<br />
Hackuarium is one of the association active at UniverCité, an innovation space under construction since May 2014 in the IRL building in Renens. We have documented our working environment as it has evolved.<br><br />
As of December 2015, UniverCité regroups a laboratory, a workshop and co-working space.<br><br />
<br><br />
<br />
=Events=<br />
<br />
<br><br />
<big>'''[[Open_Hackuarium | OpenHackuarium]]: Every Wednesday, 19:00-22:00'''</big><br />
<br />
Our lab and space are open to the public. Please come and have a chat! And if you have any questions [mailto:hello@hackuarium.ch get in touch!]<br />
<br />
==Upcoming Hackuarium Events==<br />
<br><br />
:<li>'''2017.02.08''' Wednesday 19:30-21:30: [[Openhackuarium_vol._136 | General Assembly]]<br />
:<li>'''2017.02.01''' Wednesday 19:30-20:30: [[20170201_Board_meeting | Board meeting]]<br />
<br>or follow our [https://calendar.google.com/calendar/embed?src=mgvq9goephpmna0kb7rj9ipei8%40group.calendar.google.com&ctz=Europe/Zurich | google calendar]<br><br />
<br />
==Other Upcoming Events at [http://www.univercite.ch UniverCité]==<br />
<br><br />
<br />
:<li>'''2016.12.09-11''' Friday-Sunday 9:30-18:30: [http://openscienceschool.org/about/co-lab-epfl/ Co-Lab Biomaterial] at EPFL & Hackuarium, apply [https://docs.google.com/forms/d/e/1FAIpQLSeRIYETBMSqWHywvLlHOgTURqD1xWU-WoihwODMF-cyG0JaXg/viewform?entry.45591608&entry.1546709342&entry.850914894&entry.1164969935&entry.1675893756 here] before November 30th!<br />
:<li>'''2016.11.25-27''' Friday-Sunday 9:30-18:30: [[Science_Hackathon_#SHUC2016 | Science Hackathon 2016]] The first ever Science Hackathon at UniverCité: let's hack research!<br />
<br />
==Other Upcoming Events==<br />
<br><br />
<br />
:<li>'''2017.02.11-12''' Friday-Saturday: The [https://food.opendata.ch Food Hackdays] by [https://fr.opendata.ch the OpenData.ch association]<br />
<br />
==Past Hackuarium Events==<br />
<br><br />
You can find the complete list of our '''past events''' [[past events | here]].<br />
<br />
<br><br />
<br />
=Projects=<br />
<br />
Here, you will find the projects going on in the Hackuarium.<br />
<br />
== Active Projects ==<br />
<br />
* [[Hacktion | Hacktion challenges]]<br />
* [[Pushing_the_P1 | The P1 project]]<br />
* [[BeerDeCoded]]<br />
* [[Living Instruments]]<br />
* [[Protein purification systems]]<br />
* [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Micro to Macro Water Pollution]] - with [http://www.hammerdirt.ch/ Hammerdirt] and [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Spectro-pointer]]<br />
* [[Darty_Monkeys]]<br />
* [[Octanis]] - with more information about their Rover / Balloon [http://octanis.org/rover here]<br />
* [[Grow%26Mix_Bioink]]<br />
* [[unmapping]]<br />
* [[AGiR! for genomic integrity]]<br />
* [[Moss Menageries with AGiR!]]<br />
* [[Open_Source_Bioreactor | Open Source Bioreactor]]<br />
* [[Bioreactor | Steady state bioreactor]]<br />
* [[Workshop_Bioprinter| Workshop Bioprinter]]<br />
<br />
== Archived Projects ==<br />
<br />
* [[Open-Food-DNA |Open-Food-DNA]]<br />
* [[Bience | Bience (Beer and Science!)]]<br />
* [[Mycelium Structures]]<br />
* [[Live Type]]<br />
* [[Projects:LivingLab Design|LivingLab Design]]<br />
* [[Projects:bioluminescence|Bioluminescence]]<br />
* [[Projects:Quantitative Anthropology|Quantitative Anthropology]]<br />
* [[Projects:Impression 3D|Impression 3D]]<br />
* [[Projects:Dépollution des stands de tirs Suisses]]<br />
* [[Incubateur bon marché]]<br />
* [[Space Seed]]<br />
* [[Reception d'images satellites]]<br />
* [[Edible wall]]<br />
* [[ZéBU CH]]<br />
* [[Compost Bacteria]]<br />
<br />
<br><br><br />
<br />
= Practical Informations =<br />
<br />
Following this [[ Media:Univercite map2-01.png | link]] you will find a general plan of Hackuarium.<br><br />
Following this [[ Media:Map 2-01.png | link]], you will find the plan of Hackuarium with the position of equipment.<br />
<br />
== [[Life_Main | Rules at Hackuarium]] ==<br />
[[Life_Main | This page ]] describe the code of conduct for Hackuarium members.<br />
<br />
<br />
==[[Create an Event! | Create an Event!]]== <br />
<br />
Wiki express for EVENT organisation: <br />
<br><br />
*Want to organise an event with particulars/companies/universities/your grandpapa and mama???? <br />
Talk to Juliette Davenne juliette@univercite.ch for checking if the space is free <br />
AND<br />
Talk to the community, to spread the word (not for permission) —> slack UC Events (best) and/or board board@hackuarium.ch<br />
<br><br />
Go for it!<br />
<br><br />
*Is it a WORKSHOP?? All the previousTalk ALSO to Marie Lou marielou.ravet@gmail.com for the workshop scheduling, she is doing the "dirty job" of scheduling everything nicely and communicate it to the whole community at UC. <br />
*Is there a SIMILAR workshop ALREADY planned? If yes, negotiate dates and: Do you target the SAME people? If yes, negotiate. If not, no problem. Maybe interesting to see what others do. <br />
*Go for it! and spread the love for tech, science, art and design. <br />
<br><br />
<br />
== [[Protocols | Protocols]] ==<br />
All the protocols that we use at Hackuarium can be found [[ BioP_Main | here ]]<br />
They are detailed and structured so that the main focus is on applications. The idea is to give crucial information on how to apply the most common techniques of the Biology toolbox. The protocols are structured as follow:<br />
::<li> A scheme describing each <br />
::<li> A brief description of the protocol and its use<br />
::<li> A description of the different ways of carrying out the protocol. Ideally there should be a description of a commercial kit and a DIY kit.<br />
::<li> A description of the safety issues and best practice<br />
::<li> Information specific to Hackuarium and where to find the components, tools and reagents.<br />
<br />
== [[Instru_Main | Instruments available]] ==<br />
[[Instru_Main | This page ]] describes all the instruments available at Hackuarium (work in progress..), their location and how to use them.<br />
<br />
== Up-to-date list of instruments we still need ==<br />
This [https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing on-line document] contains all the instruments, tools and consumables we are looking for. Our standard donation contract (French) [[Contrat_de_donation]]. If your organisation happen to discard a piece of equipment we are (or may be) looking for, [mailto:hello@hackuarium.ch contact us]!<br />
<br />
== [[Where we shop | Where we shop]] ==<br />
===Wetware===<br />
Consumables can be purchased from [http://www.huberlab.ch Huber Lab].<br />
<br />
Swiss-based [http://www.smiples.ch Smiples] has a very extensive listing of second hand laboratory and technical items. These can be bought from their online shop or from [https://www.ricardo.ch/online-shop/smiples/?SellerNickName=Smiples Ricardo].<br />
<br />
===Hardware===<br />
Options for electronic parts<br />
* [http://www.ebay.com Ebay] (international)<br />
* [http://www.aliexpress.com AliExpress] (China)<br />
* [https://www.adafruit.com Adafruit] (UK)<br />
* [http://www.seeedstudio.com/depot/ Seeedstudio] (China)<br />
* [http://www.tmart.com/ Tmart] (Hong Kong)<br />
* [https://www.pi-shop.ch/ Rasberry pi shop] (Switzerland)<br />
* [http://www.distrelec.ch/ Distrilec] (Switzerland)<br />
<br />
==How to built a new project page on our Wiki==<br />
<br />
If you want to start or edit a project page on Hackuarium's wiki, please follow these [[Editing the wiki | instructions]].<br />
<br><br />
<br />
==Library and ReadingList ==<br />
<br />
=== The DIY biology / Biohacking movement ===<br />
<li>[http://delfanti.org/biohackers/ Biohackers. The politics of open science] by Alessandro Delfanti (2013) London: Pluto Press.<br />
::[http://delfanti.org/wp-content/uploads/2013/05/Science-2014-Golinelli-521.pdf A review] by [[User:luchenry | Luc Henry]]<br />
<li>[http://link.springer.com/article/10.1186/s40504-016-0039-1 DIY-Bio – economic, epistemological and ethical implications and ambivalences] by Jozef Keulartz and Henk van den Belt (2016) Life Sciences, Society and Policy<br />
<li>[http://www.biobasedworldnews.com/biohacking-everything-you-need-to-know-about-diy-biology Biohacking] everything you need to know about diy biology, (Accessed 05.2016)<br><br />
<li>[http://www.prnewswire.com/news-releases/genspace-nyc-receives-350000-in-support-from-the-simons-foundation-300237457.html Genspace gets funding], PRNewswire, (Accessed 05.2016)<br><br />
<li>[http://www.nature.com/news/governance-learn-from-diy-biologists-1.19507 Learn from DIY biologists], Todd Kuiken, Nature, (Accessed 05.2016)<br><br />
<br />
=== Open Hardware ===<br />
<li>[http://www.nature.com/news/open-hardware-pioneers-push-for-low-cost-lab-kit-1.19518 Open-hardware, pioneers push for low-cost lab kit]Elizabeth Gibney, Nature, (Accessed 05.2016)<br><br />
<li>[http://www.appropedia.org/Open-source_Lab#Examples Appropedia] a source of DIY instruments builds, Dr. Joshua Pearce, (Accessed 05.2016)<br><br />
<li>[http://www.ohwr.org/projects/fr_pcb_mm The PCB milling machine], Open Hardware Repository, (Accessed 05.2016)<br><br />
:: [https://pt.wikiversity.org/wiki/Pesquisa:Ferramentas_livres:Work_group_for_development_of_the_hyperobject_workbench More]<br />
<li>http://www.creativeapplications.net/processing/sensortape-3d-aware-dense-sensor-network-on-a-tape/, Sensory network on a roll of tape, Filip Visnjic, (Accessed 05.2016)<br><br />
<li>[http://oceanoptics.com/product/redeye-oxygen-sensing-patches/ RedEye Oxygen Sensing Patches], Ocean Optics, (Accessed 05.2016) <br><br />
<br><br />
<br />
=== Art ===<br />
<li> [http://www.booooooom.com/2016/04/04/mattia-menchetti-gives-wasps-coloured-paper-to-create-rainbow-nests/#more-78906 Rainbow wasp nests], Mattia Menchetti, (Accessed 05.2016)<br><br />
<li> [http://thecreatorsproject.vice.com/blog/dirty-beats-hear-music-generated-from-bacteria Dirty beats] making music with bacteria, Interspecifics(Accessed 05.2016)<br><br />
::[http://www.interspecifics.cc/-/ More1], [http://www.ncbi.nlm.nih.gov/pubmed/21239171, More2], [http://www.ncbi.nlm.nih.gov/pubmed/12501293, More3]<br><br />
<br><br />
<br />
=== Ideas/Concepts/Science ===<br />
<li>[http://ideas.ted.com/a-newly-drawn-tree-of-life-reminds-us-to-question-what-we-know/ The new tree of life] TED (Accessed 05.2016)<br><br />
<li>[https://medium.com/now-of-work/the-workplace-of-the-future-work-of-today-16c58df1fa29#.zhbu0c57f Rethinking work], Yann Heurtaux, (Accessed 05.2016)<br><br />
<li>[https://www.kickstarter.com/projects/910418035/plastic-bottle-cutter That plastic bottle cutter], Pavel & Ian, (Accessed 05.2016)<br><br />
<br><br />
<br />
=== Open Source ===<br />
<li>[https://blogs.openaire.eu/?p=882 Results held hostage], Francesco Mondada, (Accessed 05.2016)<br><br />
<br><br />
<br />
== Media and Press ==<br />
<br />
* 2016.09.27 - Hackuarium is mentioned in a paper by Celia Luterbacher on citizen science: [http://www.swissinfo.ch/eng/democratisation_citizen-science--not-a-scientist--not-a-problem/42437940 Citizen science: Not a scientist? Not a problem]<br />
<br />
*2016.09.18 - [[User:Luchenry | Luc Henry]], co-founder of Hackuarium, is interviewed in this podcast on citizen science: [http://www.swissinfo.ch/eng/podcast_science-for-non-scientists/42438132 Science for non-scientists]<br />
<br />
*<br />
<br />
== Wanted ==<br />
Do you want to contribute to making Hackuarium a diverse and lively community? Check out our wanted lists:<br />
::<li>Skills<br />
::<li>Ideas<br />
::<li>[https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing Equipment]<br />
::<li>Consumables<br />
<br />
<br><br></div>Sachikohttps://wiki.hackuarium.ch/index.php?title=CBEMresults&diff=7403CBEMresults2016-06-29T15:33:06Z<p>Sachiko: </p>
<hr />
<div><br />
== Data from the Summer 2016 Water Quality Testing Campaign==<br />
<br />
<br />
[[file:Beach.jpg|thumb|300px|right| Vidy sampling location, June 2016.]]<br />
[[file:Vaucherelocation.jpg|thumb|300px|right|Positive control river, June 2016.]]<br />
[[file:Vaucheresign.jpg|thumb|300px|right|Sign from the beach where the positive control river flows into the lake, June 2016.]]<br />
[[file:Glovesand samples.jpg|thumb|300px|right|Labled sampling tube Vidy, June 2016.]]<br />
[[file:Capunderwater.jpg|thumb|300px|right|Collecting sample Vidy, June 2016.]]<br />
[[file:Looksready.jpg|thumb|300px|right|Removing from autoclave, Hackuarium 2016.]]<br />
[[file:Lessons.jpg|thumb|300px|right|Levine media plate pouring, Hackuarium 2016]]<br />
[[file:Grownplates.jpg|thumb|400px|right| Vidy and Vauchère 24hours, fresh Levine media plates, June 2016.]]<br />
[[file:Upclose2.png |thumb|400px|right|''E.coli'' colony from the Vauchère River on a very fresh (too wet!) Levine media plate, June 2016.]] <br />
<br />
<nowiki>Hammerdirt, Biodesign for the Real World, AGiR! and the Hackuarium are doing community based environmental monitoring, specifically testing water quality around Montreux Bay in Lake Geneva.</nowiki><br />
<br />
The first 'qualification' day to make sure the protocols and facilities were set to go was run on 7 June 2016. <br><br />
'''Qualification Day'''<br><br />
Hammerdirt volunteers met with the technical advisor from AGiR! and held a water sampling and processing 'qualification' day (Q-Day) prior to the beginning of the Water Quality Testing (WQT) pilot project.<br />
<br />
===Objectives of Q-Day ===<br />
<br />
# Combine a litter survey with the collection of water samples<br />
# Collect samples in accordance with the protocol for the WQT project<br />
# Prepare culture medium using available laboratory equipment<br />
# Collect samples without introducing contaminants<br />
# Prepare samples without introducing contaminants<br />
# Execute all tasks following laboratory safety regulations<br />
# Verify that all laboratory equipment is operational<br />
<br />
=== Meeting objectives ===<br />
<br />
The success of Q-Day was based on the response to the following questions:<br />
<br />
# Were the samples collected and plated within a 6-hour window?<br />
# Was the litter inventory completed prior to leaving the site?<br />
# Did field team observe proper hygiene and sampling protocols?<br />
# Did all laboratory equipment function? Were the team members able to use equipment?<br />
# Did the negative controls show any signs of growth? <br />
# Did the positive controls show growth in accordance with historical results?<br />
<br />
=== The survey sites for Q-Day ===<br />
<br />
# Positive control Vauchère river<br />
# Negative control : tap water<br />
# Unknown : Bay de Vidy<br />
<br />
=== Combining a litter survey with water sampling ===<br />
A comprehensive litter survey can take up to two hours (depending on the size of the beach). For the Q-day exercise hammerdirt chose a small beach (Vidy) not far from an urban center (Lausanne). Two risks were immediately identified:<br />
<br />
# Cross contamination of samples from handling litter and water sampling<br />
# Running out of time within a 6-hour window to plate the samples<br />
<br />
It was decided that initially the litter would be collected at the site by all team members and then, at the discretion of the team members, one individual would cease handling litter and collect the required samples.<br />
<br />
11:50 Litter collection and inventory<br><br />
12:50 Sample collection<br><br />
13:40 Arrival at the laboratory<br><br />
<br />
=== Collect samples in accordance with the protocol ===<br />
The location was easy to access. The team packed soap, hand sanitizer and disposable gloves specifically for water sampling operations. The designated individual ceased handling litter and washed hands with soap and water. Clean, disposable gloves were used for the sampling process. Samples were collected by wading into the water and plunging the sampling tube roughly 50cm deep. The sampling tube was uncapped underwater and filled completely. Once the sampling tube was out of the water a portion was poured off and the sampling tube was capped and put on ice. All team members washed hands and used hand sanitizer at the end of the operation.<br><br />
<br />
=== Prepare culture medium using available laboratory equipment ===<br />
For Q-Day operations we used a dehydrated culture media, eosin methylene blue agar or Levine media produced by Oxoid (product number CM0069). The culture media that was ordered and that will be used for the WQT project, ECA Check Easygel, had not arrived by the scheduled date for this exercise.<br />
Such media requires significantly more preparation and handling than the ECA Check Easygel. The following steps needed to be completed prior to plating (within the 6-hour limit):<br />
<br />
# Suspend 37.5g in 1 litre of distilled water. <br />
# Bring to a boil to dissolve completely. <br />
# Sterilise by autoclaving at 121°C for 15 minutes. <br />
# Cool to 60°C<br />
# Shake the medium in order to oxidise the methylene blue<br />
# Pour medium into sterile petri dishes<br />
# Cool medium to solid and introduce water samples<br />
# Prepare samples without introducing contaminants<br />
<br />
Collected samples were stored in the laboratory specimen refrigerator at 4c while the chromogenic medium was prepared. The work surface, a fume hood, was sterilized with 70% ethanol prior to pouring the chromogenic media into disposable, sterile petri dishes. The surface was sterilized again prior to plating of the water samples.<br />
<br><br><br />
Sterile, disposable pipettes were used and changed for each water sample. Participants used disposable latex gloves and a Bunsen burner was lit during all pouring and plating operations.<br />
<br><br><br />
Three samples from the positive control and the unknown were plated as well as one sample from the negative control (tap water).<br />
Plated samples were covered and placed in the incubator at 37<sup>o</sup>C for 24hours.<br />
<br />
=== Were the objectives met? ===<br />
# ''Were the samples collected and plated within a 6-hour window?'' '''Yes, samples were collected at 12:50 and plated at 18:30.'''<br />
# ''Was the litter inventory completed prior to leaving the site?'' '''Yes the results can be seen here :[https://kc.kobotoolbox.org/hammerdirt/forms/Veveyse/instance#/1124418 Vidy inventory]<br />
# ''Did field team observe proper hygiene and sampling protocols?'' '''Yes, field participants prepared and utilized a field hygiene kit including soap, hand sanitizer and disposable gloves. The depth of water sample was observed.'''<br />
# ''Did all laboratory equipment function? Were the team members able to use equipment?'' '''Yes, although prior organization and identification of the proper functioning equipment could have reduced the preparation time.''' <br />
# ''Did the negative controls show any signs of growth?'' '''No, the negative controls exhibited no growth. Indicating that no contamination occurred during sample handling and processing.'''<br />
# ''Did the positive controls show growth in accordance with historical results?'' '''Yes, in accordance with the experience of the technical advisor.'''<br />
<br><br />
<br />
=== Remarks ===<br />
# Field staff will need to organize activities appropriately especially in regards to the times required to inventory litter and the 6-hour time limit for water samples. <br />
# A bottle of water should be included in the field hygiene kit to rinse hands. <br />
# A dedicated space needs to be attributed in the lab for this project. <br />
# The incubator needs to be reserved ahead of time for sample processing (avoid conflicts with other projects).<br />
# The level of the fume hood should be verified, the cooled plates showed a slight unequal distribution.<br />
# A training session with ECA Check Easygel should be scheduled.<br />
<br />
=== Conclusion ===<br />
'''An opening day can be scheduled, hammerdirt staff are competent and all the necessary equipment is available at the lab.''' <br />
<gallery><br />
file:Washhands.jpg| Handwashing Vidy, June 2016.<br />
file:Pouroff.jpg|Pouring off Vidy, June 2016.<br />
file:Samples.jpg|Collected samples Vidy, June 2016.<br />
file:Onice.jpg|Samples on ice Vidy, June 2016.<br />
file:Bringtoboil.jpg|Boiling medium, June 2016.<br />
file:Makingjam.jpg|In the autoclave, June 2016.<br />
file:Oxidize.jpg|Oxidizing the medium, June 2016.<br />
file:Incubate.jpg|Incubator, June 2016.<br />
</gallery> <br />
<br><br />
<br />
=== Results of Microbiological Analyses ===<br />
<br />
The samples were removed from the incubator after 24hours of incubation at 37°C. At least 4 colony morphologies were visible on the Levine media plates, including metallic green ''E. coli'' and various purple and pink colonies, and scored.<br />
<br><br><br />
There were no visible colony forming units in the tap water or the sample taken from Vidy beach. The number colony forming units of ''E.coli'' counted from the Vauchère samples are presented in the table below.<br />
<br><br />
==== Colony forming units counted Vauchere ====<br />
{| class="wikitable"<br />
! style="text-align:left;"|Counts<br />
!Vauchere 1<br />
!Vauchere 2<br />
!Vauchere 3<br />
!Avg<br />
!Std Dev<br />
|-<br />
| AGiR! counts<br />
|style="text-align:center;"|7<br />
|style="text-align:center;"|3<br />
|style="text-align:center;"|29<br />
|style="text-align:center;"|13<br />
|style="text-align:center;"|14<br />
|-<br />
| Hammerdirt counts<br />
|style="text-align:center;"|7<br />
|style="text-align:center;"|3<br />
|style="text-align:center;"|27<br />
|style="text-align:center;"|12<br />
|style="text-align:center;"|13<br />
|}<br />
<br />
The ECA Check EasyGel material (pre-treated plates and individual liquid media bottles) arrived on June 11th. A control of 0.5ml of the same tap Water and Vauchère (saved in the refrigerator) samples were plated. With the EasyGel plates, it is much simpler to score the colony forming units than on the Levine media plates. Thank you, Hackuarium, for the microgrant!<br />
<br> <br />
[[file:Easygelplates3.jpg|thumb|650px|none| Positive and negative control samples on EasyGel medium, June 2016.]]<br />
<br><br />
<br />
[http://wiki.hackuarium.ch/w/Micro_to_Macro_Water_Pollution To go back to the initial project page ]<br />
<br />
<br />
[[Category:Projects]]<br />
[[Category:Work In Progress]]<br />
[[Category:Environment]]</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=7402Micro to Macro Water Pollution2016-06-29T15:13:41Z<p>Sachiko: /* Results */</p>
<hr />
<div>Community based environmental monitoring has been proven effective in a variety of fields, water quality monitoring by volunteers is in wide practice across North America. Four Swiss nonprofit associations use visible pollution inventories, microbiological monitoring and chemical analysis by combining classic laboratory techniques and the use of innovative bio-reporters to expand the capabilities of community based environmental monitoring.<br><br />
<br />
[[file:Sortingdebris.jpg|thumb|500px|right| hammerdirt team sorting debris at Vevey, Jan 2016. Source: MCBPII]]<br />
[[file : Pierrier.jpg |thumb|500px|right| Sorted debris Plage du Pierrier, Mar 2016. Source: MCBPII]]<br />
== Aims ==<br />
To effectively integrate more advanced and innovative water quality monitoring techniques to classic community based environmental monitoring (and trash collecting) activites.<br />
<br><br><br />
<br />
== Collaboration Defined ==<br />
{| class="wikitable"<br />
! Partner<br />
! Role<br />
|-<br />
| [http://www.genomicintegrity.org/ ACTION FOR GENOMIC INTEGRITY THROUGH RESEARCH!] <br />
| Technical oversight for the microbial assays, training of hammerdirt staff, quality control of laboratory operations and of sample processing and analyses.<br />
|-<br />
| [http://www.hackuarium.ch/fr/ HACKUARIUM]<br />
| Laboratory infrastructure and security, testing equipment and supplies for biologicals<br />
|-<br />
| [http://www.hammerdirt.ch/ HAMMERDIRT]<br />
| Collection and processing of samples, data storage and administration. Communication of analyses and results.<br />
|-<br />
| [https://biodesign.cc/ BIODESIGN.CC]<br />
| Analysis of samples for mercury, Cadmium Zinc, Alkanes and arsenic using the bio-reporters<br />
|}<br />
<br />
== Water Quality and Analysis ==<br />
=== Spring and Summer 2016 ===<br />
[[File:noswimming.jpg|thumb|right|400px|Location 5, Montreux rive gauche source : MCBPI July 2014]]<br />
==== Introduction ====<br />
<br />
One of the benefits of a “Community Based Environmental Monitoring” (CBEM) project is to expand the monitoring capacity of government agencies and engage the public in environmental stewardship. In response to questions from the public and our own professional curiosity we have decided to initiate a limited CBEM project (1) (2) .<br><br />
<br />
As part of the Montreux Clean Beach Project II (MCBPII), a water quality testing (WQT) program is being initiated at selected sites of the MCBPII. Symptoms reported by members and frequent bathers in the lake during previous summer seasons have sometimes been attributed to low bathing water quality, influenced by increased anthropogenic pressure of lakefront activities during certain times of the year. This year's WQT aims to gather microbiological and physical data over a six week period in order to test this hypothesis.<br><br />
<br />
<br />
Meetings at “La Maison de la Rivière” and the “Institut National de Recherche Agronomique” support the idea that the WQT information proposed is not regularly collected at the Haut-Lac locations covered by the MCBPII.<br><br />
<br><br />
<br />
==== Objectives ====<br />
CBEM programs are designed to educate the public, involve local citizens in environmental stewardship and provide reliable data for government and other interested organizations. In this regard the MCBPII CBEM program is no different than that of any other existing project. (2)(3)(4)(5)(6)<br><br />
<br />
Specifically, the goals for this project are to:<br />
# Collect reliable water quality data as defined by the World Water Monitoring Challenge <br />
# Enumerate the quantity of key bacteriological indicators, in particular those related to fecal contamination <br />
# Increase the skills of hammerdirt staff in regards to collecting and processing water samples<br />
# Make the obtained data free and open to use for all concerned <br />
# Inform the public about affordable and simple water monitoring techniques<br />
# Inform the public of community based resources designed to advance scientific literacy<br />
# Inform local authorities about the obtained results and help improve the situation<br />
<br><br />
More information [http://cbemn.ca/ CBEM Network]<br />
<br />
==== Deliverables ====<br />
[[File:Montreux_april_activity_opt_short-2.jpg|thumb|400px|right|Source: MCBPII Activity Report Nov 2015 - April 2016]]<br />
The objectives of a CBEM are designed to increase the monitoring capacity of current public systems and provide reliable, accessible data for the public and other government researchers. Data gathered from this project will be reported with our regular activity reports and the raw data will be available for download within 72 hours of the testing date from our repository on [https://github.com/hammerdirt/beachLitterSurveys Github] or through the KoboToolbox for the location in question. This document along with sampling protocols and all other supporting documents will be available on the wiki.<br />
<br><br><br />
Weekly results will be furnished to the CIPEL, SIGE and INRA:<br />
:# Location and number of tests<br />
:# Results of tests completed for the week<br />
An end of project report will be published in PDF format, available for interested parties, and include:<br />
:# Summary statistics and findings<br />
:# Graphs/plots<br />
:# Map overlay with densities and values<br />
:# Comparison with government supplied data (if available)<br />
:# Discussion of limitations and possible improvements to future CBEM projects<br />
<br />
More information [http://www.kobotoolbox.org/ KoboToolbox]<br />
<br />
=== Testing Materials ===<br />
==== Heavy Metals ====<br />
Bioreporters, designed and fabricated by biodesign.cc will be used to test for Alkanes, Arsenic, Mercury and Cadmium/Zinc. <br><br />
<br />
What are bioreporters ? Get some background information [http://wiki.biodesign.cc/wiki/Bioreporters_in_Pollutant_Detection here]<br />
<br />
==== Turbidity, temp, DO and PH ====<br />
Testing materials and supplies will be procured from the [http://www.monitorwater.org/ World Water Monitoring Challenge] an international program managed by the [http://www.iwa-network.org/ International Water Association] and the [http://www.wef.org/ Water Environment Federation].<br />
<br><br />
Assembled and sold by Lamotte company as a “basic test kit,” each kit includes one set of hardware and enough reagents to conduct up to 50 rounds of testing for pH, dissolved oxygen, temperature, and turbidity. Included are:<br />
# [[media : English-Spanish_Instructions.pdf |Instruction booklet]]<br />
# Sample collection jar<br />
# PH test tube<br />
# Dissolved oxygen vial<br />
# Secchi disk decal<br />
# Temperature strips (14-40°C and 0-12°C)<br />
# 50 pH reagent tablets (enough for 50 tests)<br />
# 100 Dissolved oxygen reagent tablets (enough for 50 tests)<br />
# Color chart for determining DO, pH and turbidity test results<br />
<br><br />
<br />
[[file:Eca_check_easygel_guide.pg1.jpg|thumb|right|400px|Visualizing organisms with ECA Check source: ECA Easygel guide]]<br />
==== Microbiological Analyses ====<br />
Presence and quantity of E.coli, other coli forms, Salmonella and Aeromonas will be tested using [http://www.micrologylabs.com/products/3/ECA-Check-Easygel ECA Check Easygel]. Easygel was first approved for [http://www.usawaterquality.org/ Water Watch] volunteer monitoring programs in the USA in 1999. A study released in 2009 compared the results of “Easygel” and “3M Petrifilm” used by volunteers to the results of laboratory analysis. Both methods had an overall accuracy rate above 80%. One big benefit of the Easygel format is that environmental samples of up to 5ml can be readily plated, with no worries about having to melt (and cool down!) agarose as used in standard microbial plates.(7)(8)(10)(14)<br><br />
<br />
Members of the Hackuarium laboratory have used “Easygel” in previous educational activities, thus facilitating the training of hammedirt staff and volunteers.<br />
<br />
=== Sampling Methods ===<br />
<br />
'''Water samples will be taken just below the surface (0.5m) and collected in sterile containers with a secure, air-tight lid.'''<br><br />
<br />
'''Advantage:''' simple and inexpensive, an important consideration to a program on a budget. It also does not require any special sampling apparatus. The volunteer holds a sampling container under the surface of the water, expells visible air bubbles, and closes the container under the water (to avoids losing dissolved gasses, particularly important if testing for volatile analytes).<br><br />
<br />
'''Disadvantage:''' vertical gradients of temperature, oxygen, nutrients, and algae may be missed in these near surface samples. Deep lakes have a thermal gradient in the summer, and Lac Leman has at least two thermal regions (and, possibly, at least two chemical regions as well). Even in shallow, usually well-mixed lakes, chemical gradients will develop during calm periods.<br><br />
<br />
Sampling methods by other CBEM projects : [[media:Stepenucketal2010.pdf | Stepenuck et all PDF]], [[media:Wfs-2005-01.pdf|Fact Sheet Volunteer Water Monitoring]], [[media : Moore_E_Coli.pdf | SOP Moore Creek E.coli sampling PDF]], [[media :Texasstream.pdf | Texas Sampling PDF]]<br />
<br />
==== Heavy Metals ====<br />
Two samples of 250ml will be taken and transported to the hackuarium for later analysis. One sample will be acidified to fix the heavy metals in solution.<br />
<br />
==== Turbidity, temp, DO and PH ====<br />
One sample will be taken using the container supplied with the testing kit and processed immediately. <br><br />
<br />
==== Microbiological samples ====<br />
'''Three independent samples will be taken from each designated site''' in conical tubes pre-labeled in the following manner:<br />
# Location<br />
# Date<br />
# Sample number for that day and location<br />
# Time of sample<br />
<br><br />
Once collected, the '''samples will be placed on ice and transported to the facility at Renens for plating on the ECA Check plates within 6 hours.''' Label information will be recorded in the field notes and the “KoboToolBox” for that sampling date and location.<br />
<br />
=== Processing samples and recording results ===<br />
==== Turbidity, temp, DO and PH ====<br />
The instructions provided with the kit will be followed and the results will be noted in the field manual and entered into the “KoboToolbox” form for that sampling date and location.<br />
<br />
==== Microbiological data ====<br />
One petri dish per sample will be labeled in the same manner as the sample container with the addition of the quantity of sample added to the media. A 1-5ml of sample water will be mixed into the provided gel media solution, plated and incubated for about 18 hours at the Hackuarium facility in Renens.<br><br />
<br />
After incubation, plates will be scored, counting total colony forming units (CFU), and each identifiable species (''E. coli'' CFUs will appear dark blue, other coliform CFUs will appear lighter blue-gray or blue-violet, ''Aeromonas spp.'' will appear as pink to very light pink, and ''Salmonella spp.'' will appear as turquoise colonies). Data will be reported as CFU/100ml of the original water sample.<br><br />
<br />
With values from three independent samples at each site, means and standard errors can be used to test significance of the obtained data over the course of the sampling period.<br />
<br />
=== Locations ===<br />
[[File:tweet.jpg|thumb|right|600px |Sampling locations for biological and chemical analysis, source: Sampling and analysis plan MCBPII]]<br />
Three of the five locations are currently part of the MCBPII beach-litter-survey project. Point 4 will be added to the beach litter survey by using a net to catch visible pollutants on the water surface below the boat dock. Point 3 will only be monitored for chemistry and biologicals. Correlations of the test results with the physical location of the sampling will be of great interest.<br />
<br />
<br />
<br />
To see a map of the locations that benefit from regular water quality monitoring : [http://www.vd.ch/themes/environnement/eaux/eau-de-baignade/qualite-de-leau-des-plages-cartographie/ Eau de baignade]<br />
<br />
=== Testing Schedule ===<br />
==== Calendar from biodesign.cc to be embedded here ====<br />
key dates to be defined :<br />
# [[#Qualification Day]] June 7, 2016 "Q-Day"<br />
# The Start date for the summer sampling campaign is 21 June 2016, with weekly microbiological and physical/chemical assays<br />
# Event public demonstration of sampling and plating<br />
# Event public discussion of results, improvements and future projects<br />
==== Microbiologicals ====<br />
Testing will begin about 20 June 2016, and weekly samples will be taken from locations 3, 4 and 5. A 'negative control' sample will also be obtained each week (tap water or a local drinking fountain, labelled 'eau potable'). A positive control from an urban river (like the Vuachère or other) is also planned.<br><br />
<br />
If a Tuesday afternoon testing protocol is followed over 7 weeks, the timeline would run from 21 June -2 August, require 21 sterile 15ml conical tubes for the water sampling, and 21 ECA Check EasyGel plates per site. After including a single 'negative control' for each sampling day, this will require 70 plates.<br><br />
<br />
In case there are too many bacteria to count (TMTC) from certain samples, samples will be saved at 4oC and further dilutions can be also plated and scored.<br><br />
<br />
==== Turbidity, temp, DO and PH ====<br />
Testing will begin on the Tuesday or Thursday the week the kits are received (late May). The kit contains enough reagents to conduct 50 tests, thus allowing us to monitor the locations for 10 weeks. Data will be carefully recorded, digitized and analyzed.<br><br />
<br />
==== Field Blanks ====<br />
Field blanks are used to assess potential contamination from sample handling, airborne materials, equipment, media, and other sources. A field blank usually consists of a sterile diluent sample of 2 mL that is taken to the site and poured into a properly labeled sample container during the first bacteria sampling event of that day. The blank sample is collected in the same type of container, labeled as a field blank, and handled and analyzed along with all the bacteria samples collected on that day. It is used to identify errors or contamination in sample collection and analysis.<br />
<br />
=== Data === <br />
==== Handling and storage ====<br />
The addition of water quality testing will require changes in our digital form and reporting methods. The form currently used by surveyors will change, thus separating the data in two sections, one section prior to WQT and one after. Data for the two sections will have to be merged prior to any analysis. The results of bacterial testing will be available 48-72 hours after sampling, thus adding another step to the survey. This should not, however, change the availability of the other survey results which is currently 24 hours after each survey.<br><br />
<br />
==== Data analysis and presentation ====<br />
<br />
The existing data set for MCBPII includes visible pollution surveys, hydrologic and meteorological data. With the addition of microbiological and basic water chemistry a more complete picture of the environmental status of the locations in question can be established.<br><br />
<br />
Two interpretations of the microbiological data will be used: the geometric mean and the 95th percentile. The geometric mean is in common use in North America and the 95th percentile method conforms to EU directive 2006/7/EC. Furthermore, any publicly available water quality data in the area will be presented and integrated where appropriate.<br><br />
<br />
The relationship between the results of WQT and the quantity and type of visible pollutants will be explored.<br><br />
<br />
'''How is the water currently monitored and evaluated ? '''Here is the source document from the Swiss Confederation [[media :Evaluation+des+eaux+de+baignade.pdf | Eaux de baignade]]<br />
<br />
=== Results ===<br />
'''[[CBEMresults]]''' : Here is a page which will lead to the '''results of this Community based Environmental Monitoring program (summer 2016) and further info.'''<br />
<br />
== References ==<br />
<br />
=== Sampling and Analysis in Community Based Environmental Monitoring ===<br />
# Assessing the performance of volunteers in monitoring Streams. Fore, Leska, Paulsen, Kit and O'Laughlin, Kate. Bellvue, WA : Blackwell Science, 2001, Fresh Water Biology. [[media:Fore,2001.pdf|Fore et all pdf]]<br />
# Volunteer environmental monitoring and the role of the universities : The case of Citizens Environment Watch. Savan, Beth, Morgan, Alexis and Gore, Chritopher. Toronto : s.n., June 2003, Environmental Management, Vol. 31, pp. 561-568.[[media:Savan+2003.pdf | Savan et all PDF]]<br />
# Nicholson, Emily, Ryan, Jane and Hodgkins, David. Community Data – where does the value lie? Assessing confidence limits of community collected water quality data. Victoria : Waterwatch Victoria c/o Department of Natural Resources & Environment, 2002. [[media:NicholsonEmily.pdf|Nicholson et all PDF]]<br />
# A review of citizen science and community-based environmental monitoring: issues and opportunities. Conrad, Cathy and Hilchey, Krista. [ed.] Springer. Halifax, Nova Scotia : s.n., 2010, Environ Monit Assess, pp. 273-291. [[media :Conrad-hilchey-2011-review.pdf | Conrad & Hilchey PDF]] <br />
# World water monitoring challenge. Instructions. Geneva : World water montioring Challenge, 2015. Instructions for the water monitoring test kit provided by the world water monitoring challenge.[[media : English-Spanish_Instructions.pdf | Instructions for PH, DO, temp and turbidity PDF]]<br />
# World Health Organization. Guidelines for safe recreational water environments. Geneva : World HEalth Organization, 2003. Vol. 1 Coastal and Fresh Waters. [[media:WhoGuideLines.pdf|WHO Guide Lines]]<br />
# Texas Stream Team Volunteer Water Quality Monitoring. E.coli Monitoring and Analysis Procedures. 2010. [[media :Texasstream.pdf | Texas Sampling PDF]]<br />
# Stepenuk, Kristine, et al. Volunteer monitoring of E. coli in streams of the upper Midwestern United States: a comparison of methods. [ed.] University of Wisconsin—Extension. Madison : Springer, 2010.[[media:Stepenucketal2010.pdf | Stepenuck et all PDF]]<br />
# Myers, D.N., et al. Fecal indicator bacteria (ver. 2.1). [book auth.] U.S. Geological survey. U.S. Geological Survey Techniques of Water-Resources Investigations. 2014, Vol. book 9, chap. A7, section 7.1.[[media :Fecalindicators.pdf | Myers et all PDF]] <br />
# Iowa Department of Natural Resources, Geological Survey. Citizens Monitoring Bacteria. Iowa City : s.n., 2005. Vols. Water Fact Sheet 2005-1.[[media:Wfs-2005-01.pdf|Fact Sheet Volunteer Water Monitoring]]<br />
# Arizona Department of Environmental Quality Water Quality Improvement Grant Program. Writing Effective Monitoring Plans. s.l. : Arizona department of environmental quality, 2008. TM 08-04.[[media:Writing.pdf | Guide to writing a sampling plan PDF]]<br />
# USEPA REGION 9 LABORATORY. STANDARD OPERATING PROCEDURE FOR VOLUNTEER MONITORING OF SURFACE WATERS FOR BACTERIA. Richmond : United States Environmental Agency, 2007.[[media:SOPEPARICHMOND.pdf| SOP Volunteer monitoring PDF]]<br />
# U.S. Geological Survey. National Field Manual for the collection of water quality data. 2006. Vol. Book 9. http://water.usgs.gov/owq/FieldManual/<br />
# Wolfson, Dr. Lois. E. coli Monitoring – Effective Techniques and Test Kits for Volunteers. Michigan Clean Water Corps Conference. s.l. : Michigan State University, October 16, 2007.[[media:WolfsonPresentation.pdf | Test Kit Presentation PDF]]<br />
# Epstein, Charlotte. KNOWLEDGE AND POWER IN GLOBAL ENVIRONMENTAL ACTIVISM. s.l. : International Journal of Peace Studies, 2005.[[media:Epstein_101IJPS.pdf | Epstein PDF]]<br />
# CH. Loi fédérale sur la protection des eaux. [Online] juin 1, 2014. https://www.admin.ch/opc/fr/classified-compilation/19910022/index.html#a4.<br />
# Kleehammer, Katie and Sigler, Adam. Moore Creek Volunteer Monitoring for Escherichia coli - Sampling and analysis. Bozeman : MSU Extension Water Quality, 2012.[[media : Moore_E_Coli.pdf | SOP Moore Creek E.coli sampling PDF]]<br />
# Homogeneous Distribution of Escherichia coli Measured within the Vertical Water Column of Small, Freshwater Streams. Buckalew, David, et al. Farmville, VA : Scientific Research Publishing, March 24, 2014, Water Resource and Protection, pp. 410-421. [[media : Distirbutionofecoliwatercolumn.pdf | Buckalew et all PDF]]<br />
# Micrology LAboratories. Easy Gel Method Procedure. Goshen, Indiana : s.n., 2015. Recomended procedures for chromogeinc media.[[media:Easygel_method_procedure.pdf | Procedure Easygel PDF]]<br />
# Micrology Laboratories. ECA Check Easy guide. Goshen : Manufacturers color guide for chromogenic media.[[media : Eca_check_easygel_guide.pdf | ECA guide to determining bacteria PDF]]<br />
# DIRECTIVE 2006/7/EC concerning the management of bathing water quality. European Union. Strassbourg : s.n., 2006, Official Journal of the European Union.[[media:DIRECTIVE2006EC_.pdf | Directive 2006/7/EC]]<br />
# Canfield, Daniel; Hoyer, Mark; Volunteer Lake Monitoring : Testing the Reliability of Data Collected by the Florida LakeWatch Program: Lake and Reservoir Management-March 2002 [[media : Floridalakes.pdf | Reliability of volunteer data PDF]]<br />
<br />
=== Documents from hammerdirt Clean Beach Projects ===<br />
* [[ Media : Montreux_april_activity_opt.pdf | Activity report Nov 2015 - April 2016]]<br />
* [[ Media : Pilot_project_cbem_montreux.pdf | Pilot project CBEM May 2016]]<br />
* [[Media:Clean_beach_pro_2015.pdf | Hammerdirt Clean Beach Project 2 2015 Draft]]<br />
* [[ Media : CH_OSPAR._COMPARISON_OPT.pdf | Comparison of Lake Geneva beaches to other OSPAR regions]]<br />
* [[ Media : Citizenscience.pdf | Citizen Science and litter studies (french)]]<br />
* [[ Media : MCBP1.pdf | MCBPI 2014-2015 results (French)]]<br />
* [[ Media : Plagespropres_nov2014_aout2015_opt.pdf | MCBPI 2014-2015 results (English)]]<br />
<br />
<br />
<br />
== Further Literature ==<br />
[[Media:07_phytoplancton_camp.2014.pdf | 2014 Report on Leman biomass ]] <br><br />
[[Media:Rapports_Leman_2014.pdf | 2014 Physico-chemical Leman report]]<br />
<br />
=== Relevant Links ===<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253<br />
<br />
== Documentation and Collaboration Tools ==<br />
----<br />
Agree on documentation and collaboration tools<br />
* Internal communication - hackuarium slack <br />
* Calendar? - we have a biodesign google calendar<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
== Water Collection Protocols ==<br />
----<br />
<br><br><br />
<br />
=== Coliform Bacteria Counting ===<br />
----<br />
The presence of ''E. coli'' in natural waters is a direct indication of fecal contamination. Coliform bacteria and other bacterial species can also be found in public waters and may contribute to human pathologies. There are several methods to distinguish ''E. coli'', coliform and other bacteria vs other microorganisms that may grow on an agar plate, of special interest 'chromogenic media' which contain substrates that form specific colors depending on enzymes produced by each species.<br />
==== Easy Gel ====<br />
Micrology Labs [http://www.micrologylabs.com/page/93/Coliscan-Easygel Coliscan Easygel]<br />
* Rachel asked for an offer including shipping and the 15% discount for the a coliform bacteria testing medium.<br />
* reminder request sent again 18 April to Jonathan Roth (CEO of Micrology Labs) and Doug Wengerd (who eventually answers notes to their 'info' address)<br />
[http://www.micrologylabs.com/page/95/Instructions Protocol] from the Micrology Labs<br><br />
* there have been some paying complications too, but their large scale order for 100 plates makes the 'per plate' cost half of another option <br><br />
<br />
<br />
To note: the Micrology Lab ECA Easygel plates are somewhat expensive, but can assay up to 5ml of sampled water per plate for ready scoring and disposal. Another currently proposed plate media would not only be less discriminating, but require more equipment for the sterile setup and final cleanup, and probably only allow 0.5ml to be assayed/plate. The Micrology plates are also used in other 'citizen science' campaigns and approved by regulatory bodies...<br />
<br />
==== Other Media ====<br />
* [https://en.wikipedia.org/wiki/Endo_agar Endo agar] where gram negatives are favored to grow. Fermentation of lactose in the medium by coliform bacteria gives metallic green sheen to those colonies.<br />
* [https://en.wikipedia.org/wiki/MacConkey_agar MacConkey agar] - also contains lactose and neutral red as a pH indicator, bile salts to inhibit gram-positive bacteria growth<br />
* [https://en.wikipedia.org/wiki/Sorbitol-MacConkey_agar MacConkey agar with sorbitol] is used to isolate E. coli O157, a pathogenic enteric bacteria<br />
* [https://en.wikipedia.org/wiki/Eosin_methylene_blue Eosin Methylene Blue agar] - Lactose fermenting bacteria turn a dark color, gram positive bacteria also inhibited<br />
<br />
<br />
<br><br />
==== DIY protocol ====<br />
<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br />
==== Other Methods ====<br />
* Good "travaux pratique" [http://www.bioutils.ch/protocoles/13-analyse-de-leau protocol] for bacterial counting and salts concentration from Bioutils, UNIGE <br><br />
* Other [[Media:Bacterial_counts.pdf | protocol]] proposing several direct and indirect methods <br><br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
----<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br />
<br />
=== Water Multi-meter ===<br />
----<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br><br />
<br />
== Press ==<br />
=== Short History of the Collaboration ===<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation from that day can be found here:[[media : Hammerdirt.pdf | How can we work together ?]]<br />
<br><br><br />
'''Brainstorm Results'''<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* Microbial testing - distinguish fecal contaminants and others with selective plates<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
[[Category:Projects]]<br />
[[Category:Work In Progress]]<br />
[[Category:Environment]]</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=7401Micro to Macro Water Pollution2016-06-29T15:13:24Z<p>Sachiko: /* Results */</p>
<hr />
<div>Community based environmental monitoring has been proven effective in a variety of fields, water quality monitoring by volunteers is in wide practice across North America. Four Swiss nonprofit associations use visible pollution inventories, microbiological monitoring and chemical analysis by combining classic laboratory techniques and the use of innovative bio-reporters to expand the capabilities of community based environmental monitoring.<br><br />
<br />
[[file:Sortingdebris.jpg|thumb|500px|right| hammerdirt team sorting debris at Vevey, Jan 2016. Source: MCBPII]]<br />
[[file : Pierrier.jpg |thumb|500px|right| Sorted debris Plage du Pierrier, Mar 2016. Source: MCBPII]]<br />
== Aims ==<br />
To effectively integrate more advanced and innovative water quality monitoring techniques to classic community based environmental monitoring (and trash collecting) activites.<br />
<br><br><br />
<br />
== Collaboration Defined ==<br />
{| class="wikitable"<br />
! Partner<br />
! Role<br />
|-<br />
| [http://www.genomicintegrity.org/ ACTION FOR GENOMIC INTEGRITY THROUGH RESEARCH!] <br />
| Technical oversight for the microbial assays, training of hammerdirt staff, quality control of laboratory operations and of sample processing and analyses.<br />
|-<br />
| [http://www.hackuarium.ch/fr/ HACKUARIUM]<br />
| Laboratory infrastructure and security, testing equipment and supplies for biologicals<br />
|-<br />
| [http://www.hammerdirt.ch/ HAMMERDIRT]<br />
| Collection and processing of samples, data storage and administration. Communication of analyses and results.<br />
|-<br />
| [https://biodesign.cc/ BIODESIGN.CC]<br />
| Analysis of samples for mercury, Cadmium Zinc, Alkanes and arsenic using the bio-reporters<br />
|}<br />
<br />
== Water Quality and Analysis ==<br />
=== Spring and Summer 2016 ===<br />
[[File:noswimming.jpg|thumb|right|400px|Location 5, Montreux rive gauche source : MCBPI July 2014]]<br />
==== Introduction ====<br />
<br />
One of the benefits of a “Community Based Environmental Monitoring” (CBEM) project is to expand the monitoring capacity of government agencies and engage the public in environmental stewardship. In response to questions from the public and our own professional curiosity we have decided to initiate a limited CBEM project (1) (2) .<br><br />
<br />
As part of the Montreux Clean Beach Project II (MCBPII), a water quality testing (WQT) program is being initiated at selected sites of the MCBPII. Symptoms reported by members and frequent bathers in the lake during previous summer seasons have sometimes been attributed to low bathing water quality, influenced by increased anthropogenic pressure of lakefront activities during certain times of the year. This year's WQT aims to gather microbiological and physical data over a six week period in order to test this hypothesis.<br><br />
<br />
<br />
Meetings at “La Maison de la Rivière” and the “Institut National de Recherche Agronomique” support the idea that the WQT information proposed is not regularly collected at the Haut-Lac locations covered by the MCBPII.<br><br />
<br><br />
<br />
==== Objectives ====<br />
CBEM programs are designed to educate the public, involve local citizens in environmental stewardship and provide reliable data for government and other interested organizations. In this regard the MCBPII CBEM program is no different than that of any other existing project. (2)(3)(4)(5)(6)<br><br />
<br />
Specifically, the goals for this project are to:<br />
# Collect reliable water quality data as defined by the World Water Monitoring Challenge <br />
# Enumerate the quantity of key bacteriological indicators, in particular those related to fecal contamination <br />
# Increase the skills of hammerdirt staff in regards to collecting and processing water samples<br />
# Make the obtained data free and open to use for all concerned <br />
# Inform the public about affordable and simple water monitoring techniques<br />
# Inform the public of community based resources designed to advance scientific literacy<br />
# Inform local authorities about the obtained results and help improve the situation<br />
<br><br />
More information [http://cbemn.ca/ CBEM Network]<br />
<br />
==== Deliverables ====<br />
[[File:Montreux_april_activity_opt_short-2.jpg|thumb|400px|right|Source: MCBPII Activity Report Nov 2015 - April 2016]]<br />
The objectives of a CBEM are designed to increase the monitoring capacity of current public systems and provide reliable, accessible data for the public and other government researchers. Data gathered from this project will be reported with our regular activity reports and the raw data will be available for download within 72 hours of the testing date from our repository on [https://github.com/hammerdirt/beachLitterSurveys Github] or through the KoboToolbox for the location in question. This document along with sampling protocols and all other supporting documents will be available on the wiki.<br />
<br><br><br />
Weekly results will be furnished to the CIPEL, SIGE and INRA:<br />
:# Location and number of tests<br />
:# Results of tests completed for the week<br />
An end of project report will be published in PDF format, available for interested parties, and include:<br />
:# Summary statistics and findings<br />
:# Graphs/plots<br />
:# Map overlay with densities and values<br />
:# Comparison with government supplied data (if available)<br />
:# Discussion of limitations and possible improvements to future CBEM projects<br />
<br />
More information [http://www.kobotoolbox.org/ KoboToolbox]<br />
<br />
=== Testing Materials ===<br />
==== Heavy Metals ====<br />
Bioreporters, designed and fabricated by biodesign.cc will be used to test for Alkanes, Arsenic, Mercury and Cadmium/Zinc. <br><br />
<br />
What are bioreporters ? Get some background information [http://wiki.biodesign.cc/wiki/Bioreporters_in_Pollutant_Detection here]<br />
<br />
==== Turbidity, temp, DO and PH ====<br />
Testing materials and supplies will be procured from the [http://www.monitorwater.org/ World Water Monitoring Challenge] an international program managed by the [http://www.iwa-network.org/ International Water Association] and the [http://www.wef.org/ Water Environment Federation].<br />
<br><br />
Assembled and sold by Lamotte company as a “basic test kit,” each kit includes one set of hardware and enough reagents to conduct up to 50 rounds of testing for pH, dissolved oxygen, temperature, and turbidity. Included are:<br />
# [[media : English-Spanish_Instructions.pdf |Instruction booklet]]<br />
# Sample collection jar<br />
# PH test tube<br />
# Dissolved oxygen vial<br />
# Secchi disk decal<br />
# Temperature strips (14-40°C and 0-12°C)<br />
# 50 pH reagent tablets (enough for 50 tests)<br />
# 100 Dissolved oxygen reagent tablets (enough for 50 tests)<br />
# Color chart for determining DO, pH and turbidity test results<br />
<br><br />
<br />
[[file:Eca_check_easygel_guide.pg1.jpg|thumb|right|400px|Visualizing organisms with ECA Check source: ECA Easygel guide]]<br />
==== Microbiological Analyses ====<br />
Presence and quantity of E.coli, other coli forms, Salmonella and Aeromonas will be tested using [http://www.micrologylabs.com/products/3/ECA-Check-Easygel ECA Check Easygel]. Easygel was first approved for [http://www.usawaterquality.org/ Water Watch] volunteer monitoring programs in the USA in 1999. A study released in 2009 compared the results of “Easygel” and “3M Petrifilm” used by volunteers to the results of laboratory analysis. Both methods had an overall accuracy rate above 80%. One big benefit of the Easygel format is that environmental samples of up to 5ml can be readily plated, with no worries about having to melt (and cool down!) agarose as used in standard microbial plates.(7)(8)(10)(14)<br><br />
<br />
Members of the Hackuarium laboratory have used “Easygel” in previous educational activities, thus facilitating the training of hammedirt staff and volunteers.<br />
<br />
=== Sampling Methods ===<br />
<br />
'''Water samples will be taken just below the surface (0.5m) and collected in sterile containers with a secure, air-tight lid.'''<br><br />
<br />
'''Advantage:''' simple and inexpensive, an important consideration to a program on a budget. It also does not require any special sampling apparatus. The volunteer holds a sampling container under the surface of the water, expells visible air bubbles, and closes the container under the water (to avoids losing dissolved gasses, particularly important if testing for volatile analytes).<br><br />
<br />
'''Disadvantage:''' vertical gradients of temperature, oxygen, nutrients, and algae may be missed in these near surface samples. Deep lakes have a thermal gradient in the summer, and Lac Leman has at least two thermal regions (and, possibly, at least two chemical regions as well). Even in shallow, usually well-mixed lakes, chemical gradients will develop during calm periods.<br><br />
<br />
Sampling methods by other CBEM projects : [[media:Stepenucketal2010.pdf | Stepenuck et all PDF]], [[media:Wfs-2005-01.pdf|Fact Sheet Volunteer Water Monitoring]], [[media : Moore_E_Coli.pdf | SOP Moore Creek E.coli sampling PDF]], [[media :Texasstream.pdf | Texas Sampling PDF]]<br />
<br />
==== Heavy Metals ====<br />
Two samples of 250ml will be taken and transported to the hackuarium for later analysis. One sample will be acidified to fix the heavy metals in solution.<br />
<br />
==== Turbidity, temp, DO and PH ====<br />
One sample will be taken using the container supplied with the testing kit and processed immediately. <br><br />
<br />
==== Microbiological samples ====<br />
'''Three independent samples will be taken from each designated site''' in conical tubes pre-labeled in the following manner:<br />
# Location<br />
# Date<br />
# Sample number for that day and location<br />
# Time of sample<br />
<br><br />
Once collected, the '''samples will be placed on ice and transported to the facility at Renens for plating on the ECA Check plates within 6 hours.''' Label information will be recorded in the field notes and the “KoboToolBox” for that sampling date and location.<br />
<br />
=== Processing samples and recording results ===<br />
==== Turbidity, temp, DO and PH ====<br />
The instructions provided with the kit will be followed and the results will be noted in the field manual and entered into the “KoboToolbox” form for that sampling date and location.<br />
<br />
==== Microbiological data ====<br />
One petri dish per sample will be labeled in the same manner as the sample container with the addition of the quantity of sample added to the media. A 1-5ml of sample water will be mixed into the provided gel media solution, plated and incubated for about 18 hours at the Hackuarium facility in Renens.<br><br />
<br />
After incubation, plates will be scored, counting total colony forming units (CFU), and each identifiable species (''E. coli'' CFUs will appear dark blue, other coliform CFUs will appear lighter blue-gray or blue-violet, ''Aeromonas spp.'' will appear as pink to very light pink, and ''Salmonella spp.'' will appear as turquoise colonies). Data will be reported as CFU/100ml of the original water sample.<br><br />
<br />
With values from three independent samples at each site, means and standard errors can be used to test significance of the obtained data over the course of the sampling period.<br />
<br />
=== Locations ===<br />
[[File:tweet.jpg|thumb|right|600px |Sampling locations for biological and chemical analysis, source: Sampling and analysis plan MCBPII]]<br />
Three of the five locations are currently part of the MCBPII beach-litter-survey project. Point 4 will be added to the beach litter survey by using a net to catch visible pollutants on the water surface below the boat dock. Point 3 will only be monitored for chemistry and biologicals. Correlations of the test results with the physical location of the sampling will be of great interest.<br />
<br />
<br />
<br />
To see a map of the locations that benefit from regular water quality monitoring : [http://www.vd.ch/themes/environnement/eaux/eau-de-baignade/qualite-de-leau-des-plages-cartographie/ Eau de baignade]<br />
<br />
=== Testing Schedule ===<br />
==== Calendar from biodesign.cc to be embedded here ====<br />
key dates to be defined :<br />
# [[#Qualification Day]] June 7, 2016 "Q-Day"<br />
# The Start date for the summer sampling campaign is 21 June 2016, with weekly microbiological and physical/chemical assays<br />
# Event public demonstration of sampling and plating<br />
# Event public discussion of results, improvements and future projects<br />
==== Microbiologicals ====<br />
Testing will begin about 20 June 2016, and weekly samples will be taken from locations 3, 4 and 5. A 'negative control' sample will also be obtained each week (tap water or a local drinking fountain, labelled 'eau potable'). A positive control from an urban river (like the Vuachère or other) is also planned.<br><br />
<br />
If a Tuesday afternoon testing protocol is followed over 7 weeks, the timeline would run from 21 June -2 August, require 21 sterile 15ml conical tubes for the water sampling, and 21 ECA Check EasyGel plates per site. After including a single 'negative control' for each sampling day, this will require 70 plates.<br><br />
<br />
In case there are too many bacteria to count (TMTC) from certain samples, samples will be saved at 4oC and further dilutions can be also plated and scored.<br><br />
<br />
==== Turbidity, temp, DO and PH ====<br />
Testing will begin on the Tuesday or Thursday the week the kits are received (late May). The kit contains enough reagents to conduct 50 tests, thus allowing us to monitor the locations for 10 weeks. Data will be carefully recorded, digitized and analyzed.<br><br />
<br />
==== Field Blanks ====<br />
Field blanks are used to assess potential contamination from sample handling, airborne materials, equipment, media, and other sources. A field blank usually consists of a sterile diluent sample of 2 mL that is taken to the site and poured into a properly labeled sample container during the first bacteria sampling event of that day. The blank sample is collected in the same type of container, labeled as a field blank, and handled and analyzed along with all the bacteria samples collected on that day. It is used to identify errors or contamination in sample collection and analysis.<br />
<br />
=== Data === <br />
==== Handling and storage ====<br />
The addition of water quality testing will require changes in our digital form and reporting methods. The form currently used by surveyors will change, thus separating the data in two sections, one section prior to WQT and one after. Data for the two sections will have to be merged prior to any analysis. The results of bacterial testing will be available 48-72 hours after sampling, thus adding another step to the survey. This should not, however, change the availability of the other survey results which is currently 24 hours after each survey.<br><br />
<br />
==== Data analysis and presentation ====<br />
<br />
The existing data set for MCBPII includes visible pollution surveys, hydrologic and meteorological data. With the addition of microbiological and basic water chemistry a more complete picture of the environmental status of the locations in question can be established.<br><br />
<br />
Two interpretations of the microbiological data will be used: the geometric mean and the 95th percentile. The geometric mean is in common use in North America and the 95th percentile method conforms to EU directive 2006/7/EC. Furthermore, any publicly available water quality data in the area will be presented and integrated where appropriate.<br><br />
<br />
The relationship between the results of WQT and the quantity and type of visible pollutants will be explored.<br><br />
<br />
'''How is the water currently monitored and evaluated ? '''Here is the source document from the Swiss Confederation [[media :Evaluation+des+eaux+de+baignade.pdf | Eaux de baignade]]<br />
<br />
=== Results ===<br />
[['''CBEMresults''']] : Here is a page which will lead to the '''results of this Community based Environmental Monitoring program (summer 2016) and further info.'''<br />
<br />
== References ==<br />
<br />
=== Sampling and Analysis in Community Based Environmental Monitoring ===<br />
# Assessing the performance of volunteers in monitoring Streams. Fore, Leska, Paulsen, Kit and O'Laughlin, Kate. Bellvue, WA : Blackwell Science, 2001, Fresh Water Biology. [[media:Fore,2001.pdf|Fore et all pdf]]<br />
# Volunteer environmental monitoring and the role of the universities : The case of Citizens Environment Watch. Savan, Beth, Morgan, Alexis and Gore, Chritopher. Toronto : s.n., June 2003, Environmental Management, Vol. 31, pp. 561-568.[[media:Savan+2003.pdf | Savan et all PDF]]<br />
# Nicholson, Emily, Ryan, Jane and Hodgkins, David. Community Data – where does the value lie? Assessing confidence limits of community collected water quality data. Victoria : Waterwatch Victoria c/o Department of Natural Resources & Environment, 2002. [[media:NicholsonEmily.pdf|Nicholson et all PDF]]<br />
# A review of citizen science and community-based environmental monitoring: issues and opportunities. Conrad, Cathy and Hilchey, Krista. [ed.] Springer. Halifax, Nova Scotia : s.n., 2010, Environ Monit Assess, pp. 273-291. [[media :Conrad-hilchey-2011-review.pdf | Conrad & Hilchey PDF]] <br />
# World water monitoring challenge. Instructions. Geneva : World water montioring Challenge, 2015. Instructions for the water monitoring test kit provided by the world water monitoring challenge.[[media : English-Spanish_Instructions.pdf | Instructions for PH, DO, temp and turbidity PDF]]<br />
# World Health Organization. Guidelines for safe recreational water environments. Geneva : World HEalth Organization, 2003. Vol. 1 Coastal and Fresh Waters. [[media:WhoGuideLines.pdf|WHO Guide Lines]]<br />
# Texas Stream Team Volunteer Water Quality Monitoring. E.coli Monitoring and Analysis Procedures. 2010. [[media :Texasstream.pdf | Texas Sampling PDF]]<br />
# Stepenuk, Kristine, et al. Volunteer monitoring of E. coli in streams of the upper Midwestern United States: a comparison of methods. [ed.] University of Wisconsin—Extension. Madison : Springer, 2010.[[media:Stepenucketal2010.pdf | Stepenuck et all PDF]]<br />
# Myers, D.N., et al. Fecal indicator bacteria (ver. 2.1). [book auth.] U.S. Geological survey. U.S. Geological Survey Techniques of Water-Resources Investigations. 2014, Vol. book 9, chap. A7, section 7.1.[[media :Fecalindicators.pdf | Myers et all PDF]] <br />
# Iowa Department of Natural Resources, Geological Survey. Citizens Monitoring Bacteria. Iowa City : s.n., 2005. Vols. Water Fact Sheet 2005-1.[[media:Wfs-2005-01.pdf|Fact Sheet Volunteer Water Monitoring]]<br />
# Arizona Department of Environmental Quality Water Quality Improvement Grant Program. Writing Effective Monitoring Plans. s.l. : Arizona department of environmental quality, 2008. TM 08-04.[[media:Writing.pdf | Guide to writing a sampling plan PDF]]<br />
# USEPA REGION 9 LABORATORY. STANDARD OPERATING PROCEDURE FOR VOLUNTEER MONITORING OF SURFACE WATERS FOR BACTERIA. Richmond : United States Environmental Agency, 2007.[[media:SOPEPARICHMOND.pdf| SOP Volunteer monitoring PDF]]<br />
# U.S. Geological Survey. National Field Manual for the collection of water quality data. 2006. Vol. Book 9. http://water.usgs.gov/owq/FieldManual/<br />
# Wolfson, Dr. Lois. E. coli Monitoring – Effective Techniques and Test Kits for Volunteers. Michigan Clean Water Corps Conference. s.l. : Michigan State University, October 16, 2007.[[media:WolfsonPresentation.pdf | Test Kit Presentation PDF]]<br />
# Epstein, Charlotte. KNOWLEDGE AND POWER IN GLOBAL ENVIRONMENTAL ACTIVISM. s.l. : International Journal of Peace Studies, 2005.[[media:Epstein_101IJPS.pdf | Epstein PDF]]<br />
# CH. Loi fédérale sur la protection des eaux. [Online] juin 1, 2014. https://www.admin.ch/opc/fr/classified-compilation/19910022/index.html#a4.<br />
# Kleehammer, Katie and Sigler, Adam. Moore Creek Volunteer Monitoring for Escherichia coli - Sampling and analysis. Bozeman : MSU Extension Water Quality, 2012.[[media : Moore_E_Coli.pdf | SOP Moore Creek E.coli sampling PDF]]<br />
# Homogeneous Distribution of Escherichia coli Measured within the Vertical Water Column of Small, Freshwater Streams. Buckalew, David, et al. Farmville, VA : Scientific Research Publishing, March 24, 2014, Water Resource and Protection, pp. 410-421. [[media : Distirbutionofecoliwatercolumn.pdf | Buckalew et all PDF]]<br />
# Micrology LAboratories. Easy Gel Method Procedure. Goshen, Indiana : s.n., 2015. Recomended procedures for chromogeinc media.[[media:Easygel_method_procedure.pdf | Procedure Easygel PDF]]<br />
# Micrology Laboratories. ECA Check Easy guide. Goshen : Manufacturers color guide for chromogenic media.[[media : Eca_check_easygel_guide.pdf | ECA guide to determining bacteria PDF]]<br />
# DIRECTIVE 2006/7/EC concerning the management of bathing water quality. European Union. Strassbourg : s.n., 2006, Official Journal of the European Union.[[media:DIRECTIVE2006EC_.pdf | Directive 2006/7/EC]]<br />
# Canfield, Daniel; Hoyer, Mark; Volunteer Lake Monitoring : Testing the Reliability of Data Collected by the Florida LakeWatch Program: Lake and Reservoir Management-March 2002 [[media : Floridalakes.pdf | Reliability of volunteer data PDF]]<br />
<br />
=== Documents from hammerdirt Clean Beach Projects ===<br />
* [[ Media : Montreux_april_activity_opt.pdf | Activity report Nov 2015 - April 2016]]<br />
* [[ Media : Pilot_project_cbem_montreux.pdf | Pilot project CBEM May 2016]]<br />
* [[Media:Clean_beach_pro_2015.pdf | Hammerdirt Clean Beach Project 2 2015 Draft]]<br />
* [[ Media : CH_OSPAR._COMPARISON_OPT.pdf | Comparison of Lake Geneva beaches to other OSPAR regions]]<br />
* [[ Media : Citizenscience.pdf | Citizen Science and litter studies (french)]]<br />
* [[ Media : MCBP1.pdf | MCBPI 2014-2015 results (French)]]<br />
* [[ Media : Plagespropres_nov2014_aout2015_opt.pdf | MCBPI 2014-2015 results (English)]]<br />
<br />
<br />
<br />
== Further Literature ==<br />
[[Media:07_phytoplancton_camp.2014.pdf | 2014 Report on Leman biomass ]] <br><br />
[[Media:Rapports_Leman_2014.pdf | 2014 Physico-chemical Leman report]]<br />
<br />
=== Relevant Links ===<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253<br />
<br />
== Documentation and Collaboration Tools ==<br />
----<br />
Agree on documentation and collaboration tools<br />
* Internal communication - hackuarium slack <br />
* Calendar? - we have a biodesign google calendar<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
== Water Collection Protocols ==<br />
----<br />
<br><br><br />
<br />
=== Coliform Bacteria Counting ===<br />
----<br />
The presence of ''E. coli'' in natural waters is a direct indication of fecal contamination. Coliform bacteria and other bacterial species can also be found in public waters and may contribute to human pathologies. There are several methods to distinguish ''E. coli'', coliform and other bacteria vs other microorganisms that may grow on an agar plate, of special interest 'chromogenic media' which contain substrates that form specific colors depending on enzymes produced by each species.<br />
==== Easy Gel ====<br />
Micrology Labs [http://www.micrologylabs.com/page/93/Coliscan-Easygel Coliscan Easygel]<br />
* Rachel asked for an offer including shipping and the 15% discount for the a coliform bacteria testing medium.<br />
* reminder request sent again 18 April to Jonathan Roth (CEO of Micrology Labs) and Doug Wengerd (who eventually answers notes to their 'info' address)<br />
[http://www.micrologylabs.com/page/95/Instructions Protocol] from the Micrology Labs<br><br />
* there have been some paying complications too, but their large scale order for 100 plates makes the 'per plate' cost half of another option <br><br />
<br />
<br />
To note: the Micrology Lab ECA Easygel plates are somewhat expensive, but can assay up to 5ml of sampled water per plate for ready scoring and disposal. Another currently proposed plate media would not only be less discriminating, but require more equipment for the sterile setup and final cleanup, and probably only allow 0.5ml to be assayed/plate. The Micrology plates are also used in other 'citizen science' campaigns and approved by regulatory bodies...<br />
<br />
==== Other Media ====<br />
* [https://en.wikipedia.org/wiki/Endo_agar Endo agar] where gram negatives are favored to grow. Fermentation of lactose in the medium by coliform bacteria gives metallic green sheen to those colonies.<br />
* [https://en.wikipedia.org/wiki/MacConkey_agar MacConkey agar] - also contains lactose and neutral red as a pH indicator, bile salts to inhibit gram-positive bacteria growth<br />
* [https://en.wikipedia.org/wiki/Sorbitol-MacConkey_agar MacConkey agar with sorbitol] is used to isolate E. coli O157, a pathogenic enteric bacteria<br />
* [https://en.wikipedia.org/wiki/Eosin_methylene_blue Eosin Methylene Blue agar] - Lactose fermenting bacteria turn a dark color, gram positive bacteria also inhibited<br />
<br />
<br />
<br><br />
==== DIY protocol ====<br />
<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br />
==== Other Methods ====<br />
* Good "travaux pratique" [http://www.bioutils.ch/protocoles/13-analyse-de-leau protocol] for bacterial counting and salts concentration from Bioutils, UNIGE <br><br />
* Other [[Media:Bacterial_counts.pdf | protocol]] proposing several direct and indirect methods <br><br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
----<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br />
<br />
=== Water Multi-meter ===<br />
----<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br><br />
<br />
== Press ==<br />
=== Short History of the Collaboration ===<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation from that day can be found here:[[media : Hammerdirt.pdf | How can we work together ?]]<br />
<br><br><br />
'''Brainstorm Results'''<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* Microbial testing - distinguish fecal contaminants and others with selective plates<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
[[Category:Projects]]<br />
[[Category:Work In Progress]]<br />
[[Category:Environment]]</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=7400Micro to Macro Water Pollution2016-06-29T15:13:06Z<p>Sachiko: /* Results */</p>
<hr />
<div>Community based environmental monitoring has been proven effective in a variety of fields, water quality monitoring by volunteers is in wide practice across North America. Four Swiss nonprofit associations use visible pollution inventories, microbiological monitoring and chemical analysis by combining classic laboratory techniques and the use of innovative bio-reporters to expand the capabilities of community based environmental monitoring.<br><br />
<br />
[[file:Sortingdebris.jpg|thumb|500px|right| hammerdirt team sorting debris at Vevey, Jan 2016. Source: MCBPII]]<br />
[[file : Pierrier.jpg |thumb|500px|right| Sorted debris Plage du Pierrier, Mar 2016. Source: MCBPII]]<br />
== Aims ==<br />
To effectively integrate more advanced and innovative water quality monitoring techniques to classic community based environmental monitoring (and trash collecting) activites.<br />
<br><br><br />
<br />
== Collaboration Defined ==<br />
{| class="wikitable"<br />
! Partner<br />
! Role<br />
|-<br />
| [http://www.genomicintegrity.org/ ACTION FOR GENOMIC INTEGRITY THROUGH RESEARCH!] <br />
| Technical oversight for the microbial assays, training of hammerdirt staff, quality control of laboratory operations and of sample processing and analyses.<br />
|-<br />
| [http://www.hackuarium.ch/fr/ HACKUARIUM]<br />
| Laboratory infrastructure and security, testing equipment and supplies for biologicals<br />
|-<br />
| [http://www.hammerdirt.ch/ HAMMERDIRT]<br />
| Collection and processing of samples, data storage and administration. Communication of analyses and results.<br />
|-<br />
| [https://biodesign.cc/ BIODESIGN.CC]<br />
| Analysis of samples for mercury, Cadmium Zinc, Alkanes and arsenic using the bio-reporters<br />
|}<br />
<br />
== Water Quality and Analysis ==<br />
=== Spring and Summer 2016 ===<br />
[[File:noswimming.jpg|thumb|right|400px|Location 5, Montreux rive gauche source : MCBPI July 2014]]<br />
==== Introduction ====<br />
<br />
One of the benefits of a “Community Based Environmental Monitoring” (CBEM) project is to expand the monitoring capacity of government agencies and engage the public in environmental stewardship. In response to questions from the public and our own professional curiosity we have decided to initiate a limited CBEM project (1) (2) .<br><br />
<br />
As part of the Montreux Clean Beach Project II (MCBPII), a water quality testing (WQT) program is being initiated at selected sites of the MCBPII. Symptoms reported by members and frequent bathers in the lake during previous summer seasons have sometimes been attributed to low bathing water quality, influenced by increased anthropogenic pressure of lakefront activities during certain times of the year. This year's WQT aims to gather microbiological and physical data over a six week period in order to test this hypothesis.<br><br />
<br />
<br />
Meetings at “La Maison de la Rivière” and the “Institut National de Recherche Agronomique” support the idea that the WQT information proposed is not regularly collected at the Haut-Lac locations covered by the MCBPII.<br><br />
<br><br />
<br />
==== Objectives ====<br />
CBEM programs are designed to educate the public, involve local citizens in environmental stewardship and provide reliable data for government and other interested organizations. In this regard the MCBPII CBEM program is no different than that of any other existing project. (2)(3)(4)(5)(6)<br><br />
<br />
Specifically, the goals for this project are to:<br />
# Collect reliable water quality data as defined by the World Water Monitoring Challenge <br />
# Enumerate the quantity of key bacteriological indicators, in particular those related to fecal contamination <br />
# Increase the skills of hammerdirt staff in regards to collecting and processing water samples<br />
# Make the obtained data free and open to use for all concerned <br />
# Inform the public about affordable and simple water monitoring techniques<br />
# Inform the public of community based resources designed to advance scientific literacy<br />
# Inform local authorities about the obtained results and help improve the situation<br />
<br><br />
More information [http://cbemn.ca/ CBEM Network]<br />
<br />
==== Deliverables ====<br />
[[File:Montreux_april_activity_opt_short-2.jpg|thumb|400px|right|Source: MCBPII Activity Report Nov 2015 - April 2016]]<br />
The objectives of a CBEM are designed to increase the monitoring capacity of current public systems and provide reliable, accessible data for the public and other government researchers. Data gathered from this project will be reported with our regular activity reports and the raw data will be available for download within 72 hours of the testing date from our repository on [https://github.com/hammerdirt/beachLitterSurveys Github] or through the KoboToolbox for the location in question. This document along with sampling protocols and all other supporting documents will be available on the wiki.<br />
<br><br><br />
Weekly results will be furnished to the CIPEL, SIGE and INRA:<br />
:# Location and number of tests<br />
:# Results of tests completed for the week<br />
An end of project report will be published in PDF format, available for interested parties, and include:<br />
:# Summary statistics and findings<br />
:# Graphs/plots<br />
:# Map overlay with densities and values<br />
:# Comparison with government supplied data (if available)<br />
:# Discussion of limitations and possible improvements to future CBEM projects<br />
<br />
More information [http://www.kobotoolbox.org/ KoboToolbox]<br />
<br />
=== Testing Materials ===<br />
==== Heavy Metals ====<br />
Bioreporters, designed and fabricated by biodesign.cc will be used to test for Alkanes, Arsenic, Mercury and Cadmium/Zinc. <br><br />
<br />
What are bioreporters ? Get some background information [http://wiki.biodesign.cc/wiki/Bioreporters_in_Pollutant_Detection here]<br />
<br />
==== Turbidity, temp, DO and PH ====<br />
Testing materials and supplies will be procured from the [http://www.monitorwater.org/ World Water Monitoring Challenge] an international program managed by the [http://www.iwa-network.org/ International Water Association] and the [http://www.wef.org/ Water Environment Federation].<br />
<br><br />
Assembled and sold by Lamotte company as a “basic test kit,” each kit includes one set of hardware and enough reagents to conduct up to 50 rounds of testing for pH, dissolved oxygen, temperature, and turbidity. Included are:<br />
# [[media : English-Spanish_Instructions.pdf |Instruction booklet]]<br />
# Sample collection jar<br />
# PH test tube<br />
# Dissolved oxygen vial<br />
# Secchi disk decal<br />
# Temperature strips (14-40°C and 0-12°C)<br />
# 50 pH reagent tablets (enough for 50 tests)<br />
# 100 Dissolved oxygen reagent tablets (enough for 50 tests)<br />
# Color chart for determining DO, pH and turbidity test results<br />
<br><br />
<br />
[[file:Eca_check_easygel_guide.pg1.jpg|thumb|right|400px|Visualizing organisms with ECA Check source: ECA Easygel guide]]<br />
==== Microbiological Analyses ====<br />
Presence and quantity of E.coli, other coli forms, Salmonella and Aeromonas will be tested using [http://www.micrologylabs.com/products/3/ECA-Check-Easygel ECA Check Easygel]. Easygel was first approved for [http://www.usawaterquality.org/ Water Watch] volunteer monitoring programs in the USA in 1999. A study released in 2009 compared the results of “Easygel” and “3M Petrifilm” used by volunteers to the results of laboratory analysis. Both methods had an overall accuracy rate above 80%. One big benefit of the Easygel format is that environmental samples of up to 5ml can be readily plated, with no worries about having to melt (and cool down!) agarose as used in standard microbial plates.(7)(8)(10)(14)<br><br />
<br />
Members of the Hackuarium laboratory have used “Easygel” in previous educational activities, thus facilitating the training of hammedirt staff and volunteers.<br />
<br />
=== Sampling Methods ===<br />
<br />
'''Water samples will be taken just below the surface (0.5m) and collected in sterile containers with a secure, air-tight lid.'''<br><br />
<br />
'''Advantage:''' simple and inexpensive, an important consideration to a program on a budget. It also does not require any special sampling apparatus. The volunteer holds a sampling container under the surface of the water, expells visible air bubbles, and closes the container under the water (to avoids losing dissolved gasses, particularly important if testing for volatile analytes).<br><br />
<br />
'''Disadvantage:''' vertical gradients of temperature, oxygen, nutrients, and algae may be missed in these near surface samples. Deep lakes have a thermal gradient in the summer, and Lac Leman has at least two thermal regions (and, possibly, at least two chemical regions as well). Even in shallow, usually well-mixed lakes, chemical gradients will develop during calm periods.<br><br />
<br />
Sampling methods by other CBEM projects : [[media:Stepenucketal2010.pdf | Stepenuck et all PDF]], [[media:Wfs-2005-01.pdf|Fact Sheet Volunteer Water Monitoring]], [[media : Moore_E_Coli.pdf | SOP Moore Creek E.coli sampling PDF]], [[media :Texasstream.pdf | Texas Sampling PDF]]<br />
<br />
==== Heavy Metals ====<br />
Two samples of 250ml will be taken and transported to the hackuarium for later analysis. One sample will be acidified to fix the heavy metals in solution.<br />
<br />
==== Turbidity, temp, DO and PH ====<br />
One sample will be taken using the container supplied with the testing kit and processed immediately. <br><br />
<br />
==== Microbiological samples ====<br />
'''Three independent samples will be taken from each designated site''' in conical tubes pre-labeled in the following manner:<br />
# Location<br />
# Date<br />
# Sample number for that day and location<br />
# Time of sample<br />
<br><br />
Once collected, the '''samples will be placed on ice and transported to the facility at Renens for plating on the ECA Check plates within 6 hours.''' Label information will be recorded in the field notes and the “KoboToolBox” for that sampling date and location.<br />
<br />
=== Processing samples and recording results ===<br />
==== Turbidity, temp, DO and PH ====<br />
The instructions provided with the kit will be followed and the results will be noted in the field manual and entered into the “KoboToolbox” form for that sampling date and location.<br />
<br />
==== Microbiological data ====<br />
One petri dish per sample will be labeled in the same manner as the sample container with the addition of the quantity of sample added to the media. A 1-5ml of sample water will be mixed into the provided gel media solution, plated and incubated for about 18 hours at the Hackuarium facility in Renens.<br><br />
<br />
After incubation, plates will be scored, counting total colony forming units (CFU), and each identifiable species (''E. coli'' CFUs will appear dark blue, other coliform CFUs will appear lighter blue-gray or blue-violet, ''Aeromonas spp.'' will appear as pink to very light pink, and ''Salmonella spp.'' will appear as turquoise colonies). Data will be reported as CFU/100ml of the original water sample.<br><br />
<br />
With values from three independent samples at each site, means and standard errors can be used to test significance of the obtained data over the course of the sampling period.<br />
<br />
=== Locations ===<br />
[[File:tweet.jpg|thumb|right|600px |Sampling locations for biological and chemical analysis, source: Sampling and analysis plan MCBPII]]<br />
Three of the five locations are currently part of the MCBPII beach-litter-survey project. Point 4 will be added to the beach litter survey by using a net to catch visible pollutants on the water surface below the boat dock. Point 3 will only be monitored for chemistry and biologicals. Correlations of the test results with the physical location of the sampling will be of great interest.<br />
<br />
<br />
<br />
To see a map of the locations that benefit from regular water quality monitoring : [http://www.vd.ch/themes/environnement/eaux/eau-de-baignade/qualite-de-leau-des-plages-cartographie/ Eau de baignade]<br />
<br />
=== Testing Schedule ===<br />
==== Calendar from biodesign.cc to be embedded here ====<br />
key dates to be defined :<br />
# [[#Qualification Day]] June 7, 2016 "Q-Day"<br />
# The Start date for the summer sampling campaign is 21 June 2016, with weekly microbiological and physical/chemical assays<br />
# Event public demonstration of sampling and plating<br />
# Event public discussion of results, improvements and future projects<br />
==== Microbiologicals ====<br />
Testing will begin about 20 June 2016, and weekly samples will be taken from locations 3, 4 and 5. A 'negative control' sample will also be obtained each week (tap water or a local drinking fountain, labelled 'eau potable'). A positive control from an urban river (like the Vuachère or other) is also planned.<br><br />
<br />
If a Tuesday afternoon testing protocol is followed over 7 weeks, the timeline would run from 21 June -2 August, require 21 sterile 15ml conical tubes for the water sampling, and 21 ECA Check EasyGel plates per site. After including a single 'negative control' for each sampling day, this will require 70 plates.<br><br />
<br />
In case there are too many bacteria to count (TMTC) from certain samples, samples will be saved at 4oC and further dilutions can be also plated and scored.<br><br />
<br />
==== Turbidity, temp, DO and PH ====<br />
Testing will begin on the Tuesday or Thursday the week the kits are received (late May). The kit contains enough reagents to conduct 50 tests, thus allowing us to monitor the locations for 10 weeks. Data will be carefully recorded, digitized and analyzed.<br><br />
<br />
==== Field Blanks ====<br />
Field blanks are used to assess potential contamination from sample handling, airborne materials, equipment, media, and other sources. A field blank usually consists of a sterile diluent sample of 2 mL that is taken to the site and poured into a properly labeled sample container during the first bacteria sampling event of that day. The blank sample is collected in the same type of container, labeled as a field blank, and handled and analyzed along with all the bacteria samples collected on that day. It is used to identify errors or contamination in sample collection and analysis.<br />
<br />
=== Data === <br />
==== Handling and storage ====<br />
The addition of water quality testing will require changes in our digital form and reporting methods. The form currently used by surveyors will change, thus separating the data in two sections, one section prior to WQT and one after. Data for the two sections will have to be merged prior to any analysis. The results of bacterial testing will be available 48-72 hours after sampling, thus adding another step to the survey. This should not, however, change the availability of the other survey results which is currently 24 hours after each survey.<br><br />
<br />
==== Data analysis and presentation ====<br />
<br />
The existing data set for MCBPII includes visible pollution surveys, hydrologic and meteorological data. With the addition of microbiological and basic water chemistry a more complete picture of the environmental status of the locations in question can be established.<br><br />
<br />
Two interpretations of the microbiological data will be used: the geometric mean and the 95th percentile. The geometric mean is in common use in North America and the 95th percentile method conforms to EU directive 2006/7/EC. Furthermore, any publicly available water quality data in the area will be presented and integrated where appropriate.<br><br />
<br />
The relationship between the results of WQT and the quantity and type of visible pollutants will be explored.<br><br />
<br />
'''How is the water currently monitored and evaluated ? '''Here is the source document from the Swiss Confederation [[media :Evaluation+des+eaux+de+baignade.pdf | Eaux de baignade]]<br />
<br />
=== Results ===<br />
[[CBEMresults]] Here is a page which will lead to the '''results of this Community based Environmental Monitoring program (summer 2016) and further info.'''<br />
<br />
== References ==<br />
<br />
=== Sampling and Analysis in Community Based Environmental Monitoring ===<br />
# Assessing the performance of volunteers in monitoring Streams. Fore, Leska, Paulsen, Kit and O'Laughlin, Kate. Bellvue, WA : Blackwell Science, 2001, Fresh Water Biology. [[media:Fore,2001.pdf|Fore et all pdf]]<br />
# Volunteer environmental monitoring and the role of the universities : The case of Citizens Environment Watch. Savan, Beth, Morgan, Alexis and Gore, Chritopher. Toronto : s.n., June 2003, Environmental Management, Vol. 31, pp. 561-568.[[media:Savan+2003.pdf | Savan et all PDF]]<br />
# Nicholson, Emily, Ryan, Jane and Hodgkins, David. Community Data – where does the value lie? Assessing confidence limits of community collected water quality data. Victoria : Waterwatch Victoria c/o Department of Natural Resources & Environment, 2002. [[media:NicholsonEmily.pdf|Nicholson et all PDF]]<br />
# A review of citizen science and community-based environmental monitoring: issues and opportunities. Conrad, Cathy and Hilchey, Krista. [ed.] Springer. Halifax, Nova Scotia : s.n., 2010, Environ Monit Assess, pp. 273-291. [[media :Conrad-hilchey-2011-review.pdf | Conrad & Hilchey PDF]] <br />
# World water monitoring challenge. Instructions. Geneva : World water montioring Challenge, 2015. Instructions for the water monitoring test kit provided by the world water monitoring challenge.[[media : English-Spanish_Instructions.pdf | Instructions for PH, DO, temp and turbidity PDF]]<br />
# World Health Organization. Guidelines for safe recreational water environments. Geneva : World HEalth Organization, 2003. Vol. 1 Coastal and Fresh Waters. [[media:WhoGuideLines.pdf|WHO Guide Lines]]<br />
# Texas Stream Team Volunteer Water Quality Monitoring. E.coli Monitoring and Analysis Procedures. 2010. [[media :Texasstream.pdf | Texas Sampling PDF]]<br />
# Stepenuk, Kristine, et al. Volunteer monitoring of E. coli in streams of the upper Midwestern United States: a comparison of methods. [ed.] University of Wisconsin—Extension. Madison : Springer, 2010.[[media:Stepenucketal2010.pdf | Stepenuck et all PDF]]<br />
# Myers, D.N., et al. Fecal indicator bacteria (ver. 2.1). [book auth.] U.S. Geological survey. U.S. Geological Survey Techniques of Water-Resources Investigations. 2014, Vol. book 9, chap. A7, section 7.1.[[media :Fecalindicators.pdf | Myers et all PDF]] <br />
# Iowa Department of Natural Resources, Geological Survey. Citizens Monitoring Bacteria. Iowa City : s.n., 2005. Vols. Water Fact Sheet 2005-1.[[media:Wfs-2005-01.pdf|Fact Sheet Volunteer Water Monitoring]]<br />
# Arizona Department of Environmental Quality Water Quality Improvement Grant Program. Writing Effective Monitoring Plans. s.l. : Arizona department of environmental quality, 2008. TM 08-04.[[media:Writing.pdf | Guide to writing a sampling plan PDF]]<br />
# USEPA REGION 9 LABORATORY. STANDARD OPERATING PROCEDURE FOR VOLUNTEER MONITORING OF SURFACE WATERS FOR BACTERIA. Richmond : United States Environmental Agency, 2007.[[media:SOPEPARICHMOND.pdf| SOP Volunteer monitoring PDF]]<br />
# U.S. Geological Survey. National Field Manual for the collection of water quality data. 2006. Vol. Book 9. http://water.usgs.gov/owq/FieldManual/<br />
# Wolfson, Dr. Lois. E. coli Monitoring – Effective Techniques and Test Kits for Volunteers. Michigan Clean Water Corps Conference. s.l. : Michigan State University, October 16, 2007.[[media:WolfsonPresentation.pdf | Test Kit Presentation PDF]]<br />
# Epstein, Charlotte. KNOWLEDGE AND POWER IN GLOBAL ENVIRONMENTAL ACTIVISM. s.l. : International Journal of Peace Studies, 2005.[[media:Epstein_101IJPS.pdf | Epstein PDF]]<br />
# CH. Loi fédérale sur la protection des eaux. [Online] juin 1, 2014. https://www.admin.ch/opc/fr/classified-compilation/19910022/index.html#a4.<br />
# Kleehammer, Katie and Sigler, Adam. Moore Creek Volunteer Monitoring for Escherichia coli - Sampling and analysis. Bozeman : MSU Extension Water Quality, 2012.[[media : Moore_E_Coli.pdf | SOP Moore Creek E.coli sampling PDF]]<br />
# Homogeneous Distribution of Escherichia coli Measured within the Vertical Water Column of Small, Freshwater Streams. Buckalew, David, et al. Farmville, VA : Scientific Research Publishing, March 24, 2014, Water Resource and Protection, pp. 410-421. [[media : Distirbutionofecoliwatercolumn.pdf | Buckalew et all PDF]]<br />
# Micrology LAboratories. Easy Gel Method Procedure. Goshen, Indiana : s.n., 2015. Recomended procedures for chromogeinc media.[[media:Easygel_method_procedure.pdf | Procedure Easygel PDF]]<br />
# Micrology Laboratories. ECA Check Easy guide. Goshen : Manufacturers color guide for chromogenic media.[[media : Eca_check_easygel_guide.pdf | ECA guide to determining bacteria PDF]]<br />
# DIRECTIVE 2006/7/EC concerning the management of bathing water quality. European Union. Strassbourg : s.n., 2006, Official Journal of the European Union.[[media:DIRECTIVE2006EC_.pdf | Directive 2006/7/EC]]<br />
# Canfield, Daniel; Hoyer, Mark; Volunteer Lake Monitoring : Testing the Reliability of Data Collected by the Florida LakeWatch Program: Lake and Reservoir Management-March 2002 [[media : Floridalakes.pdf | Reliability of volunteer data PDF]]<br />
<br />
=== Documents from hammerdirt Clean Beach Projects ===<br />
* [[ Media : Montreux_april_activity_opt.pdf | Activity report Nov 2015 - April 2016]]<br />
* [[ Media : Pilot_project_cbem_montreux.pdf | Pilot project CBEM May 2016]]<br />
* [[Media:Clean_beach_pro_2015.pdf | Hammerdirt Clean Beach Project 2 2015 Draft]]<br />
* [[ Media : CH_OSPAR._COMPARISON_OPT.pdf | Comparison of Lake Geneva beaches to other OSPAR regions]]<br />
* [[ Media : Citizenscience.pdf | Citizen Science and litter studies (french)]]<br />
* [[ Media : MCBP1.pdf | MCBPI 2014-2015 results (French)]]<br />
* [[ Media : Plagespropres_nov2014_aout2015_opt.pdf | MCBPI 2014-2015 results (English)]]<br />
<br />
<br />
<br />
== Further Literature ==<br />
[[Media:07_phytoplancton_camp.2014.pdf | 2014 Report on Leman biomass ]] <br><br />
[[Media:Rapports_Leman_2014.pdf | 2014 Physico-chemical Leman report]]<br />
<br />
=== Relevant Links ===<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253<br />
<br />
== Documentation and Collaboration Tools ==<br />
----<br />
Agree on documentation and collaboration tools<br />
* Internal communication - hackuarium slack <br />
* Calendar? - we have a biodesign google calendar<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
== Water Collection Protocols ==<br />
----<br />
<br><br><br />
<br />
=== Coliform Bacteria Counting ===<br />
----<br />
The presence of ''E. coli'' in natural waters is a direct indication of fecal contamination. Coliform bacteria and other bacterial species can also be found in public waters and may contribute to human pathologies. There are several methods to distinguish ''E. coli'', coliform and other bacteria vs other microorganisms that may grow on an agar plate, of special interest 'chromogenic media' which contain substrates that form specific colors depending on enzymes produced by each species.<br />
==== Easy Gel ====<br />
Micrology Labs [http://www.micrologylabs.com/page/93/Coliscan-Easygel Coliscan Easygel]<br />
* Rachel asked for an offer including shipping and the 15% discount for the a coliform bacteria testing medium.<br />
* reminder request sent again 18 April to Jonathan Roth (CEO of Micrology Labs) and Doug Wengerd (who eventually answers notes to their 'info' address)<br />
[http://www.micrologylabs.com/page/95/Instructions Protocol] from the Micrology Labs<br><br />
* there have been some paying complications too, but their large scale order for 100 plates makes the 'per plate' cost half of another option <br><br />
<br />
<br />
To note: the Micrology Lab ECA Easygel plates are somewhat expensive, but can assay up to 5ml of sampled water per plate for ready scoring and disposal. Another currently proposed plate media would not only be less discriminating, but require more equipment for the sterile setup and final cleanup, and probably only allow 0.5ml to be assayed/plate. The Micrology plates are also used in other 'citizen science' campaigns and approved by regulatory bodies...<br />
<br />
==== Other Media ====<br />
* [https://en.wikipedia.org/wiki/Endo_agar Endo agar] where gram negatives are favored to grow. Fermentation of lactose in the medium by coliform bacteria gives metallic green sheen to those colonies.<br />
* [https://en.wikipedia.org/wiki/MacConkey_agar MacConkey agar] - also contains lactose and neutral red as a pH indicator, bile salts to inhibit gram-positive bacteria growth<br />
* [https://en.wikipedia.org/wiki/Sorbitol-MacConkey_agar MacConkey agar with sorbitol] is used to isolate E. coli O157, a pathogenic enteric bacteria<br />
* [https://en.wikipedia.org/wiki/Eosin_methylene_blue Eosin Methylene Blue agar] - Lactose fermenting bacteria turn a dark color, gram positive bacteria also inhibited<br />
<br />
<br />
<br><br />
==== DIY protocol ====<br />
<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br />
==== Other Methods ====<br />
* Good "travaux pratique" [http://www.bioutils.ch/protocoles/13-analyse-de-leau protocol] for bacterial counting and salts concentration from Bioutils, UNIGE <br><br />
* Other [[Media:Bacterial_counts.pdf | protocol]] proposing several direct and indirect methods <br><br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
----<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br />
<br />
=== Water Multi-meter ===<br />
----<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br><br />
<br />
== Press ==<br />
=== Short History of the Collaboration ===<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation from that day can be found here:[[media : Hammerdirt.pdf | How can we work together ?]]<br />
<br><br><br />
'''Brainstorm Results'''<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* Microbial testing - distinguish fecal contaminants and others with selective plates<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
[[Category:Projects]]<br />
[[Category:Work In Progress]]<br />
[[Category:Environment]]</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=7327Micro to Macro Water Pollution2016-06-20T13:31:33Z<p>Sachiko: /* Were the objectives met? */</p>
<hr />
<div>Community based environmental monitoring has been proven effective in a variety of fields, water quality monitoring by volunteers is in wide practice across North America. Four Swiss nonprofit associations use visible pollution inventories, microbiological monitoring and chemical analysis by combining classic laboratory techniques and the use of innovative bio-reporters to expand the capabilities of community based environmental monitoring.<br><br />
<br />
[[file:Sortingdebris.jpg|thumb|500px|right| hammerdirt team sorting debris at Vevey, Jan 2016. Source: MCBPII]]<br />
[[file : Pierrier.jpg |thumb|500px|right| Sorted debris Plage du Pierrier, Mar 2016. Source: MCBPII]]<br />
== Aims ==<br />
To effectively integrate more advanced and innovative water quality monitoring techniques to classic community based environmental monitoring activites.<br />
<br><br><br />
<br />
<br />
== Collaboration Defined ==<br />
{| class="wikitable"<br />
! Partner<br />
! Role<br />
|-<br />
| [http://www.genomicintegrity.org/ ACTION FOR GENOMIC INTEGRITY THROUGH RESEARCH!] <br />
| Technical oversight for the microbial assays, training of hammerdirt staff, quality control of laboratory operations and of sample processing and analyses.<br />
|-<br />
| [http://www.hackuarium.ch/fr/ HACKUARIUM]<br />
| Laboratory infrastructure and security, testing equipment and supplies for biologicals<br />
|-<br />
| [http://www.hammerdirt.ch/ HAMMERDIRT]<br />
| Collection and processing of samples, data storage and administration. Communication of analyses and results.<br />
|-<br />
| [https://biodesign.cc/ BIODESIGN.CC]<br />
| Analysis of samples for mercury, Cadmium Zinc, Alkanes and arsenic using the bio-reporters<br />
|}<br />
<br />
== Water Quality and Analysis ==<br />
=== Spring and Summer 2016 ===<br />
[[File:noswimming.jpg|thumb|right|400px|Location 5, Montreux rive gauche source : MCBPI July 2014]]<br />
==== Introduction ====<br />
<br />
One of the benefits of a “Community Based Environmental Monitoring” (CBEM) project is to expand the monitoring capacity of government agencies and engage the public in environmental stewardship. In response to questions from the public and our own professional curiosity we have decided to initiate a limited CBEM project (1) (2) .<br><br />
<br />
As part of the Montreux Clean Beach Project II(MCBPII), a water quality testing (WQT) program is being initiated at selected sites of the MCBPII. Symptoms reported by members and frequent bathers in the lake during previous summer seasons have sometimes been attributed to low bathing water quality, influenced by increased anthropogenic pressure of lakefront activities during certain times of the year. This year's WQT aims to gather microbiological data over a six week period in order to test this hypothesis.<br><br />
<br />
<br />
Meetings at “La Maison de la Rivière” and the “Institut National de Recherche Agronomique” support the idea that the WQT information proposed is not regularly collected at the Haut-Lac locations covered by the MCBPII.<br><br />
<br><br />
<br />
==== Objectives ====<br />
CBEM programs are designed to educate the public, involve local citizens in environmental stewardship and provide reliable data for government and other interested organizations. In this regard the MCBPII CBEM program is no different than that of any other existing project. (2)(3)(4)(5)(6)<br><br />
<br />
Specifically, the goals for this project are to:<br />
# Collect reliable water quality data as defined by the World Water Monitoring Challenge <br />
# Collect and enumerate the quantity of key bacteriological indicators, in particular those related to fecal contamination <br />
# Increase the skills of hammerdirt staff in regards to collecting and processing water samples.<br />
# Make the obtained data free and open to use for all concerned <br />
# Inform the public about affordable and simple water monitoring techniques<br />
# Inform the public of community based resources designed to advance scientific literacy<br />
<br><br />
More information [http://cbemn.ca/ CBEM Network]<br />
<br />
==== Deliverables ====<br />
[[File:Montreux_april_activity_opt_short-2.jpg|thumb|400px|right|Source: MCBPII Activity Report Nov 2015 - April 2016]]<br />
The objectives of a CBEM are designed to increase the monitoring capacity of current public systems and provide reliable, accessible data for the public and other government researchers. Data gathered from this project will be reported with our regular activity reports and the raw data will be available for download within 72 hours of the testing date from our repository on [https://github.com/hammerdirt/beachLitterSurveys Github] or through the KoboToolbox for the location in question. This document along with sampling protocols and all other supporting documents will be available on the wiki.<br />
<br><br><br />
Weekly results will be furnished to the CIPEL, SIGE and INRA:<br />
:# Location and number of tests<br />
:# Results of tests completed for the week<br />
An end of project report will be published in PDF format, available for interested parties, and include:<br />
:# Summary statistics and findings<br />
:# Graphs/plots<br />
:# Map overlay with densities and values<br />
:# Comparison with government supplied data (if available)<br />
:# Discussion of limitations and possible improvements to future CBEM projects<br />
<br />
More information [http://www.kobotoolbox.org/ KoboToolbox]<br />
<br />
=== Testing Materials ===<br />
==== Heavy Metals ====<br />
Bioreporters, designed and fabricated by biodesign.cc will be used to test for Alkanes, Arsenic, Mercury and Cadmium/Zinc. <br><br />
<br />
What are bioreporters ? Get some background information [http://wiki.biodesign.cc/wiki/Bioreporters_in_Pollutant_Detection here]<br />
<br />
==== Turbidity, temp, DO and PH ====<br />
Testing materials and supplies will be procured from the [http://www.monitorwater.org/ World Water Monitoring Challenge] an international program managed by the [http://www.iwa-network.org/ International Water Association] and the [http://www.wef.org/ Water Environment Federation].<br />
<br><br />
Assembled and sold by Lamotte company as a “basic test kit,” each kit includes one set of hardware and enough reagents to conduct up to 50 rounds of testing for pH, dissolved oxygen, temperature, and turbidity. Included are:<br />
# [[media : English-Spanish_Instructions.pdf |Instruction booklet]]<br />
# Sample collection jar<br />
# PH test tube<br />
# Dissolved oxygen vial<br />
# Secchi disk decal<br />
# Temperature strips (14-40°C and 0-12°C)<br />
# 50 pH reagent tablets (enough for 50 tests)<br />
# 100 Dissolved oxygen reagent tablets (enough for 50 tests)<br />
# Color chart for determining DO, pH and turbidity test results<br />
<br><br />
<br />
[[file:Eca_check_easygel_guide.pg1.jpg|thumb|right|400px|Visualizing organisms with ECA Check source: ECA Easygel guide]]<br />
==== Microbiological Analyses ====<br />
Presence and quantity of E.coli, other coli forms, Salmonella and Aeromonas will be tested using [http://www.micrologylabs.com/products/3/ECA-Check-Easygel ECA Check Easygel]. Easygel was first approved for [http://www.usawaterquality.org/ Water Watch] volunteer monitoring programs in the USA in 1999. A study released in 2009 compared the results of “Easygel” and “3M Petrifilm” used by volunteers to the results of laboratory analysis. Both methods had an overall accuracy rate above 80%. One big benefit of the Easygel format is that environmental samples of up to 5ml can be readily plated, with no worries about having to melt (and cool down!) agarose as used in standard microbial plates.(7)(8)(10)(14)<br><br />
<br />
Members of the Hackuarium laboratory have used “Easygel” in previous educational activities, thus facilitating the training of hammedirt staff and volunteers.<br />
<br />
=== Sampling Methods ===<br />
<br />
'''Water samples will be taken just below the surface (0.5m) and collected in sterile containers with a secure, air-tight lid.'''<br><br />
<br />
'''Advantage:''' simple and inexpensive, an important consideration to a program on a budget. It also does not require any special sampling apparatus. The volunteer holds a sampling container under the surface of the water, expells visible air bubbles, and closes the container under the water (to avoids losing dissolved gasses, particularly important if testing for volatile analytes).<br><br />
<br />
'''Disadvantage:''' vertical gradients of temperature, oxygen, nutrients, and algae may be missed in these near surface samples. Deep lakes have a thermal gradient in the summer, and Lac Leman has at least two thermal regions (and, possibly, at least two chemical regions as well). Even in shallow, usually well-mixed lakes, chemical gradients will develop during calm periods.<br><br />
<br />
Sampling methods by other CBEM projects : [[media:Stepenucketal2010.pdf | Stepenuck et all PDF]], [[media:Wfs-2005-01.pdf|Fact Sheet Volunteer Water Monitoring]], [[media : Moore_E_Coli.pdf | SOP Moore Creek E.coli sampling PDF]], [[media :Texasstream.pdf | Texas Sampling PDF]]<br />
<br />
==== Heavy Metals ====<br />
Two samples of 250ml will be taken and transported to the hackuarium for later analysis. One sample will be acidified to fix the heavy metals in solution.<br />
<br />
==== Turbidity, temp, DO and PH ====<br />
One sample will be taken using the container supplied with the testing kit and processed immediately. <br><br />
<br />
==== Microbiological samples ====<br />
'''Three independent samples will be taken from each designated site''' in 15ml conical tubes pre-labeled in the following manner:<br />
# Location<br />
# Date<br />
# Sample number for that day and location<br />
# Time of sample<br />
<br><br />
Once collected, the '''samples will be placed on ice and transported to the facility at Renens for plating on the ECA Check plates within 6 hours.''' Label information will be recorded in the field notes and the “KoboToolBox” for that sampling date and location.<br />
<br />
=== Processing samples and recording results ===<br />
==== Turbidity, temp, DO and PH ====<br />
The instructions provided with the kit will be followed and the results will be noted in the field manual and entered into the “KoboToolbox” form for that sampling date and location.<br />
<br />
==== Microbiologicals ====<br />
One petri dish per sample will be labeled in the same manner as the sample container with the addition of the quantity of sample added to the media. A 1-5ml of sample water will be mixed into the provided gel media solution, plated and incubated for about 18 hours at the Hackuarium facility in Renens.<br><br />
<br />
After incubation, plates will be scored, counting total colony forming units (CFU), and each identifiable species (E. coli CFUs will appear dark blue, other coliform CFUs will appear lighter blue-gray or blue-violet, Aeromonas spp. will appear as pink to very light pink, and Salmonella spp. will appear as light green colonies). Data will be reported as CFU/100ml of sample.<br><br />
<br />
With values from three independent samples at each site, means and standard errors can be used to test significance of the obtained data over the course of the sampling period.<br />
<br />
=== Locations ===<br />
[[File:tweet.jpg|thumb|right|600px |Sampling locations for biological and chemical analysis, source: Sampling and analysis plan MCBPII]]<br />
Three of the five locations are currently part of the MCBPII beach-litter-survey project. Point 4 will be added to the beach litter survey by using a net to catch visible pollutants on the water surface below the boat dock. Point 3 will only be monitored for chemistry and biologicals. Correlations of the test results with the physical location of the sampling will be of great interest.<br />
<br />
<br />
<br />
To see a map of the locations that benefit from regular water quality monitoring : [http://www.vd.ch/themes/environnement/eaux/eau-de-baignade/qualite-de-leau-des-plages-cartographie/ Eau de baignade]<br />
<br />
=== Testing Schedule ===<br />
==== Calendar from biodesign.cc to be embedded here ====<br />
key dates to be defined :<br />
# [[#Qualification Day]] June 7, 2016 "Q-Day"<br />
# Event public demonstration of sampling and plating<br />
# Start date for chemical samples<br />
# Start date for microbiologicals<br />
# Event public discussion of results, improvements and future projects<br />
==== Microbiologicals ====<br />
Testing will begin about 20 June 2016, and weekly samples will be taken from locations 3, 4 and 5. A 'negative control' sample will also be obtained each week from a local drinking fountain (labelled 'eau potable'). A positive control from an urban river (like the Vuachère or other) is also possible.<br><br />
<br />
If a Tuesday afternoon testing protocol is followed over 7 weeks, the timeline would run from 21 June -2 August, require 21 sterile 15ml conical tubes for the water sampling, and 21 ECA Check EasyGel plates per site. After including a single 'negative control' for each sampling day, this will require 70 plates.<br><br />
<br />
In case there are too many bacteria to count (TMTC) from certain samples, samples will be saved at 4oC and further dilutions can be also plated and scored.<br><br />
<br />
==== Turbidity, temp, DO and PH ====<br />
Testing will begin on the Tuesday or Thursday the week the kits are received (late May). The kit contains enough reagents to conduct 50 tests, thus allowing us to monitor the locations for 10 weeks. Data will be carefully recorded, digitized and analyzed.<br><br />
<br />
==== Field Blanks ====<br />
Field blanks are used to assess potential contamination from sample handling, airborne materials, equipment, media, and other sources. A field blank usually consists of a sterile diluent sample of 2 mL that is taken to the site and poured into a properly labeled sample container during the first bacteria sampling event of that day. The blank sample is collected in the same type of container, labeled as a field blank, and handled and analyzed along with all the bacteria samples collected on that day. It is used to identify errors or contamination in sample collection and analysis.<br />
<br />
=== Data === <br />
==== Handling and storage ====<br />
The addition of water quality testing will require changes in our digital form and reporting methods. The form currently used by surveyors will change, thus separating the data in two sections, one section prior to WQT and one after. Data for the two sections will have to be merged prior to any analysis. The results of bacterial testing will be available 48-72 hours after sampling, thus adding another step to the survey. This should not, however, change the availability of the other survey results which is currently 24 hours after each survey.<br><br />
<br />
==== Data analysis and presentation ====<br />
<br />
The existing data set for MCBPII includes visible pollution surveys, hydrologic and meteorological data. With the addition of microbiological and basic water chemistry a more complete picture of the environmental status of the locations in question can be established.<br><br />
<br />
Two interpretations of the microbiological data will be used: the geometric mean and the 95th percentile. The geometric mean is in common use in North America and the 95th percentile method conforms to EU directive 2006/7/EC. Furthermore, any publicly available water quality data in the area will be presented and integrated where appropriate.<br><br />
<br />
The relationship between the results of WQT and the quantity and type of visible pollutants will be explored.<br><br />
<br />
'''How is the water currently monitored and evaluated ? '''Here is the source document from the Swiss Confederation [[media :Evaluation+des+eaux+de+baignade.pdf | Eaux de baignade]]<br />
<br />
== References ==<br />
<br />
=== Sampling and Analysis in Community Based Environmental Monitoring ===<br />
# Assessing the performance of volunteers in monitoring Streams. Fore, Leska, Paulsen, Kit and O'Laughlin, Kate. Bellvue, WA : Blackwell Science, 2001, Fresh Water Biology. [[media:Fore,2001.pdf|Fore et all pdf]]<br />
# Volunteer environmental monitoring and the role of the universities : The case of Citizens Environment Watch. Savan, Beth, Morgan, Alexis and Gore, Chritopher. Toronto : s.n., June 2003, Environmental Management, Vol. 31, pp. 561-568.[[media:Savan+2003.pdf | Savan et all PDF]]<br />
# Nicholson, Emily, Ryan, Jane and Hodgkins, David. Community Data – where does the value lie? Assessing confidence limits of community collected water quality data. Victoria : Waterwatch Victoria c/o Department of Natural Resources & Environment, 2002. [[media:NicholsonEmily.pdf|Nicholson et all PDF]]<br />
# A review of citizen science and community-based environmental monitoring: issues and opportunities. Conrad, Cathy and Hilchey, Krista. [ed.] Springer. Halifax, Nova Scotia : s.n., 2010, Environ Monit Assess, pp. 273-291. [[media :Conrad-hilchey-2011-review.pdf | Conrad & Hilchey PDF]] <br />
# World water monitoring challenge. Instructions. Geneva : World water montioring Challenge, 2015. Instructions for the water monitoring test kit provided by the world water monitoring challenge.[[media : English-Spanish_Instructions.pdf | Instructions for PH, DO, temp and turbidity PDF]]<br />
# World Health Organization. Guidelines for safe recreational water environments. Geneva : World HEalth Organization, 2003. Vol. 1 Coastal and Fresh Waters. [[media:WhoGuideLines.pdf|WHO Guide Lines]]<br />
# Texas Stream Team Volunteer Water Quality Monitoring. E.coli Monitoring and Analysis Procedures. 2010. [[media :Texasstream.pdf | Texas Sampling PDF]]<br />
# Stepenuk, Kristine, et al. Volunteer monitoring of E. coli in streams of the upper Midwestern United States: a comparison of methods. [ed.] University of Wisconsin—Extension. Madison : Springer, 2010.[[media:Stepenucketal2010.pdf | Stepenuck et all PDF]]<br />
# Myers, D.N., et al. Fecal indicator bacteria (ver. 2.1). [book auth.] U.S. Geological survey. U.S. Geological Survey Techniques of Water-Resources Investigations. 2014, Vol. book 9, chap. A7, section 7.1.[[media :Fecalindicators.pdf | Myers et all PDF]] <br />
# Iowa Department of Natural Resources, Geological Survey. Citizens Monitoring Bacteria. Iowa City : s.n., 2005. Vols. Water Fact Sheet 2005-1.[[media:Wfs-2005-01.pdf|Fact Sheet Volunteer Water Monitoring]]<br />
# Arizona Department of Environmental Quality Water Quality Improvement Grant Program. Writing Effective Monitoring Plans. s.l. : Arizona department of environmental quality, 2008. TM 08-04.[[media:Writing.pdf | Guide to writing a sampling plan PDF]]<br />
# USEPA REGION 9 LABORATORY. STANDARD OPERATING PROCEDURE FOR VOLUNTEER MONITORING OF SURFACE WATERS FOR BACTERIA. Richmond : United States Environmental Agency, 2007.[[media:SOPEPARICHMOND.pdf| SOP Volunteer monitoring PDF]]<br />
# U.S. Geological Survey. National Field Manual for the collection of water quality data. 2006. Vol. Book 9. http://water.usgs.gov/owq/FieldManual/<br />
# Wolfson, Dr. Lois. E. coli Monitoring – Effective Techniques and Test Kits for Volunteers. Michigan Clean Water Corps Conference. s.l. : Michigan State University, October 16, 2007.[[media:WolfsonPresentation.pdf | Test Kit Presentation PDF]]<br />
# Epstein, Charlotte. KNOWLEDGE AND POWER IN GLOBAL ENVIRONMENTAL ACTIVISM. s.l. : International Journal of Peace Studies, 2005.[[media:Epstein_101IJPS.pdf | Epstein PDF]]<br />
# CH. Loi fédérale sur la protection des eaux. [Online] juin 1, 2014. https://www.admin.ch/opc/fr/classified-compilation/19910022/index.html#a4.<br />
# Kleehammer, Katie and Sigler, Adam. Moore Creek Volunteer Monitoring for Escherichia coli - Sampling and analysis. Bozeman : MSU Extension Water Quality, 2012.[[media : Moore_E_Coli.pdf | SOP Moore Creek E.coli sampling PDF]]<br />
# Homogeneous Distribution of Escherichia coli Measured within the Vertical Water Column of Small, Freshwater Streams. Buckalew, David, et al. Farmville, VA : Scientific Research Publishing, March 24, 2014, Water Resource and Protection, pp. 410-421. [[media : Distirbutionofecoliwatercolumn.pdf | Buckalew et all PDF]]<br />
# Micrology LAboratories. Easy Gel Method Procedure. Goshen, Indiana : s.n., 2015. Recomended procedures for chromogeinc media.[[media:Easygel_method_procedure.pdf | Procedure Easygel PDF]]<br />
# Micrology Laboratories. ECA Check Easy guide. Goshen : Manufacturers color guide for chromogenic media.[[media : Eca_check_easygel_guide.pdf | ECA guide to determining bacteria PDF]]<br />
# DIRECTIVE 2006/7/EC concerning the management of bathing water quality. European Union. Strassbourg : s.n., 2006, Official Journal of the European Union.[[media:DIRECTIVE2006EC_.pdf | Directive 2006/7/EC]]<br />
# Canfield, Daniel; Hoyer, Mark; Volunteer Lake Monitoring : Testing the Reliability of Data Collected by the Florida LakeWatch Program: Lake and Reservoir Management-March 2002 [[media : Floridalakes.pdf | Reliability of volunteer data PDF]]<br />
<br />
=== Documents from hammerdirt Clean Beach Projects ===<br />
* [[ Media : Montreux_april_activity_opt.pdf | Activity report Nov 2015 - April 2016]]<br />
* [[ Media : Pilot_project_cbem_montreux.pdf | Pilot project CBEM May 2016]]<br />
* [[Media:Clean_beach_pro_2015.pdf | Hammerdirt Clean Beach Project 2 2015 Draft]]<br />
* [[ Media : CH_OSPAR._COMPARISON_OPT.pdf | Comparison of Lake Geneva beaches to other OSPAR regions]]<br />
* [[ Media : Citizenscience.pdf | Citizen Science and litter studies (french)]]<br />
* [[ Media : MCBP1.pdf | MCBPI 2014-2015 results (French)]]<br />
* [[ Media : Plagespropres_nov2014_aout2015_opt.pdf | MCBPI 2014-2015 results (English)]]<br />
<br />
== Qualification Day ==<br />
[[file:Beach.jpg|thumb|300px|right| Vidy sampling location, June 2016.]]<br />
[[file:Vaucherelocation.jpg|thumb|300px|right|Positive control location, June 2016.]]<br />
[[file:Vaucheresign.jpg|thumb|300px|right|Positive control location, June 2016.]]<br />
[[file:Glovesand samples.jpg|thumb|300px|right|Labled sampling tube Vidy, June 2016.]]<br />
[[file:Capunderwater.jpg|thumb|300px|right|Collecting sample Vidy, June 2016.]]<br />
[[file:Looksready.jpg|thumb|300px|right|Removing from autoclave, Hackuarium 2016.]]<br />
[[file:Lessons.jpg|thumb|300px|right|Rachel demonstrating, Hackuarium 2016]]<br />
[[file:Grownplates.jpg|thumb|400px|right| Vidy and Vauchère 24hours methylene blue agar, June 2016.]]<br />
[[file:Upclose2.png |thumb|400px|right|E.coli colony Vauchère methylene blue agar, June 2016.]] <br />
As indicated in the project plan hammerdirt volunteers met with the technical advisor from AGIR and agreed to hold a water sampling and sample handling qualification day (Q-Day) prior to the beginning of the Water Quality Testing (WQT) pilot project.<br />
<br />
===Objectives of Q-Day ===<br />
<br />
# Combine a litter survey with the collection of water samples<br />
# Collect samples in accordance with the protocol for the WQT project<br />
# Prepare culture medium using available laboratory equipment<br />
# Collect samples without introducing contaminants<br />
# Prepare samples without introducing contaminants<br />
# Execute all tasks following laboratory safety regulations<br />
# Verify that all laboratory equipment is operational<br />
<br />
=== Meeting objectives ===<br />
<br />
The success of Q-Day was based on the response to the following questions:<br />
<br />
# Were the samples collected and plated within a 6-hour window?<br />
# Was the litter inventory completed prior to leaving the site?<br />
# Did field team observe proper hygiene and sampling protocols?<br />
# Did all laboratory equipment function? Were the team members able to use equipment?<br />
# Did the negative controls show any signs of growth? <br />
# Did the positive controls show growth in accordance with historical results?<br />
<br />
=== The survey sites for Q-Day ===<br />
<br />
# Positive control Vauchère river<br />
# Negative control : tap water<br />
# Unknown : Bay de Vidy<br />
<br />
=== Combining a litter survey with water sampling ===<br />
A comprehensive litter survey can take up to two hours (depending on the size of the beach). For the Q-day exercise hammerdirt chose a small beach in an urban center. Two risks were immediately identified:<br />
<br />
# Cross contamination of samples from handling litter and water sampling<br />
# Running out of time within a 6-hour window to plate the samples<br />
<br />
It was decided that initially the litter would be collected at the site by all team members and then, at the discretion of the team members, one individual would cease handling litter and collect the required samples.<br />
<br />
11:50 Litter collection and inventory<br><br />
12:50 Sample collection<br><br />
13:40 Arrival at the laboratory<br><br />
<br />
=== Collect samples in accordance with the protocol ===<br />
The location was easy to access. The team packed soap, hand sanitizer and disposable gloves specifically for water sampling operations. The designated individual ceased handling litter and washed hands with soap and water. Clean, disposable gloves were used for the sampling process. Samples were collected by wading into the water and plunging the sampling tube roughly 50cm deep. The sampling tube was uncapped underwater and filled completely. Once the sampling tube was out of the water a portion was poured off and the sampling tube was capped and put on ice. All team members washed hands and used hand sanitizer at the end of the operation.<br><br />
<br />
=== Prepare culture medium using available laboratory equipment ===<br />
For Q-Day operations we used a dehydrated culture media, eosin methylene blue agar, produced by Oxoid and sold under product number CM0069. The culture media that was ordered and that will be used for the WQT project, ECA Check Easygel, had not arrived by the scheduled date.<br />
The methylene blue agar requires significantly more preparation and handling than the ECA Check Easygel. The following steps needed to be completed prior to plating (within the 6-hour limit):<br />
<br />
# Suspend 37.5g in 1 litre of distilled water. <br />
# Bring to a boil to dissolve completely. <br />
# Sterilise by autoclaving at 121°C for 15 minutes. <br />
# Cool to 60°C<br />
# Shake the medium in order to oxidise the methylene blue<br />
# Pour medium into sterile petri dishes<br />
# Cool medium to solid and introduce water samples<br />
# Prepare samples without introducing contaminants<br />
<br />
Collected samples were stored in the laboratory specimen refrigerator at 4c while the chromogenic medium was prepared. The work surface, a fume hood, was sterilized with 70% ethanol prior to pouring the chromogenic media into disposable, sterile petri dishes. The surface was sterilized again prior to plating of the water samples.<br />
<br><br><br />
Sterile, disposable pipettes were used and changed for each water sample. Participants used disposable latex gloves and a Bunsen burner was lit during all pouring and plating operations.<br />
<br><br><br />
Three samples from the positive control and the unknown were plated as well as one sample from the negative control (tap water).<br />
Plated samples were covered and placed in the incubator at 37c for 24hours.<br />
<br />
=== Were the objectives met? ===<br />
# ''Were the samples collected and plated within a 6-hour window?'' '''Yes, samples were collected at 12:50 and plated at 18:30.'''<br />
# ''Was the litter inventory completed prior to leaving the site?'' '''Yes the results can be seen here :[https://kc.kobotoolbox.org/hammerdirt/forms/Veveyse/instance#/1124418 Vidy inventory]<br />
# ''Did field team observe proper hygiene and sampling protocols?'' '''Yes, field participants prepared and utilized a field hygiene kit including soap, hand sanitizer and disposable gloves. The depth of water sample was observed.'''<br />
# ''Did all laboratory equipment function? Were the team members able to use equipment?'' '''Yes, although prior organization and identification of the proper functioning equipment could have reduced the preparation time.''' <br />
# ''Did the negative controls show any signs of growth?'' '''No, the negative controls exhibited no growth. Indicating that no contamination occurred during sample handling and processing.'''<br />
# ''Did the positive controls show growth in accordance with historical results?'' '''Yes, in accordance with the experience of the technical advisor.'''<br />
<br><br />
<br />
=== Remarks ===<br />
# Field staff will need to organize activities appropriately especially in regards to the times required to inventory litter and the 6-hour time limit for water samples. <br />
# A bottle of water should be included in the field hygiene kit to rinse hands. <br />
# A dedicated space needs to be attributed in the lab for this project. <br />
# The incubator needs to be reserved ahead of time for sample processing (avoid conflicts with other projects).<br />
# The level of the fume hood should be verified, the cooled plates showed a slight unequal distribution.<br />
# A training session with ECA Check Easygel should be scheduled.<br />
<br />
=== Conclusion ===<br />
'''An opening day can be scheduled, hammerdirt staff are competent and all the necessary equipment is available at the lab.''' <br />
<gallery><br />
file:Washhands.jpg| Handwashing Vidy, June 2016.<br />
file:Pouroff.jpg|Pouring off Vidy, June 2016.<br />
file:Samples.jpg|Collected samples Vidy, June 2016.<br />
file:Onice.jpg|Samples on ice Vidy, June 2016.<br />
file:Bringtoboil.jpg|Boiling medium, June 2016.<br />
file:Makingjam.jpg|In the autoclave, June 2016.<br />
file:Oxidize.jpg|Oxidizing the medium, June 2016.<br />
file:Incubate.jpg|Incubator, June 2016.<br />
</gallery> <br />
<br><br />
<br />
=== Results of Microbiological Analyses ===<br />
<br />
The samples were removed from the incubator after 24hours of incubation at 37c. Mulitple colonies were noted in the methlylene blue agar, we are displaying only the counts of the ''E.coli'' colony forming units.<br />
<br><br><br />
There was no visible colony forming units in the tap water or the sample taken from Vidy (the unknown). The colony forming units of ''E.coli'' counted from the Vauchère samples are presented in the table below.<br />
<br><br />
==== Colony forming units counted Vauchere ====<br />
{| class="wikitable"<br />
! style="text-align:left;"|Counts<br />
!Vauchere 1<br />
!Vauchere 2<br />
!Vauchere 3<br />
!Avg<br />
!Std Dev<br />
|-<br />
| Agir<br />
|style="text-align:center;"|7<br />
|style="text-align:center;"|3<br />
|style="text-align:center;"|29<br />
|style="text-align:center;"|13<br />
|style="text-align:center;"|14<br />
|-<br />
| hammerdirt<br />
|style="text-align:center;"|7<br />
|style="text-align:center;"|3<br />
|style="text-align:center;"|27<br />
|style="text-align:center;"|12<br />
|style="text-align:center;"|13<br />
|}<br />
<br />
The ECA Check Easygel material arrived on June 11th. A control of 0.5ml of the same tap Water and Vauchère (saved in the refrigerator) samples were plated. The EasyGel is much easier to distinguish the colony forming units than the methylene blue agar.<br />
<br> <br />
[[file:Easygelplates3.jpg|thumb|650px|none| Positive and negative control samples on Easygel medium, June 2016.]]<br />
<br><br />
== Literature ==<br />
[[Media:07_phytoplancton_camp.2014.pdf | 2014 Report on Leman biomass ]] <br><br />
[[Media:Rapports_Leman_2014.pdf | 2014 Physico-chemical Leman report]]<br />
<br />
=== Relevant Links ===<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253<br />
<br />
== Documentation and Collaboration Tools ==<br />
----<br />
Agree on documentation and collaboration tools<br />
* Internal communication - hackuarium slack <br />
* Calendar? - we have a biodesign google calendar<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
== Water Collection Protocols ==<br />
----<br />
<br><br><br />
<br />
=== Coliform Bacteria Counting ===<br />
----<br />
The presence of ''E. coli'' in natural waters is a direct indication of fecal contamination of water. Coliform bacteria and other bacterial species can also be found in public waters and contribute to human pathologies. There are several methods to distinguish ''E. coli'', coliform and other bacteria vs other microorganisms that may grow on an agar plate, of special interest 'chromogenic media' which contain substrates that form specific colors depending on enzymes produced by each species.<br />
==== Easy Gel ====<br />
Micrology Labs [http://www.micrologylabs.com/page/93/Coliscan-Easygel Coliscan Easygel]<br />
* Rachel asked for an offer including shipping and the 15% discount for the a coliform bacteria testing medium.<br />
* reminder request sent again 18 April to Jonathan Roth (CEO of Micrology Labs) and Doug Wengerd (who eventually answers notes to their 'info' address)<br />
[http://www.micrologylabs.com/page/95/Instructions Protocol] from the Micrology Labs<br><br />
* there have been some paying complications too, but their large scale order for 100 plates makes the 'per plate' cost half of another option <br><br />
<br />
<br />
To note: the Micrology Lab ECA Easygel plates are somewhat expensive, but can assay up to 5ml of sampled water per plate for ready scoring and disposal. Another currently proposed plate media would not only be less discriminating, but require more equipment for the sterile setup and final cleanup, and probably only allow 0.5ml to be assayed/plate. The Micrology plates are also used in other 'citizen science' campaigns and approved by regulatory bodies...<br />
<br />
==== Other Media ====<br />
* [https://en.wikipedia.org/wiki/Endo_agar Endo agar] where gram negatives are favored to grow. Fermentation of lactose in the medium by coliform bacteria gives metallic green sheen to those colonies.<br />
* [https://en.wikipedia.org/wiki/MacConkey_agar MacConkey agar] - also contains lactose and neutral red as a pH indicator, bile salts to inhibit gram-positive bacteria growth<br />
* [https://en.wikipedia.org/wiki/Sorbitol-MacConkey_agar MacConkey agar with sorbitol] is used to isolate E. coli O157, a pathogenic enteric bacteria<br />
* [https://en.wikipedia.org/wiki/Eosin_methylene_blue Eosin Methylene Blue agar] - Lactose fermenting bacteria turn a dark color, gram positive bacteria also inhibited<br />
<br />
<br />
<br><br />
==== DIY protocol ====<br />
<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br />
==== Other Methods ====<br />
* Good "travaux pratique" [http://www.bioutils.ch/protocoles/13-analyse-de-leau protocol] for bacterial counting and salts concentration from Bioutils, UNIGE <br><br />
* Other [[Media:Bacterial_counts.pdf | protocol]] proposing several direct and indirect methods <br><br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
----<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br />
<br />
=== Water Multi-meter ===<br />
----<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br><br />
<br />
== Press ==<br />
=== Short History of the Collaboration ===<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation from that day can be found here:[[media : Hammerdirt.pdf | How can we work together ?]]<br />
<br><br><br />
'''Brainstorm Results'''<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* Microbial testing - distinguish fecal contaminants and others with selective plates<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
[[Category:Projects]]<br />
[[Category:Work In Progress]]<br />
[[Category:Environment]]</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=7103Micro to Macro Water Pollution2016-05-23T11:20:28Z<p>Sachiko: /* Water Collection Protocols */</p>
<hr />
<div>Community based environmental monitoring has been proven effective in a variety of fields, water quality monitoring by volunteers is in wide practice across North America. Four Swiss nonprofit associations use visible pollution inventories, microbiological monitoring and chemical analysis by combining classic laboratory techniques and the use of innovative bio-reporters to expand the capabilities of community based environmental monitoring.<br><br />
<br />
[[file:Sortingdebris.jpg|thumb|500px|right| hammerdirt team sorting debris at Vevey, Jan 2016. Source: MCBPII]]<br />
[[file : Pierrier.jpg |thumb|500px|right| Sorted debris Plage du Pierrier, Mar 2016. Source: MCBPII]]<br />
== Aims ==<br />
To effectively integrate more advanced and innovative water quality monitoring techniques to classic community based environmental monitoring activites.<br />
<br><br><br />
<br />
<br />
== Collaboration Defined ==<br />
{| class="wikitable"<br />
! Partner<br />
! Role<br />
|-<br />
| [http://www.genomicintegrity.org/ ACTION FOR GENOMIC INTEGRITY THROUGH RESEARCH!] <br />
| Technical oversight for the microbial assays, training of hammerdirt staff, quality control of laboratory operations and of sample processing and analyses.<br />
|-<br />
| [http://www.hackuarium.ch/fr/ HACKUARIUM]<br />
| Laboratory infrastructure and security, testing equipment and supplies for biologicals<br />
|-<br />
| [http://www.hammerdirt.ch/ HAMMERDIRT]<br />
| Collection and processing of samples, data storage and administration. Communication of analyses and results.<br />
|-<br />
| [https://biodesign.cc/ BIODESIGN.CC]<br />
| Analysis of samples for mercury, Cadmium Zinc, Alkanes and arsenic using the bio-reporters<br />
|}<br />
<br />
== Water Quality and Analysis ==<br />
=== Spring and Summer 2016 ===<br />
[[File:noswimming.jpg|thumb|right|400px|Location 5, Montreux rive gauche source : MCBPI July 2014]]<br />
==== Introduction ====<br />
<br />
One of the benefits of a “Community Based Environmental Monitoring” (CBEM) project is to expand the monitoring capacity of government agencies and engage the public in environmental stewardship. In response to questions from the public and our own professional curiosity we have decided to initiate a limited CBEM project (1) (2) .<br><br />
<br />
As part of the Montreux Clean Beach Project II(MCBPII), a water quality testing (WQT) program is being initiated at selected sites of the MCBPII. Symptoms reported by members and frequent bathers in the lake during previous summer seasons have sometimes been attributed to low bathing water quality, influenced by increased anthropogenic pressure of lakefront activities during certain times of the year. This year's WQT aims to gather microbiological data over a six week period in order to test this hypothesis.<br><br />
<br />
<br />
Meetings at “La Maison de la Rivière” and the “Institut National de Recherche Agronomique” support the idea that the WQT information proposed is not regularly collected at the Haut-Lac locations covered by the MCBPII.<br><br />
<br><br />
<br />
==== Objectives ====<br />
CBEM programs are designed to educate the public, involve local citizens in environmental stewardship and provide reliable data for government and other interested organizations. In this regard the MCBPII CBEM program is no different than that of any other existing project. (2)(3)(4)(5)(6)<br><br />
<br />
Specifically, the goals for this project are to:<br />
# Collect reliable water quality data as defined by the World Water Monitoring Challenge <br />
# Collect and enumerate the quantity of key bacteriological indicators, in particular those related to fecal contamination <br />
# Increase the skills of hammerdirt staff in regards to collecting and processing water samples.<br />
# Make the obtained data free and open to use for all concerned <br />
# Inform the public about affordable and simple water monitoring techniques<br />
# Inform the public of community based resources designed to advance scientific literacy<br />
<br><br />
More information [http://cbemn.ca/ CBEM Network]<br />
<br />
==== Deliverables ====<br />
[[File:Montreux_april_activity_opt_short-2.jpg|thumb|400px|right|Source: MCBPII Activity Report Nov 2015 - April 2016]]<br />
The objectives of a CBEM are designed to increase the monitoring capacity of current public systems and provide reliable, accessible data for the public and other government researchers. Data gathered from this project will be reported with our regular activity reports and the raw data will be available for download within 72 hours of the testing date from our repository on [https://github.com/hammerdirt/beachLitterSurveys Github] or through the KoboToolbox for the location in question. This document along with sampling protocols and all other supporting documents will be available on the wiki.<br />
<br><br><br />
Weekly results will be furnished to the CIPEL, SIGE and INRA:<br />
:# Location and number of tests<br />
:# Results of tests completed for the week<br />
An end of project report will be published in PDF format, available for interested parties, and include:<br />
:# Summary statistics and findings<br />
:# Graphs/plots<br />
:# Map overlay with densities and values<br />
:# Comparison with government supplied data (if available)<br />
:# Discussion of limitations and possible improvements to future CBEM projects<br />
<br />
More information [http://www.kobotoolbox.org/ KoboToolbox]<br />
<br />
=== Testing Materials ===<br />
==== Heavy Metals ====<br />
Bioreporters, designed and fabricated by biodesign.cc will be used to test for Alkanes, Arsenic, Mercury and Cadmium/Zinc. <br><br />
<br />
What are bioreporters ? Get some background information [http://wiki.biodesign.cc/wiki/Bioreporters_in_Pollutant_Detection here]<br />
<br />
==== Turbidity, temp, DO and PH ====<br />
Testing materials and supplies will be procured from the [http://www.monitorwater.org/ World Water Monitoring Challenge] an international program managed by the [http://www.iwa-network.org/ International Water Association] and the [http://www.wef.org/ Water Environment Federation].<br />
<br><br />
Assembled and sold by Lamotte company as a “basic test kit,” each kit includes one set of hardware and enough reagents to conduct up to 50 rounds of testing for pH, dissolved oxygen, temperature, and turbidity. Included are:<br />
# [[media : English-Spanish_Instructions.pdf |Instruction booklet]]<br />
# Sample collection jar<br />
# PH test tube<br />
# Dissolved oxygen vial<br />
# Secchi disk decal<br />
# Temperature strips (14-40°C and 0-12°C)<br />
# 50 pH reagent tablets (enough for 50 tests)<br />
# 100 Dissolved oxygen reagent tablets (enough for 50 tests)<br />
# Color chart for determining DO, pH and turbidity test results<br />
<br><br />
<br />
[[file:Eca_check_easygel_guide.pg1.jpg|thumb|right|400px|Visualizing organisms with ECA Check source: ECA Easygel guide]]<br />
==== Microbiological Analyses ====<br />
Presence and quantity of E.coli, other coli forms, Salmonella and Aeromonas will be tested using [http://www.micrologylabs.com/products/3/ECA-Check-Easygel ECA Check Easygel]. Easygel was first approved for [http://www.usawaterquality.org/ Water Watch] volunteer monitoring programs in the USA in 1999. A study released in 2009 compared the results of “Easygel” and “3M Petrifilm” used by volunteers to the results of laboratory analysis. Both methods had an overall accuracy rate above 80%. One big benefit of the Easygel format is that environmental samples of up to 5ml can be readily plated, with no worries about having to melt (and cool down!) agarose as used in standard microbial plates.(7)(8)(10)(14)<br><br />
<br />
Members of the Hackuarium laboratory have used “Easygel” in previous educational activities, thus facilitating the training of hammedirt staff and volunteers.<br />
<br />
=== Sampling Methods ===<br />
<br />
'''Water samples will be taken just below the surface (0.5m) and collected in sterile containers with a secure, air-tight lid.'''<br><br />
<br />
'''Advantage:''' simple and inexpensive, an important consideration to a program on a budget. It also does not require any special sampling apparatus. The volunteer holds a sampling container under the surface of the water, expells visible air bubbles, and closes the container under the water (to avoids losing dissolved gasses, particularly important if testing for volatile analytes).<br><br />
<br />
'''Disadvantage:''' vertical gradients of temperature, oxygen, nutrients, and algae may be missed in these near surface samples. Deep lakes have a thermal gradient in the summer, and Lac Leman has at least two thermal regions (and, possibly, at least two chemical regions as well). Even in shallow, usually well-mixed lakes, chemical gradients will develop during calm periods.<br><br />
<br />
Sampling methods by other CBEM projects : [[media:Stepenucketal2010.pdf | Stepenuck et all PDF]], [[media:Wfs-2005-01.pdf|Fact Sheet Volunteer Water Monitoring]], [[media : Moore_E_Coli.pdf | SOP Moore Creek E.coli sampling PDF]], [[media :Texasstream.pdf | Texas Sampling PDF]]<br />
<br />
==== Heavy Metals ====<br />
Two samples of 250ml will be taken and transported to the hackuarium for later analysis. One sample will be acidified to fix the heavy metals in solution.<br />
<br />
==== Turbidity, temp, DO and PH ====<br />
One sample will be taken using the container supplied with the testing kit and processed immediately. <br><br />
<br />
==== Microbiological samples ====<br />
'''Three independent samples will be taken from each designated site''' in 15ml conical tubes pre-labeled in the following manner:<br />
# Location<br />
# Date<br />
# Sample number for that day and location<br />
# Time of sample<br />
<br><br />
Once collected, the '''samples will be placed on ice and transported to the facility at Renens for plating on the ECA Check plates within 6 hours.''' Label information will be recorded in the field notes and the “KoboToolBox” for that sampling date and location.<br />
<br />
=== Processing samples and recording results ===<br />
==== Turbidity, temp, DO and PH ====<br />
The instructions provided with the kit will be followed and the results will be noted in the field manual and entered into the “KoboToolbox” form for that sampling date and location.<br />
<br />
==== Microbiologicals ====<br />
One petri dish per sample will be labeled in the same manner as the sample container with the addition of the quantity of sample added to the media. A 1-5ml of sample water will be mixed into the provided gel media solution, plated and incubated for about 18 hours at the Hackuarium facility in Renens.<br><br />
<br />
After incubation, plates will be scored, counting total colony forming units (CFU), and each identifiable species (E. coli CFUs will appear dark blue, other coliform CFUs will appear lighter blue-gray or blue-violet, Aeromonas spp. will appear as pink to very light pink, and Salmonella spp. will appear as light green colonies). Data will be reported as CFU/100ml of sample.<br><br />
<br />
With values from three independent samples at each site, means and standard errors can be used to test significance of the obtained data over the course of the sampling period.<br />
<br />
=== Locations ===<br />
[[File:tweet.jpg|thumb|right|600px |Sampling locations for biological and chemical analysis, source: Sampling and analysis plan MCBPII]]<br />
Three of the five locations are currently part of the MCBPII beach-litter-survey project. Point 4 will be added to the beach litter survey by using a net to catch visible pollutants on the water surface below the boat dock. Point 3 will only be monitored for chemistry and biologicals. Correlations of the test results with the physical location of the sampling will be of great interest.<br />
<br />
<br />
<br />
To see a map of the locations that benefit from regular water quality monitoring : [http://www.vd.ch/themes/environnement/eaux/eau-de-baignade/qualite-de-leau-des-plages-cartographie/ Eau de baignade]<br />
<br />
=== Testing Schedule ===<br />
==== Calendar from biodesign.cc to be embedded here ====<br />
key dates to be defined :<br />
# Training for sampling and plating<br />
# Event public demonstration of sampling and plating<br />
# Start date for chemical samples<br />
# Start date for microbiologicals<br />
# Event public discussion of results, improvements and future projects<br />
==== Microbiologicals ====<br />
Testing will begin about 20 June 2016, and weekly samples will be taken from locations 3, 4 and 5. A 'negative control' sample will also be obtained each week from a local drinking fountain (labelled 'eau potable'). A positive control from an urban river (like the Vuachère or other) is also possible.<br><br />
<br />
If a Tuesday afternoon testing protocol is followed over 7 weeks, the timeline would run from 21 June -2 August, require 21 sterile 15ml conical tubes for the water sampling, and 21 ECA Check EasyGel plates per site. After including a single 'negative control' for each sampling day, this will require 70 plates.<br><br />
<br />
In case there are too many bacteria to count (TMTC) from certain samples, samples will be saved at 4oC and further dilutions can be also plated and scored.<br><br />
<br />
==== Turbidity, temp, DO and PH ====<br />
Testing will begin on the Tuesday or Thursday the week the kits are received (late May). The kit contains enough reagents to conduct 50 tests, thus allowing us to monitor the locations for 10 weeks. Data will be carefully recorded, digitized and analyzed.<br><br />
<br />
==== Field Blanks ====<br />
Field blanks are used to assess potential contamination from sample handling, airborne materials, equipment, media, and other sources. A field blank usually consists of a sterile diluent sample of 2 mL that is taken to the site and poured into a properly labeled sample container during the first bacteria sampling event of that day. The blank sample is collected in the same type of container, labeled as a field blank, and handled and analyzed along with all the bacteria samples collected on that day. It is used to identify errors or contamination in sample collection and analysis.<br />
<br />
=== Data === <br />
==== Handling and storage ====<br />
The addition of water quality testing will require changes in our digital form and reporting methods. The form currently used by surveyors will change, thus separating the data in two sections, one section prior to WQT and one after. Data for the two sections will have to be merged prior to any analysis. The results of bacterial testing will be available 48-72 hours after sampling, thus adding another step to the survey. This should not, however, change the availability of the other survey results which is currently 24 hours after each survey.<br><br />
<br />
==== Data analysis and presentation ====<br />
<br />
The existing data set for MCBPII includes visible pollution surveys, hydrologic and meteorological data. With the addition of microbiological and basic water chemistry a more complete picture of the environmental status of the locations in question can be established.<br><br />
<br />
Two interpretations of the microbiological data will be used: the geometric mean and the 95th percentile. The geometric mean is in common use in North America and the 95th percentile method conforms to EU directive 2006/7/EC. Furthermore, any publicly available water quality data in the area will be presented and integrated where appropriate.<br><br />
<br />
The relationship between the results of WQT and the quantity and type of visible pollutants will be explored.<br><br />
<br />
'''How is the water currently monitored and evaluated ? '''Here is the source document from the Swiss Confederation [[media :Evaluation+des+eaux+de+baignade.pdf | Eaux de baignade]]<br />
<br />
== References ==<br />
<br />
=== Sampling and Analysis in Community Based Environmental Monitoring ===<br />
# Assessing the performance of volunteers in monitoring Streams. Fore, Leska, Paulsen, Kit and O'Laughlin, Kate. Bellvue, WA : Blackwell Science, 2001, Fresh Water Biology. [[media:Fore,2001.pdf|Fore et all pdf]]<br />
# Volunteer environmental monitoring and the role of the universities : The case of Citizens Environment Watch. Savan, Beth, Morgan, Alexis and Gore, Chritopher. Toronto : s.n., June 2003, Environmental Management, Vol. 31, pp. 561-568.[[media:Savan+2003.pdf | Savan et all PDF]]<br />
# Nicholson, Emily, Ryan, Jane and Hodgkins, David. Community Data – where does the value lie? Assessing confidence limits of community collected water quality data. Victoria : Waterwatch Victoria c/o Department of Natural Resources & Environment, 2002. [[media:NicholsonEmily.pdf|Nicholson et all PDF]]<br />
# A review of citizen science and community-based environmental monitoring: issues and opportunities. Conrad, Cathy and Hilchey, Krista. [ed.] Springer. Halifax, Nova Scotia : s.n., 2010, Environ Monit Assess, pp. 273-291. [[media :Conrad-hilchey-2011-review.pdf | Conrad & Hilchey PDF]] <br />
# World water monitoring challenge. Instructions. Geneva : World water montioring Challenge, 2015. Instructions for the water monitoring test kit provided by the world water monitoring challenge.[[media : English-Spanish_Instructions.pdf | Instructions for PH, DO, temp and turbidity PDF]]<br />
# World Health Organization. Guidelines for safe recreational water environments. Geneva : World HEalth Organization, 2003. Vol. 1 Coastal and Fresh Waters. [[media:WhoGuideLines.pdf|WHO Guide Lines]]<br />
# Texas Stream Team Volunteer Water Quality Monitoring. E.coli Monitoring and Analysis Procedures. 2010. [[media :Texasstream.pdf | Texas Sampling PDF]]<br />
# Stepenuk, Kristine, et al. Volunteer monitoring of E. coli in streams of the upper Midwestern United States: a comparison of methods. [ed.] University of Wisconsin—Extension. Madison : Springer, 2010.[[media:Stepenucketal2010.pdf | Stepenuck et all PDF]]<br />
# Myers, D.N., et al. Fecal indicator bacteria (ver. 2.1). [book auth.] U.S. Geological survey. U.S. Geological Survey Techniques of Water-Resources Investigations. 2014, Vol. book 9, chap. A7, section 7.1.[[media :Fecalindicators.pdf | Myers et all PDF]] <br />
# Iowa Department of Natural Resources, Geological Survey. Citizens Monitoring Bacteria. Iowa City : s.n., 2005. Vols. Water Fact Sheet 2005-1.[[media:Wfs-2005-01.pdf|Fact Sheet Volunteer Water Monitoring]]<br />
# Arizona Department of Environmental Quality Water Quality Improvement Grant Program. Writing Effective Monitoring Plans. s.l. : Arizona department of environmental quality, 2008. TM 08-04.[[media:Writing.pdf | Guide to writing a sampling plan PDF]]<br />
# USEPA REGION 9 LABORATORY. STANDARD OPERATING PROCEDURE FOR VOLUNTEER MONITORING OF SURFACE WATERS FOR BACTERIA. Richmond : United States Environmental Agency, 2007.[[media:SOPEPARICHMOND.pdf| SOP Volunteer monitoring PDF]]<br />
# U.S. Geological Survey. National Field Manual for the collection of water quality data. 2006. Vol. Book 9. http://water.usgs.gov/owq/FieldManual/<br />
# Wolfson, Dr. Lois. E. coli Monitoring – Effective Techniques and Test Kits for Volunteers. Michigan Clean Water Corps Conference. s.l. : Michigan State University, October 16, 2007.[[media:WolfsonPresentation.pdf | Test Kit Presentation PDF]]<br />
# Epstein, Charlotte. KNOWLEDGE AND POWER IN GLOBAL ENVIRONMENTAL ACTIVISM. s.l. : International Journal of Peace Studies, 2005.[[media:Epstein_101IJPS.pdf | Epstein PDF]]<br />
# CH. Loi fédérale sur la protection des eaux. [Online] juin 1, 2014. https://www.admin.ch/opc/fr/classified-compilation/19910022/index.html#a4.<br />
# Kleehammer, Katie and Sigler, Adam. Moore Creek Volunteer Monitoring for Escherichia coli - Sampling and analysis. Bozeman : MSU Extension Water Quality, 2012.[[media : Moore_E_Coli.pdf | SOP Moore Creek E.coli sampling PDF]]<br />
# Homogeneous Distribution of Escherichia coli Measured within the Vertical Water Column of Small, Freshwater Streams. Buckalew, David, et al. Farmville, VA : Scientific Research Publishing, March 24, 2014, Water Resource and Protection, pp. 410-421. [[media : Distirbutionofecoliwatercolumn.pdf | Buckalew et all PDF]]<br />
# Micrology LAboratories. Easy Gel Method Procedure. Goshen, Indiana : s.n., 2015. Recomended procedures for chromogeinc media.[[media:Easygel_method_procedure.pdf | Procedure Easygel PDF]]<br />
# Micrology Laboratories. ECA Check Easy guide. Goshen : Manufacturers color guide for chromogenic media.[[media : Eca_check_easygel_guide.pdf | ECA guide to determining bacteria PDF]]<br />
# DIRECTIVE 2006/7/EC concerning the management of bathing water quality. European Union. Strassbourg : s.n., 2006, Official Journal of the European Union.[[media:DIRECTIVE2006EC_.pdf | Directive 2006/7/EC]]<br />
# Canfield, Daniel; Hoyer, Mark; Volunteer Lake Monitoring : Testing the Reliability of Data Collected by the Florida LakeWatch Program: Lake and Reservoir Management-March 2002 [[media : Floridalakes.pdf | Reliability of volunteer data PDF]]<br />
<br />
=== Documents from hammerdirt Clean Beach Projects ===<br />
* [[ Media : Montreux_april_activity_opt.pdf | Activity report Nov 2015 - April 2016]]<br />
* [[ Media : Pilot_project_cbem_montreux.pdf | Pilot project CBEM May 2016]]<br />
* [[Media:Clean_beach_pro_2015.pdf | Hammerdirt Clean Beach Project 2 2015 Draft]]<br />
* [[ Media : CH_OSPAR._COMPARISON_OPT.pdf | Comparison of Lake Geneva beaches to other OSPAR regions]]<br />
* [[ Media : Citizenscience.pdf | Citizen Science and litter studies (french)]]<br />
* [[ Media : MCBP1.pdf | MCBPI 2014-2015 results (French)]]<br />
* [[ Media : Plagespropres_nov2014_aout2015_opt.pdf | MCBPI 2014-2015 results (English)]]<br />
<br />
=== Literature ===<br />
[[Media:07_phytoplancton_camp.2014.pdf | 2014 Report on Leman biomass ]] <br><br />
[[Media:Rapports_Leman_2014.pdf | 2014 Physico-chemical Leman report]]<br />
<br />
=== Relevant Links ===<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253<br />
<br />
<br />
== Documentation and Collaboration Tools ==<br />
----<br />
Agree on documentation and collaboration tools<br />
* Internal communication - hackuarium slack <br />
* Calendar? - we have a biodesign google calendar<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
== Water Collection Protocols ==<br />
----<br />
<br><br><br />
<br />
=== Coliform Bacteria Counting ===<br />
----<br />
The presence of ''E. coli'' in natural waters is a direct indication of fecal contamination of water. Coliform bacteria and other bacterial species can also be found in public waters and contribute to human pathologies. There are several methods to distinguish ''E. coli'', coliform and other bacteria vs other microorganisms that may grow on an agar plate, of special interest 'chromogenic media' which contain substrates that form specific colors depending on enzymes produced by each species.<br />
==== Easy Gel ====<br />
Micrology Labs [http://www.micrologylabs.com/page/93/Coliscan-Easygel Coliscan Easygel]<br />
* Rachel asked for an offer including shipping and the 15% discount for the a coliform bacteria testing medium.<br />
* reminder request sent again 18 April to Jonathan Roth (CEO of Micrology Labs) and Doug Wengerd (who eventually answers notes to their 'info' address)<br />
[http://www.micrologylabs.com/page/95/Instructions Protocol] from the Micrology Labs<br><br />
* there have been some paying complications too, but their large scale order for 100 plates makes the 'per plate' cost half of another option <br><br />
<br />
<br />
To note: the Micrology Lab ECA Easygel plates are somewhat expensive, but can assay up to 5ml of sampled water per plate for ready scoring and disposal. Another currently proposed plate media would not only be less discriminating, but require more equipment for the sterile setup and final cleanup, and probably only allow 0.5ml to be assayed/plate. The Micrology plates are also used in other 'citizen science' campaigns and approved by regulatory bodies...<br />
<br />
==== Other Media ====<br />
* [https://en.wikipedia.org/wiki/Endo_agar Endo agar] where gram negatives are favored to grow. Fermentation of lactose in the medium by coliform bacteria gives metallic green sheen to those colonies.<br />
* [https://en.wikipedia.org/wiki/MacConkey_agar MacConkey agar] - also contains lactose and neutral red as a pH indicator, bile salts to inhibit gram-positive bacteria growth<br />
* [https://en.wikipedia.org/wiki/Sorbitol-MacConkey_agar MacConkey agar with sorbitol] is used to isolate E. coli O157, a pathogenic enteric bacteria<br />
* [https://en.wikipedia.org/wiki/Eosin_methylene_blue Eosin Methylene Blue agar] - Lactose fermenting bacteria turn a dark color, gram positive bacteria also inhibited<br />
<br />
<br />
<br><br />
==== DIY protocol ====<br />
<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br />
==== Other Methods ====<br />
* Good "travaux pratique" [http://www.bioutils.ch/protocoles/13-analyse-de-leau protocol] for bacterial counting and salts concentration from Bioutils, UNIGE <br><br />
* Other [[Media:Bacterial_counts.pdf | protocol]] proposing several direct and indirect methods <br><br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
----<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br />
<br />
=== Water Multi-meter ===<br />
----<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br><br />
<br />
== Press ==<br />
=== Short History of the Collaboration ===<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation from that day can be found here:[[media : Hammerdirt.pdf | How can we work together ?]]<br />
<br><br><br />
'''Brainstorm Results'''<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* Microbial testing - distinguish fecal contaminants and others with selective plates<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
[[Category:Projects]]<br />
[[Category:Work In Progress]]<br />
[[Category:Environment]]</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=7102Micro to Macro Water Pollution2016-05-23T11:19:49Z<p>Sachiko: </p>
<hr />
<div>Community based environmental monitoring has been proven effective in a variety of fields, water quality monitoring by volunteers is in wide practice across North America. Four Swiss nonprofit associations use visible pollution inventories, microbiological monitoring and chemical analysis by combining classic laboratory techniques and the use of innovative bio-reporters to expand the capabilities of community based environmental monitoring.<br><br />
<br />
[[file:Sortingdebris.jpg|thumb|500px|right| hammerdirt team sorting debris at Vevey, Jan 2016. Source: MCBPII]]<br />
[[file : Pierrier.jpg |thumb|500px|right| Sorted debris Plage du Pierrier, Mar 2016. Source: MCBPII]]<br />
== Aims ==<br />
To effectively integrate more advanced and innovative water quality monitoring techniques to classic community based environmental monitoring activites.<br />
<br><br><br />
<br />
<br />
== Collaboration Defined ==<br />
{| class="wikitable"<br />
! Partner<br />
! Role<br />
|-<br />
| [http://www.genomicintegrity.org/ ACTION FOR GENOMIC INTEGRITY THROUGH RESEARCH!] <br />
| Technical oversight for the microbial assays, training of hammerdirt staff, quality control of laboratory operations and of sample processing and analyses.<br />
|-<br />
| [http://www.hackuarium.ch/fr/ HACKUARIUM]<br />
| Laboratory infrastructure and security, testing equipment and supplies for biologicals<br />
|-<br />
| [http://www.hammerdirt.ch/ HAMMERDIRT]<br />
| Collection and processing of samples, data storage and administration. Communication of analyses and results.<br />
|-<br />
| [https://biodesign.cc/ BIODESIGN.CC]<br />
| Analysis of samples for mercury, Cadmium Zinc, Alkanes and arsenic using the bio-reporters<br />
|}<br />
<br />
== Water Quality and Analysis ==<br />
=== Spring and Summer 2016 ===<br />
[[File:noswimming.jpg|thumb|right|400px|Location 5, Montreux rive gauche source : MCBPI July 2014]]<br />
==== Introduction ====<br />
<br />
One of the benefits of a “Community Based Environmental Monitoring” (CBEM) project is to expand the monitoring capacity of government agencies and engage the public in environmental stewardship. In response to questions from the public and our own professional curiosity we have decided to initiate a limited CBEM project (1) (2) .<br><br />
<br />
As part of the Montreux Clean Beach Project II(MCBPII), a water quality testing (WQT) program is being initiated at selected sites of the MCBPII. Symptoms reported by members and frequent bathers in the lake during previous summer seasons have sometimes been attributed to low bathing water quality, influenced by increased anthropogenic pressure of lakefront activities during certain times of the year. This year's WQT aims to gather microbiological data over a six week period in order to test this hypothesis.<br><br />
<br />
<br />
Meetings at “La Maison de la Rivière” and the “Institut National de Recherche Agronomique” support the idea that the WQT information proposed is not regularly collected at the Haut-Lac locations covered by the MCBPII.<br><br />
<br><br />
<br />
==== Objectives ====<br />
CBEM programs are designed to educate the public, involve local citizens in environmental stewardship and provide reliable data for government and other interested organizations. In this regard the MCBPII CBEM program is no different than that of any other existing project. (2)(3)(4)(5)(6)<br><br />
<br />
Specifically, the goals for this project are to:<br />
# Collect reliable water quality data as defined by the World Water Monitoring Challenge <br />
# Collect and enumerate the quantity of key bacteriological indicators, in particular those related to fecal contamination <br />
# Increase the skills of hammerdirt staff in regards to collecting and processing water samples.<br />
# Make the obtained data free and open to use for all concerned <br />
# Inform the public about affordable and simple water monitoring techniques<br />
# Inform the public of community based resources designed to advance scientific literacy<br />
<br><br />
More information [http://cbemn.ca/ CBEM Network]<br />
<br />
==== Deliverables ====<br />
[[File:Montreux_april_activity_opt_short-2.jpg|thumb|400px|right|Source: MCBPII Activity Report Nov 2015 - April 2016]]<br />
The objectives of a CBEM are designed to increase the monitoring capacity of current public systems and provide reliable, accessible data for the public and other government researchers. Data gathered from this project will be reported with our regular activity reports and the raw data will be available for download within 72 hours of the testing date from our repository on [https://github.com/hammerdirt/beachLitterSurveys Github] or through the KoboToolbox for the location in question. This document along with sampling protocols and all other supporting documents will be available on the wiki.<br />
<br><br><br />
Weekly results will be furnished to the CIPEL, SIGE and INRA:<br />
:# Location and number of tests<br />
:# Results of tests completed for the week<br />
An end of project report will be published in PDF format, available for interested parties, and include:<br />
:# Summary statistics and findings<br />
:# Graphs/plots<br />
:# Map overlay with densities and values<br />
:# Comparison with government supplied data (if available)<br />
:# Discussion of limitations and possible improvements to future CBEM projects<br />
<br />
More information [http://www.kobotoolbox.org/ KoboToolbox]<br />
<br />
=== Testing Materials ===<br />
==== Heavy Metals ====<br />
Bioreporters, designed and fabricated by biodesign.cc will be used to test for Alkanes, Arsenic, Mercury and Cadmium/Zinc. <br><br />
<br />
What are bioreporters ? Get some background information [http://wiki.biodesign.cc/wiki/Bioreporters_in_Pollutant_Detection here]<br />
<br />
==== Turbidity, temp, DO and PH ====<br />
Testing materials and supplies will be procured from the [http://www.monitorwater.org/ World Water Monitoring Challenge] an international program managed by the [http://www.iwa-network.org/ International Water Association] and the [http://www.wef.org/ Water Environment Federation].<br />
<br><br />
Assembled and sold by Lamotte company as a “basic test kit,” each kit includes one set of hardware and enough reagents to conduct up to 50 rounds of testing for pH, dissolved oxygen, temperature, and turbidity. Included are:<br />
# [[media : English-Spanish_Instructions.pdf |Instruction booklet]]<br />
# Sample collection jar<br />
# PH test tube<br />
# Dissolved oxygen vial<br />
# Secchi disk decal<br />
# Temperature strips (14-40°C and 0-12°C)<br />
# 50 pH reagent tablets (enough for 50 tests)<br />
# 100 Dissolved oxygen reagent tablets (enough for 50 tests)<br />
# Color chart for determining DO, pH and turbidity test results<br />
<br><br />
<br />
[[file:Eca_check_easygel_guide.pg1.jpg|thumb|right|400px|Visualizing organisms with ECA Check source: ECA Easygel guide]]<br />
==== Microbiological Analyses ====<br />
Presence and quantity of E.coli, other coli forms, Salmonella and Aeromonas will be tested using [http://www.micrologylabs.com/products/3/ECA-Check-Easygel ECA Check Easygel]. Easygel was first approved for [http://www.usawaterquality.org/ Water Watch] volunteer monitoring programs in the USA in 1999. A study released in 2009 compared the results of “Easygel” and “3M Petrifilm” used by volunteers to the results of laboratory analysis. Both methods had an overall accuracy rate above 80%. One big benefit of the Easygel format is that environmental samples of up to 5ml can be readily plated, with no worries about having to melt (and cool down!) agarose as used in standard microbial plates.(7)(8)(10)(14)<br><br />
<br />
Members of the Hackuarium laboratory have used “Easygel” in previous educational activities, thus facilitating the training of hammedirt staff and volunteers.<br />
<br />
=== Sampling Methods ===<br />
<br />
'''Water samples will be taken just below the surface (0.5m) and collected in sterile containers with a secure, air-tight lid.'''<br><br />
<br />
'''Advantage:''' simple and inexpensive, an important consideration to a program on a budget. It also does not require any special sampling apparatus. The volunteer holds a sampling container under the surface of the water, expells visible air bubbles, and closes the container under the water (to avoids losing dissolved gasses, particularly important if testing for volatile analytes).<br><br />
<br />
'''Disadvantage:''' vertical gradients of temperature, oxygen, nutrients, and algae may be missed in these near surface samples. Deep lakes have a thermal gradient in the summer, and Lac Leman has at least two thermal regions (and, possibly, at least two chemical regions as well). Even in shallow, usually well-mixed lakes, chemical gradients will develop during calm periods.<br><br />
<br />
Sampling methods by other CBEM projects : [[media:Stepenucketal2010.pdf | Stepenuck et all PDF]], [[media:Wfs-2005-01.pdf|Fact Sheet Volunteer Water Monitoring]], [[media : Moore_E_Coli.pdf | SOP Moore Creek E.coli sampling PDF]], [[media :Texasstream.pdf | Texas Sampling PDF]]<br />
<br />
==== Heavy Metals ====<br />
Two samples of 250ml will be taken and transported to the hackuarium for later analysis. One sample will be acidified to fix the heavy metals in solution.<br />
<br />
==== Turbidity, temp, DO and PH ====<br />
One sample will be taken using the container supplied with the testing kit and processed immediately. <br><br />
<br />
==== Microbiological samples ====<br />
'''Three independent samples will be taken from each designated site''' in 15ml conical tubes pre-labeled in the following manner:<br />
# Location<br />
# Date<br />
# Sample number for that day and location<br />
# Time of sample<br />
<br><br />
Once collected, the '''samples will be placed on ice and transported to the facility at Renens for plating on the ECA Check plates within 6 hours.''' Label information will be recorded in the field notes and the “KoboToolBox” for that sampling date and location.<br />
<br />
=== Processing samples and recording results ===<br />
==== Turbidity, temp, DO and PH ====<br />
The instructions provided with the kit will be followed and the results will be noted in the field manual and entered into the “KoboToolbox” form for that sampling date and location.<br />
<br />
==== Microbiologicals ====<br />
One petri dish per sample will be labeled in the same manner as the sample container with the addition of the quantity of sample added to the media. A 1-5ml of sample water will be mixed into the provided gel media solution, plated and incubated for about 18 hours at the Hackuarium facility in Renens.<br><br />
<br />
After incubation, plates will be scored, counting total colony forming units (CFU), and each identifiable species (E. coli CFUs will appear dark blue, other coliform CFUs will appear lighter blue-gray or blue-violet, Aeromonas spp. will appear as pink to very light pink, and Salmonella spp. will appear as light green colonies). Data will be reported as CFU/100ml of sample.<br><br />
<br />
With values from three independent samples at each site, means and standard errors can be used to test significance of the obtained data over the course of the sampling period.<br />
<br />
=== Locations ===<br />
[[File:tweet.jpg|thumb|right|600px |Sampling locations for biological and chemical analysis, source: Sampling and analysis plan MCBPII]]<br />
Three of the five locations are currently part of the MCBPII beach-litter-survey project. Point 4 will be added to the beach litter survey by using a net to catch visible pollutants on the water surface below the boat dock. Point 3 will only be monitored for chemistry and biologicals. Correlations of the test results with the physical location of the sampling will be of great interest.<br />
<br />
<br />
<br />
To see a map of the locations that benefit from regular water quality monitoring : [http://www.vd.ch/themes/environnement/eaux/eau-de-baignade/qualite-de-leau-des-plages-cartographie/ Eau de baignade]<br />
<br />
=== Testing Schedule ===<br />
==== Calendar from biodesign.cc to be embedded here ====<br />
key dates to be defined :<br />
# Training for sampling and plating<br />
# Event public demonstration of sampling and plating<br />
# Start date for chemical samples<br />
# Start date for microbiologicals<br />
# Event public discussion of results, improvements and future projects<br />
==== Microbiologicals ====<br />
Testing will begin about 20 June 2016, and weekly samples will be taken from locations 3, 4 and 5. A 'negative control' sample will also be obtained each week from a local drinking fountain (labelled 'eau potable'). A positive control from an urban river (like the Vuachère or other) is also possible.<br><br />
<br />
If a Tuesday afternoon testing protocol is followed over 7 weeks, the timeline would run from 21 June -2 August, require 21 sterile 15ml conical tubes for the water sampling, and 21 ECA Check EasyGel plates per site. After including a single 'negative control' for each sampling day, this will require 70 plates.<br><br />
<br />
In case there are too many bacteria to count (TMTC) from certain samples, samples will be saved at 4oC and further dilutions can be also plated and scored.<br><br />
<br />
==== Turbidity, temp, DO and PH ====<br />
Testing will begin on the Tuesday or Thursday the week the kits are received (late May). The kit contains enough reagents to conduct 50 tests, thus allowing us to monitor the locations for 10 weeks. Data will be carefully recorded, digitized and analyzed.<br><br />
<br />
==== Field Blanks ====<br />
Field blanks are used to assess potential contamination from sample handling, airborne materials, equipment, media, and other sources. A field blank usually consists of a sterile diluent sample of 2 mL that is taken to the site and poured into a properly labeled sample container during the first bacteria sampling event of that day. The blank sample is collected in the same type of container, labeled as a field blank, and handled and analyzed along with all the bacteria samples collected on that day. It is used to identify errors or contamination in sample collection and analysis.<br />
<br />
=== Data === <br />
==== Handling and storage ====<br />
The addition of water quality testing will require changes in our digital form and reporting methods. The form currently used by surveyors will change, thus separating the data in two sections, one section prior to WQT and one after. Data for the two sections will have to be merged prior to any analysis. The results of bacterial testing will be available 48-72 hours after sampling, thus adding another step to the survey. This should not, however, change the availability of the other survey results which is currently 24 hours after each survey.<br><br />
<br />
==== Data analysis and presentation ====<br />
<br />
The existing data set for MCBPII includes visible pollution surveys, hydrologic and meteorological data. With the addition of microbiological and basic water chemistry a more complete picture of the environmental status of the locations in question can be established.<br><br />
<br />
Two interpretations of the microbiological data will be used: the geometric mean and the 95th percentile. The geometric mean is in common use in North America and the 95th percentile method conforms to EU directive 2006/7/EC. Furthermore, any publicly available water quality data in the area will be presented and integrated where appropriate.<br><br />
<br />
The relationship between the results of WQT and the quantity and type of visible pollutants will be explored.<br><br />
<br />
'''How is the water currently monitored and evaluated ? '''Here is the source document from the Swiss Confederation [[media :Evaluation+des+eaux+de+baignade.pdf | Eaux de baignade]]<br />
<br />
== References ==<br />
<br />
=== Sampling and Analysis in Community Based Environmental Monitoring ===<br />
# Assessing the performance of volunteers in monitoring Streams. Fore, Leska, Paulsen, Kit and O'Laughlin, Kate. Bellvue, WA : Blackwell Science, 2001, Fresh Water Biology. [[media:Fore,2001.pdf|Fore et all pdf]]<br />
# Volunteer environmental monitoring and the role of the universities : The case of Citizens Environment Watch. Savan, Beth, Morgan, Alexis and Gore, Chritopher. Toronto : s.n., June 2003, Environmental Management, Vol. 31, pp. 561-568.[[media:Savan+2003.pdf | Savan et all PDF]]<br />
# Nicholson, Emily, Ryan, Jane and Hodgkins, David. Community Data – where does the value lie? Assessing confidence limits of community collected water quality data. Victoria : Waterwatch Victoria c/o Department of Natural Resources & Environment, 2002. [[media:NicholsonEmily.pdf|Nicholson et all PDF]]<br />
# A review of citizen science and community-based environmental monitoring: issues and opportunities. Conrad, Cathy and Hilchey, Krista. [ed.] Springer. Halifax, Nova Scotia : s.n., 2010, Environ Monit Assess, pp. 273-291. [[media :Conrad-hilchey-2011-review.pdf | Conrad & Hilchey PDF]] <br />
# World water monitoring challenge. Instructions. Geneva : World water montioring Challenge, 2015. Instructions for the water monitoring test kit provided by the world water monitoring challenge.[[media : English-Spanish_Instructions.pdf | Instructions for PH, DO, temp and turbidity PDF]]<br />
# World Health Organization. Guidelines for safe recreational water environments. Geneva : World HEalth Organization, 2003. Vol. 1 Coastal and Fresh Waters. [[media:WhoGuideLines.pdf|WHO Guide Lines]]<br />
# Texas Stream Team Volunteer Water Quality Monitoring. E.coli Monitoring and Analysis Procedures. 2010. [[media :Texasstream.pdf | Texas Sampling PDF]]<br />
# Stepenuk, Kristine, et al. Volunteer monitoring of E. coli in streams of the upper Midwestern United States: a comparison of methods. [ed.] University of Wisconsin—Extension. Madison : Springer, 2010.[[media:Stepenucketal2010.pdf | Stepenuck et all PDF]]<br />
# Myers, D.N., et al. Fecal indicator bacteria (ver. 2.1). [book auth.] U.S. Geological survey. U.S. Geological Survey Techniques of Water-Resources Investigations. 2014, Vol. book 9, chap. A7, section 7.1.[[media :Fecalindicators.pdf | Myers et all PDF]] <br />
# Iowa Department of Natural Resources, Geological Survey. Citizens Monitoring Bacteria. Iowa City : s.n., 2005. Vols. Water Fact Sheet 2005-1.[[media:Wfs-2005-01.pdf|Fact Sheet Volunteer Water Monitoring]]<br />
# Arizona Department of Environmental Quality Water Quality Improvement Grant Program. Writing Effective Monitoring Plans. s.l. : Arizona department of environmental quality, 2008. TM 08-04.[[media:Writing.pdf | Guide to writing a sampling plan PDF]]<br />
# USEPA REGION 9 LABORATORY. STANDARD OPERATING PROCEDURE FOR VOLUNTEER MONITORING OF SURFACE WATERS FOR BACTERIA. Richmond : United States Environmental Agency, 2007.[[media:SOPEPARICHMOND.pdf| SOP Volunteer monitoring PDF]]<br />
# U.S. Geological Survey. National Field Manual for the collection of water quality data. 2006. Vol. Book 9. http://water.usgs.gov/owq/FieldManual/<br />
# Wolfson, Dr. Lois. E. coli Monitoring – Effective Techniques and Test Kits for Volunteers. Michigan Clean Water Corps Conference. s.l. : Michigan State University, October 16, 2007.[[media:WolfsonPresentation.pdf | Test Kit Presentation PDF]]<br />
# Epstein, Charlotte. KNOWLEDGE AND POWER IN GLOBAL ENVIRONMENTAL ACTIVISM. s.l. : International Journal of Peace Studies, 2005.[[media:Epstein_101IJPS.pdf | Epstein PDF]]<br />
# CH. Loi fédérale sur la protection des eaux. [Online] juin 1, 2014. https://www.admin.ch/opc/fr/classified-compilation/19910022/index.html#a4.<br />
# Kleehammer, Katie and Sigler, Adam. Moore Creek Volunteer Monitoring for Escherichia coli - Sampling and analysis. Bozeman : MSU Extension Water Quality, 2012.[[media : Moore_E_Coli.pdf | SOP Moore Creek E.coli sampling PDF]]<br />
# Homogeneous Distribution of Escherichia coli Measured within the Vertical Water Column of Small, Freshwater Streams. Buckalew, David, et al. Farmville, VA : Scientific Research Publishing, March 24, 2014, Water Resource and Protection, pp. 410-421. [[media : Distirbutionofecoliwatercolumn.pdf | Buckalew et all PDF]]<br />
# Micrology LAboratories. Easy Gel Method Procedure. Goshen, Indiana : s.n., 2015. Recomended procedures for chromogeinc media.[[media:Easygel_method_procedure.pdf | Procedure Easygel PDF]]<br />
# Micrology Laboratories. ECA Check Easy guide. Goshen : Manufacturers color guide for chromogenic media.[[media : Eca_check_easygel_guide.pdf | ECA guide to determining bacteria PDF]]<br />
# DIRECTIVE 2006/7/EC concerning the management of bathing water quality. European Union. Strassbourg : s.n., 2006, Official Journal of the European Union.[[media:DIRECTIVE2006EC_.pdf | Directive 2006/7/EC]]<br />
# Canfield, Daniel; Hoyer, Mark; Volunteer Lake Monitoring : Testing the Reliability of Data Collected by the Florida LakeWatch Program: Lake and Reservoir Management-March 2002 [[media : Floridalakes.pdf | Reliability of volunteer data PDF]]<br />
<br />
=== Documents from hammerdirt Clean Beach Projects ===<br />
* [[ Media : Montreux_april_activity_opt.pdf | Activity report Nov 2015 - April 2016]]<br />
* [[ Media : Pilot_project_cbem_montreux.pdf | Pilot project CBEM May 2016]]<br />
* [[Media:Clean_beach_pro_2015.pdf | Hammerdirt Clean Beach Project 2 2015 Draft]]<br />
* [[ Media : CH_OSPAR._COMPARISON_OPT.pdf | Comparison of Lake Geneva beaches to other OSPAR regions]]<br />
* [[ Media : Citizenscience.pdf | Citizen Science and litter studies (french)]]<br />
* [[ Media : MCBP1.pdf | MCBPI 2014-2015 results (French)]]<br />
* [[ Media : Plagespropres_nov2014_aout2015_opt.pdf | MCBPI 2014-2015 results (English)]]<br />
<br />
=== Literature ===<br />
[[Media:07_phytoplancton_camp.2014.pdf | 2014 Report on Leman biomass ]] <br><br />
[[Media:Rapports_Leman_2014.pdf | 2014 Physico-chemical Leman report]]<br />
<br />
=== Relevant Links ===<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253<br />
<br />
<br />
== Documentation and Collaboration Tools ==<br />
----<br />
Agree on documentation and collaboration tools<br />
* Internal communication - hackuarium slack <br />
* Calendar? - we have a biodesign google calendar<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
== Water Collection Protocols ==<br />
----<br />
<br><br><br />
<br />
=== Coliform Bacteria Counting ===<br />
----<br />
The presence of ''E. coli'' in natural waters is a direct indication of fecal contamination of water. Coliform bacteria and other bacterial species can also be found in public waters and contribute to human pathologies. There are several methods to distinguish ''E. coli'', coliform and other bacteria vs other microorganisms that may grow on an agar plate, of special interest 'chromogenic media' which contain substrates that form specific colors depending on enzymes produced by each species.<br />
==== Easy Gel ====<br />
Micrology Labs [http://www.micrologylabs.com/page/93/Coliscan-Easygel Coliscan Easygel]<br />
* Rachel asked for an offer including shipping and the 15% discount for the a coliform bacteria testing medium.<br />
* reminder request sent again 18 April to Jonathan Roth (CEO of Micrology Labs) and Doug Wengerd (who eventually answers notes to their 'info' address)<br />
[http://www.micrologylabs.com/page/95/Instructions Protocol] from the Micrology Labs<br><br />
* there have been some paying complications too, but their large scale order for 100 plates makes the 'per plate' cost half of another option <br><br />
<br />
<br />
To note: the Micrology Lab ECA Easygel plates are somewhat expensive, but can assay up to 5ml of sampled water per plate for ready scoring and disposal. Another currently proposed plate media would not only be less discriminating, but require more equipment for the sterile setup and final cleanup, and probably only allow 0.5ml to be assayed/plate. The Micrology plates are also used in other 'citizen science' campaigns and approved by regulatory bodies...<br />
<br />
==== Other Media ====<br />
* [https://en.wikipedia.org/wiki/Endo_agar Endo agar] where gram negatives are favored to grow. Fermentation of lactose in the medium by coliform bacteria gives metallic green sheen to those colonies.<br />
* [https://en.wikipedia.org/wiki/MacConkey_agar MacConkey agar] - also contains lactose and neutral red as a pH indicator, bile salts to inhibit gram-positive bacteria growth<br />
* [https://en.wikipedia.org/wiki/Sorbitol-MacConkey_agar MacConkey agar with sorbitol] is used to isolate E. coli O157, a pathogenic enteric bacteria<br />
* [https://en.wikipedia.org/wiki/Eosin_methylene_blue Eosin Methylene Blue agar] - Lactose fermenting bacteria turn a dark color, gram positive bacteria also inhibited<br />
<br />
<br />
<br><br />
==== DIY protocol ====<br />
<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br />
==== Other Methods ====<br />
* Good "travaux pratique" [http://www.bioutils.ch/protocoles/13-analyse-de-leau protocol] for bacterial counting and salts concentration from Bioutils, UNIGE <br><br />
* Other [[Media:Bacterial_counts.pdf | protocol]] proposing several direct and indirect methods <br><br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
----<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br />
<br />
=== Water Multi-meter ===<br />
----<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br><br />
<br />
<br />
== Press ==<br />
=== Short History of the Collaboration ===<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation from that day can be found here:[[media : Hammerdirt.pdf | How can we work together ?]]<br />
<br><br><br />
'''Brainstorm Results'''<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* Microbial testing - distinguish fecal contaminants and others with selective plates<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
[[Category:Projects]]<br />
[[Category:Work In Progress]]<br />
[[Category:Environment]]</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=7101Micro to Macro Water Pollution2016-05-23T11:17:42Z<p>Sachiko: </p>
<hr />
<div>Community based environmental monitoring has been proven effective in a variety of fields, water quality monitoring by volunteers is in wide practice across North America. Four Swiss nonprofit associations use visible pollution inventories, microbiological monitoring and chemical analysis by combining classic laboratory techniques and the use of innovative bio-reporters to expand the capabilities of community based environmental monitoring.<br><br />
<br />
[[file:Sortingdebris.jpg|thumb|500px|right| hammerdirt team sorting debris at Vevey, Jan 2016. Source: MCBPII]]<br />
[[file : Pierrier.jpg |thumb|500px|right| Sorted debris Plage du Pierrier, Mar 2016. Source: MCBPII]]<br />
== Aims ==<br />
To effectively integrate more advanced and innovative water quality monitoring techniques to classic community based environmental monitoring activites.<br />
<br><br><br />
<br />
== Brainstorm Results ==<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* Microbial testing - distinguish fecal contaminants and others with selective plates<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
== Collaboration Defined ==<br />
{| class="wikitable"<br />
! Partner<br />
! Role<br />
|-<br />
| [http://www.genomicintegrity.org/ ACTION FOR GENOMIC INTEGRITY THROUGH RESEARCH!] <br />
| Technical oversight for the microbial assays, training of hammerdirt staff, quality control of laboratory operations and of sample processing and analyses.<br />
|-<br />
| [http://www.hackuarium.ch/fr/ HACKUARIUM]<br />
| Laboratory infrastructure and security, testing equipment and supplies for biologicals<br />
|-<br />
| [http://www.hammerdirt.ch/ HAMMERDIRT]<br />
| Collection and processing of samples, data storage and administration. Communication of analyses and results.<br />
|-<br />
| [https://biodesign.cc/ BIODESIGN.CC]<br />
| Analysis of samples for mercury, Cadmium Zinc, Alkanes and arsenic using the bio-reporters<br />
|}<br />
<br />
== Water Quality and Analysis ==<br />
=== Spring and Summer 2016 ===<br />
[[File:noswimming.jpg|thumb|right|400px|Location 5, Montreux rive gauche source : MCBPI July 2014]]<br />
==== Introduction ====<br />
<br />
One of the benefits of a “Community Based Environmental Monitoring” (CBEM) project is to expand the monitoring capacity of government agencies and engage the public in environmental stewardship. In response to questions from the public and our own professional curiosity we have decided to initiate a limited CBEM project (1) (2) .<br><br />
<br />
As part of the Montreux Clean Beach Project II(MCBPII), a water quality testing (WQT) program is being initiated at selected sites of the MCBPII. Symptoms reported by members and frequent bathers in the lake during previous summer seasons have sometimes been attributed to low bathing water quality, influenced by increased anthropogenic pressure of lakefront activities during certain times of the year. This year's WQT aims to gather microbiological data over a six week period in order to test this hypothesis.<br><br />
<br />
<br />
Meetings at “La Maison de la Rivière” and the “Institut National de Recherche Agronomique” support the idea that the WQT information proposed is not regularly collected at the Haut-Lac locations covered by the MCBPII.<br><br />
<br><br />
<br />
==== Objectives ====<br />
CBEM programs are designed to educate the public, involve local citizens in environmental stewardship and provide reliable data for government and other interested organizations. In this regard the MCBPII CBEM program is no different than that of any other existing project. (2)(3)(4)(5)(6)<br><br />
<br />
Specifically, the goals for this project are to:<br />
# Collect reliable water quality data as defined by the World Water Monitoring Challenge <br />
# Collect and enumerate the quantity of key bacteriological indicators, in particular those related to fecal contamination <br />
# Increase the skills of hammerdirt staff in regards to collecting and processing water samples.<br />
# Make the obtained data free and open to use for all concerned <br />
# Inform the public about affordable and simple water monitoring techniques<br />
# Inform the public of community based resources designed to advance scientific literacy<br />
<br><br />
More information [http://cbemn.ca/ CBEM Network]<br />
<br />
==== Deliverables ====<br />
[[File:Montreux_april_activity_opt_short-2.jpg|thumb|400px|right|Source: MCBPII Activity Report Nov 2015 - April 2016]]<br />
The objectives of a CBEM are designed to increase the monitoring capacity of current public systems and provide reliable, accessible data for the public and other government researchers. Data gathered from this project will be reported with our regular activity reports and the raw data will be available for download within 72 hours of the testing date from our repository on [https://github.com/hammerdirt/beachLitterSurveys Github] or through the KoboToolbox for the location in question. This document along with sampling protocols and all other supporting documents will be available on the wiki.<br />
<br><br><br />
Weekly results will be furnished to the CIPEL, SIGE and INRA:<br />
:# Location and number of tests<br />
:# Results of tests completed for the week<br />
An end of project report will be published in PDF format, available for interested parties, and include:<br />
:# Summary statistics and findings<br />
:# Graphs/plots<br />
:# Map overlay with densities and values<br />
:# Comparison with government supplied data (if available)<br />
:# Discussion of limitations and possible improvements to future CBEM projects<br />
<br />
More information [http://www.kobotoolbox.org/ KoboToolbox]<br />
<br />
=== Testing Materials ===<br />
==== Heavy Metals ====<br />
Bioreporters, designed and fabricated by biodesign.cc will be used to test for Alkanes, Arsenic, Mercury and Cadmium/Zinc. <br><br />
<br />
What are bioreporters ? Get some background information [http://wiki.biodesign.cc/wiki/Bioreporters_in_Pollutant_Detection here]<br />
<br />
==== Turbidity, temp, DO and PH ====<br />
Testing materials and supplies will be procured from the [http://www.monitorwater.org/ World Water Monitoring Challenge] an international program managed by the [http://www.iwa-network.org/ International Water Association] and the [http://www.wef.org/ Water Environment Federation].<br />
<br><br />
Assembled and sold by Lamotte company as a “basic test kit,” each kit includes one set of hardware and enough reagents to conduct up to 50 rounds of testing for pH, dissolved oxygen, temperature, and turbidity. Included are:<br />
# [[media : English-Spanish_Instructions.pdf |Instruction booklet]]<br />
# Sample collection jar<br />
# PH test tube<br />
# Dissolved oxygen vial<br />
# Secchi disk decal<br />
# Temperature strips (14-40°C and 0-12°C)<br />
# 50 pH reagent tablets (enough for 50 tests)<br />
# 100 Dissolved oxygen reagent tablets (enough for 50 tests)<br />
# Color chart for determining DO, pH and turbidity test results<br />
<br><br />
<br />
[[file:Eca_check_easygel_guide.pg1.jpg|thumb|right|400px|Visualizing organisms with ECA Check source: ECA Easygel guide]]<br />
==== Microbiological Analyses ====<br />
Presence and quantity of E.coli, other coli forms, Salmonella and Aeromonas will be tested using [http://www.micrologylabs.com/products/3/ECA-Check-Easygel ECA Check Easygel]. Easygel was first approved for [http://www.usawaterquality.org/ Water Watch] volunteer monitoring programs in the USA in 1999. A study released in 2009 compared the results of “Easygel” and “3M Petrifilm” used by volunteers to the results of laboratory analysis. Both methods had an overall accuracy rate above 80%. One big benefit of the Easygel format is that environmental samples of up to 5ml can be readily plated, with no worries about having to melt (and cool down!) agarose as used in standard microbial plates.(7)(8)(10)(14)<br><br />
<br />
Members of the Hackuarium laboratory have used “Easygel” in previous educational activities, thus facilitating the training of hammedirt staff and volunteers.<br />
<br />
=== Sampling Methods ===<br />
<br />
'''Water samples will be taken just below the surface (0.5m) and collected in sterile containers with a secure, air-tight lid.'''<br><br />
<br />
'''Advantage:''' simple and inexpensive, an important consideration to a program on a budget. It also does not require any special sampling apparatus. The volunteer holds a sampling container under the surface of the water, expells visible air bubbles, and closes the container under the water (to avoids losing dissolved gasses, particularly important if testing for volatile analytes).<br><br />
<br />
'''Disadvantage:''' vertical gradients of temperature, oxygen, nutrients, and algae may be missed in these near surface samples. Deep lakes have a thermal gradient in the summer, and Lac Leman has at least two thermal regions (and, possibly, at least two chemical regions as well). Even in shallow, usually well-mixed lakes, chemical gradients will develop during calm periods.<br><br />
<br />
Sampling methods by other CBEM projects : [[media:Stepenucketal2010.pdf | Stepenuck et all PDF]], [[media:Wfs-2005-01.pdf|Fact Sheet Volunteer Water Monitoring]], [[media : Moore_E_Coli.pdf | SOP Moore Creek E.coli sampling PDF]], [[media :Texasstream.pdf | Texas Sampling PDF]]<br />
<br />
==== Heavy Metals ====<br />
Two samples of 250ml will be taken and transported to the hackuarium for later analysis. One sample will be acidified to fix the heavy metals in solution.<br />
<br />
==== Turbidity, temp, DO and PH ====<br />
One sample will be taken using the container supplied with the testing kit and processed immediately. <br><br />
<br />
==== Microbiological samples ====<br />
'''Three independent samples will be taken from each designated site''' in 15ml conical tubes pre-labeled in the following manner:<br />
# Location<br />
# Date<br />
# Sample number for that day and location<br />
# Time of sample<br />
<br><br />
Once collected, the '''samples will be placed on ice and transported to the facility at Renens for plating on the ECA Check plates within 6 hours.''' Label information will be recorded in the field notes and the “KoboToolBox” for that sampling date and location.<br />
<br />
=== Processing samples and recording results ===<br />
==== Turbidity, temp, DO and PH ====<br />
The instructions provided with the kit will be followed and the results will be noted in the field manual and entered into the “KoboToolbox” form for that sampling date and location.<br />
<br />
==== Microbiologicals ====<br />
One petri dish per sample will be labeled in the same manner as the sample container with the addition of the quantity of sample added to the media. A 1-5ml of sample water will be mixed into the provided gel media solution, plated and incubated for about 18 hours at the Hackuarium facility in Renens.<br><br />
<br />
After incubation, plates will be scored, counting total colony forming units (CFU), and each identifiable species (E. coli CFUs will appear dark blue, other coliform CFUs will appear lighter blue-gray or blue-violet, Aeromonas spp. will appear as pink to very light pink, and Salmonella spp. will appear as light green colonies). Data will be reported as CFU/100ml of sample.<br><br />
<br />
With values from three independent samples at each site, means and standard errors can be used to test significance of the obtained data over the course of the sampling period.<br />
<br />
=== Locations ===<br />
[[File:tweet.jpg|thumb|right|600px |Sampling locations for biological and chemical analysis, source: Sampling and analysis plan MCBPII]]<br />
Three of the five locations are currently part of the MCBPII beach-litter-survey project. Point 4 will be added to the beach litter survey by using a net to catch visible pollutants on the water surface below the boat dock. Point 3 will only be monitored for chemistry and biologicals. Correlations of the test results with the physical location of the sampling will be of great interest.<br />
<br />
<br />
<br />
To see a map of the locations that benefit from regular water quality monitoring : [http://www.vd.ch/themes/environnement/eaux/eau-de-baignade/qualite-de-leau-des-plages-cartographie/ Eau de baignade]<br />
<br />
=== Testing Schedule ===<br />
==== Calendar from biodesign.cc to be embedded here ====<br />
key dates to be defined :<br />
# Training for sampling and plating<br />
# Event public demonstration of sampling and plating<br />
# Start date for chemical samples<br />
# Start date for microbiologicals<br />
# Event public discussion of results, improvements and future projects<br />
==== Microbiologicals ====<br />
Testing will begin about 20 June 2016, and weekly samples will be taken from locations 3, 4 and 5. A 'negative control' sample will also be obtained each week from a local drinking fountain (labelled 'eau potable'). A positive control from an urban river (like the Vuachère or other) is also possible.<br><br />
<br />
If a Tuesday afternoon testing protocol is followed over 7 weeks, the timeline would run from 21 June -2 August, require 21 sterile 15ml conical tubes for the water sampling, and 21 ECA Check EasyGel plates per site. After including a single 'negative control' for each sampling day, this will require 70 plates.<br><br />
<br />
In case there are too many bacteria to count (TMTC) from certain samples, samples will be saved at 4oC and further dilutions can be also plated and scored.<br><br />
<br />
==== Turbidity, temp, DO and PH ====<br />
Testing will begin on the Tuesday or Thursday the week the kits are received (late May). The kit contains enough reagents to conduct 50 tests, thus allowing us to monitor the locations for 10 weeks. Data will be carefully recorded, digitized and analyzed.<br><br />
<br />
==== Field Blanks ====<br />
Field blanks are used to assess potential contamination from sample handling, airborne materials, equipment, media, and other sources. A field blank usually consists of a sterile diluent sample of 2 mL that is taken to the site and poured into a properly labeled sample container during the first bacteria sampling event of that day. The blank sample is collected in the same type of container, labeled as a field blank, and handled and analyzed along with all the bacteria samples collected on that day. It is used to identify errors or contamination in sample collection and analysis.<br />
<br />
=== Data === <br />
==== Handling and storage ====<br />
The addition of water quality testing will require changes in our digital form and reporting methods. The form currently used by surveyors will change, thus separating the data in two sections, one section prior to WQT and one after. Data for the two sections will have to be merged prior to any analysis. The results of bacterial testing will be available 48-72 hours after sampling, thus adding another step to the survey. This should not, however, change the availability of the other survey results which is currently 24 hours after each survey.<br><br />
<br />
==== Data analysis and presentation ====<br />
<br />
The existing data set for MCBPII includes visible pollution surveys, hydrologic and meteorological data. With the addition of microbiological and basic water chemistry a more complete picture of the environmental status of the locations in question can be established.<br><br />
<br />
Two interpretations of the microbiological data will be used: the geometric mean and the 95th percentile. The geometric mean is in common use in North America and the 95th percentile method conforms to EU directive 2006/7/EC. Furthermore, any publicly available water quality data in the area will be presented and integrated where appropriate.<br><br />
<br />
The relationship between the results of WQT and the quantity and type of visible pollutants will be explored.<br><br />
<br />
'''How is the water currently monitored and evaluated ? '''Here is the source document from the Swiss Confederation [[media :Evaluation+des+eaux+de+baignade.pdf | Eaux de baignade]]<br />
<br />
== References ==<br />
<br />
=== Sampling and Analysis in Community Based Environmental Monitoring ===<br />
# Assessing the performance of volunteers in monitoring Streams. Fore, Leska, Paulsen, Kit and O'Laughlin, Kate. Bellvue, WA : Blackwell Science, 2001, Fresh Water Biology. [[media:Fore,2001.pdf|Fore et all pdf]]<br />
# Volunteer environmental monitoring and the role of the universities : The case of Citizens Environment Watch. Savan, Beth, Morgan, Alexis and Gore, Chritopher. Toronto : s.n., June 2003, Environmental Management, Vol. 31, pp. 561-568.[[media:Savan+2003.pdf | Savan et all PDF]]<br />
# Nicholson, Emily, Ryan, Jane and Hodgkins, David. Community Data – where does the value lie? Assessing confidence limits of community collected water quality data. Victoria : Waterwatch Victoria c/o Department of Natural Resources & Environment, 2002. [[media:NicholsonEmily.pdf|Nicholson et all PDF]]<br />
# A review of citizen science and community-based environmental monitoring: issues and opportunities. Conrad, Cathy and Hilchey, Krista. [ed.] Springer. Halifax, Nova Scotia : s.n., 2010, Environ Monit Assess, pp. 273-291. [[media :Conrad-hilchey-2011-review.pdf | Conrad & Hilchey PDF]] <br />
# World water monitoring challenge. Instructions. Geneva : World water montioring Challenge, 2015. Instructions for the water monitoring test kit provided by the world water monitoring challenge.[[media : English-Spanish_Instructions.pdf | Instructions for PH, DO, temp and turbidity PDF]]<br />
# World Health Organization. Guidelines for safe recreational water environments. Geneva : World HEalth Organization, 2003. Vol. 1 Coastal and Fresh Waters. [[media:WhoGuideLines.pdf|WHO Guide Lines]]<br />
# Texas Stream Team Volunteer Water Quality Monitoring. E.coli Monitoring and Analysis Procedures. 2010. [[media :Texasstream.pdf | Texas Sampling PDF]]<br />
# Stepenuk, Kristine, et al. Volunteer monitoring of E. coli in streams of the upper Midwestern United States: a comparison of methods. [ed.] University of Wisconsin—Extension. Madison : Springer, 2010.[[media:Stepenucketal2010.pdf | Stepenuck et all PDF]]<br />
# Myers, D.N., et al. Fecal indicator bacteria (ver. 2.1). [book auth.] U.S. Geological survey. U.S. Geological Survey Techniques of Water-Resources Investigations. 2014, Vol. book 9, chap. A7, section 7.1.[[media :Fecalindicators.pdf | Myers et all PDF]] <br />
# Iowa Department of Natural Resources, Geological Survey. Citizens Monitoring Bacteria. Iowa City : s.n., 2005. Vols. Water Fact Sheet 2005-1.[[media:Wfs-2005-01.pdf|Fact Sheet Volunteer Water Monitoring]]<br />
# Arizona Department of Environmental Quality Water Quality Improvement Grant Program. Writing Effective Monitoring Plans. s.l. : Arizona department of environmental quality, 2008. TM 08-04.[[media:Writing.pdf | Guide to writing a sampling plan PDF]]<br />
# USEPA REGION 9 LABORATORY. STANDARD OPERATING PROCEDURE FOR VOLUNTEER MONITORING OF SURFACE WATERS FOR BACTERIA. Richmond : United States Environmental Agency, 2007.[[media:SOPEPARICHMOND.pdf| SOP Volunteer monitoring PDF]]<br />
# U.S. Geological Survey. National Field Manual for the collection of water quality data. 2006. Vol. Book 9. http://water.usgs.gov/owq/FieldManual/<br />
# Wolfson, Dr. Lois. E. coli Monitoring – Effective Techniques and Test Kits for Volunteers. Michigan Clean Water Corps Conference. s.l. : Michigan State University, October 16, 2007.[[media:WolfsonPresentation.pdf | Test Kit Presentation PDF]]<br />
# Epstein, Charlotte. KNOWLEDGE AND POWER IN GLOBAL ENVIRONMENTAL ACTIVISM. s.l. : International Journal of Peace Studies, 2005.[[media:Epstein_101IJPS.pdf | Epstein PDF]]<br />
# CH. Loi fédérale sur la protection des eaux. [Online] juin 1, 2014. https://www.admin.ch/opc/fr/classified-compilation/19910022/index.html#a4.<br />
# Kleehammer, Katie and Sigler, Adam. Moore Creek Volunteer Monitoring for Escherichia coli - Sampling and analysis. Bozeman : MSU Extension Water Quality, 2012.[[media : Moore_E_Coli.pdf | SOP Moore Creek E.coli sampling PDF]]<br />
# Homogeneous Distribution of Escherichia coli Measured within the Vertical Water Column of Small, Freshwater Streams. Buckalew, David, et al. Farmville, VA : Scientific Research Publishing, March 24, 2014, Water Resource and Protection, pp. 410-421. [[media : Distirbutionofecoliwatercolumn.pdf | Buckalew et all PDF]]<br />
# Micrology LAboratories. Easy Gel Method Procedure. Goshen, Indiana : s.n., 2015. Recomended procedures for chromogeinc media.[[media:Easygel_method_procedure.pdf | Procedure Easygel PDF]]<br />
# Micrology Laboratories. ECA Check Easy guide. Goshen : Manufacturers color guide for chromogenic media.[[media : Eca_check_easygel_guide.pdf | ECA guide to determining bacteria PDF]]<br />
# DIRECTIVE 2006/7/EC concerning the management of bathing water quality. European Union. Strassbourg : s.n., 2006, Official Journal of the European Union.[[media:DIRECTIVE2006EC_.pdf | Directive 2006/7/EC]]<br />
# Canfield, Daniel; Hoyer, Mark; Volunteer Lake Monitoring : Testing the Reliability of Data Collected by the Florida LakeWatch Program: Lake and Reservoir Management-March 2002 [[media : Floridalakes.pdf | Reliability of volunteer data PDF]]<br />
<br />
=== Documents from hammerdirt Clean Beach Projects ===<br />
* [[ Media : Montreux_april_activity_opt.pdf | Activity report Nov 2015 - April 2016]]<br />
* [[ Media : Pilot_project_cbem_montreux.pdf | Pilot project CBEM May 2016]]<br />
* [[Media:Clean_beach_pro_2015.pdf | Hammerdirt Clean Beach Project 2 2015 Draft]]<br />
* [[ Media : CH_OSPAR._COMPARISON_OPT.pdf | Comparison of Lake Geneva beaches to other OSPAR regions]]<br />
* [[ Media : Citizenscience.pdf | Citizen Science and litter studies (french)]]<br />
* [[ Media : MCBP1.pdf | MCBPI 2014-2015 results (French)]]<br />
* [[ Media : Plagespropres_nov2014_aout2015_opt.pdf | MCBPI 2014-2015 results (English)]]<br />
<br />
=== Literature ===<br />
[[Media:07_phytoplancton_camp.2014.pdf | 2014 Report on Leman biomass ]] <br><br />
[[Media:Rapports_Leman_2014.pdf | 2014 Physico-chemical Leman report]]<br />
<br />
=== Relevant Links ===<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253<br />
<br />
<br />
== Documentation and Collaboration Tools ==<br />
----<br />
Agree on documentation and collaboration tools<br />
* Internal communication - hackuarium slack <br />
* Calendar? - we have a biodesign google calendar<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
== Water Collection Protocols ==<br />
----<br />
<br><br><br />
<br />
=== Coliform Bacteria Counting ===<br />
----<br />
The presence of ''E. coli'' in natural waters is a direct indication of fecal contamination of water. Coliform bacteria and other bacterial species can also be found in public waters and contribute to human pathologies. There are several methods to distinguish ''E. coli'', coliform and other bacteria vs other microorganisms that may grow on an agar plate, of special interest 'chromogenic media' which contain substrates that form specific colors depending on enzymes produced by each species.<br />
==== Easy Gel ====<br />
Micrology Labs [http://www.micrologylabs.com/page/93/Coliscan-Easygel Coliscan Easygel]<br />
* Rachel asked for an offer including shipping and the 15% discount for the a coliform bacteria testing medium.<br />
* reminder request sent again 18 April to Jonathan Roth (CEO of Micrology Labs) and Doug Wengerd (who eventually answers notes to their 'info' address)<br />
[http://www.micrologylabs.com/page/95/Instructions Protocol] from the Micrology Labs<br><br />
* there have been some paying complications too, but their large scale order for 100 plates makes the 'per plate' cost half of another option <br><br />
<br />
<br />
To note: the Micrology Lab ECA Easygel plates are somewhat expensive, but can assay up to 5ml of sampled water per plate for ready scoring and disposal. Another currently proposed plate media would not only be less discriminating, but require more equipment for the sterile setup and final cleanup, and probably only allow 0.5ml to be assayed/plate. The Micrology plates are also used in other 'citizen science' campaigns and approved by regulatory bodies...<br />
<br />
==== Other Media ====<br />
* [https://en.wikipedia.org/wiki/Endo_agar Endo agar] where gram negatives are favored to grow. Fermentation of lactose in the medium by coliform bacteria gives metallic green sheen to those colonies.<br />
* [https://en.wikipedia.org/wiki/MacConkey_agar MacConkey agar] - also contains lactose and neutral red as a pH indicator, bile salts to inhibit gram-positive bacteria growth<br />
* [https://en.wikipedia.org/wiki/Sorbitol-MacConkey_agar MacConkey agar with sorbitol] is used to isolate E. coli O157, a pathogenic enteric bacteria<br />
* [https://en.wikipedia.org/wiki/Eosin_methylene_blue Eosin Methylene Blue agar] - Lactose fermenting bacteria turn a dark color, gram positive bacteria also inhibited<br />
<br />
<br />
<br><br />
==== DIY protocol ====<br />
<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br />
==== Other Methods ====<br />
* Good "travaux pratique" [http://www.bioutils.ch/protocoles/13-analyse-de-leau protocol] for bacterial counting and salts concentration from Bioutils, UNIGE <br><br />
* Other [[Media:Bacterial_counts.pdf | protocol]] proposing several direct and indirect methods <br><br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
----<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br />
<br />
=== Water Multi-meter ===<br />
----<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br><br />
<br />
<br />
== Press ==<br />
=== Short History of the Collaboration ===<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation can be found here:[[media : Hammerdirt.pdf | How can we work together ?]]<br />
<br><br><br />
[[Category:Projects]]<br />
[[Category:Work In Progress]]<br />
[[Category:Environment]]</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=7100Micro to Macro Water Pollution2016-05-23T11:15:53Z<p>Sachiko: /* Press */</p>
<hr />
<div>Community based environmental monitoring has been proven effective in a variety of fields, water quality monitoring by volunteers is in wide practice across North America. Four Swiss nonprofit associations use visible pollution inventories, microbiological monitoring and chemical analysis by combining classic laboratory techniques and the use of innovative bio-reporters to expand the capabilities of community based environmental monitoring.<br><br />
<br />
[[file:Sortingdebris.jpg|thumb|500px|right| hammerdirt team sorting debris at Vevey, Jan 2016. Source: MCBPII]]<br />
[[file : Pierrier.jpg |thumb|500px|right| Sorted debris Plage du Pierrier, Mar 2016. Source: MCBPII]]<br />
== Aims ==<br />
To effectively integrate more advanced and innovative water quality monitoring techniques to classic community based environmental monitoring activites.<br />
<br><br><br />
<br />
== Brainstorm Results ==<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* Microbial testing - distinguish fecal contaminants and others with selective plates<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
== Collaboration Defined ==<br />
{| class="wikitable"<br />
! Partner<br />
! Role<br />
|-<br />
| [http://www.genomicintegrity.org/ ACTION FOR GENOMIC INTEGRITY THROUGH RESEARCH!] <br />
| Technical oversight for the microbial assays, training of hammerdirt staff, quality control of laboratory operations and of sample processing and analyses.<br />
|-<br />
| [http://www.hackuarium.ch/fr/ HACKUARIUM]<br />
| Laboratory infrastructure and security, testing equipment and supplies for biologicals<br />
|-<br />
| [http://www.hammerdirt.ch/ HAMMERDIRT]<br />
| Collection and processing of samples, data storage and administration. Communication of analyses and results.<br />
|-<br />
| [https://biodesign.cc/ BIODESIGN.CC]<br />
| Analysis of samples for mercury, Cadmium Zinc, Alkanes and arsenic using the bio-reporters<br />
|}<br />
<br />
== Water Quality and Analysis ==<br />
=== Spring and Summer 2016 ===<br />
[[File:noswimming.jpg|thumb|right|400px|Location 5, Montreux rive gauche source : MCBPI July 2014]]<br />
==== Introduction ====<br />
<br />
One of the benefits of a “Community Based Environmental Monitoring” (CBEM) project is to expand the monitoring capacity of government agencies and engage the public in environmental stewardship. In response to questions from the public and our own professional curiosity we have decided to initiate a limited CBEM project (1) (2) .<br><br />
<br />
As part of the Montreux Clean Beach Project II(MCBPII), a water quality testing (WQT) program is being initiated at selected sites of the MCBPII. Symptoms reported by members and frequent bathers in the lake during previous summer seasons have sometimes been attributed to low bathing water quality, influenced by increased anthropogenic pressure of lakefront activities during certain times of the year. This year's WQT aims to gather microbiological data over a six week period in order to test this hypothesis.<br><br />
<br />
<br />
Meetings at “La Maison de la Rivière” and the “Institut National de Recherche Agronomique” support the idea that the WQT information proposed is not regularly collected at the Haut-Lac locations covered by the MCBPII.<br><br />
<br><br />
<br />
==== Objectives ====<br />
CBEM programs are designed to educate the public, involve local citizens in environmental stewardship and provide reliable data for government and other interested organizations. In this regard the MCBPII CBEM program is no different than that of any other existing project. (2)(3)(4)(5)(6)<br><br />
<br />
Specifically, the goals for this project are to:<br />
# Collect reliable water quality data as defined by the World Water Monitoring Challenge <br />
# Collect and enumerate the quantity of key bacteriological indicators, in particular those related to fecal contamination <br />
# Increase the skills of hammerdirt staff in regards to collecting and processing water samples.<br />
# Make the obtained data free and open to use for all concerned <br />
# Inform the public about affordable and simple water monitoring techniques<br />
# Inform the public of community based resources designed to advance scientific literacy<br />
<br><br />
More information [http://cbemn.ca/ CBEM Network]<br />
<br />
==== Deliverables ====<br />
[[File:Montreux_april_activity_opt_short-2.jpg|thumb|400px|right|Source: MCBPII Activity Report Nov 2015 - April 2016]]<br />
The objectives of a CBEM are designed to increase the monitoring capacity of current public systems and provide reliable, accessible data for the public and other government researchers. Data gathered from this project will be reported with our regular activity reports and the raw data will be available for download within 72 hours of the testing date from our repository on [https://github.com/hammerdirt/beachLitterSurveys Github] or through the KoboToolbox for the location in question. This document along with sampling protocols and all other supporting documents will be available on the wiki.<br />
<br><br><br />
Weekly results will be furnished to the CIPEL, SIGE and INRA:<br />
:# Location and number of tests<br />
:# Results of tests completed for the week<br />
An end of project report will be published in PDF format, available for interested parties, and include:<br />
:# Summary statistics and findings<br />
:# Graphs/plots<br />
:# Map overlay with densities and values<br />
:# Comparison with government supplied data (if available)<br />
:# Discussion of limitations and possible improvements to future CBEM projects<br />
<br />
More information [http://www.kobotoolbox.org/ KoboToolbox]<br />
<br />
=== Testing Materials ===<br />
==== Heavy Metals ====<br />
Bioreporters, designed and fabricated by biodesign.cc will be used to test for Alkanes, Arsenic, Mercury and Cadmium/Zinc. <br><br />
<br />
What are bioreporters ? Get some background information [http://wiki.biodesign.cc/wiki/Bioreporters_in_Pollutant_Detection here]<br />
<br />
==== Turbidity, temp, DO and PH ====<br />
Testing materials and supplies will be procured from the [http://www.monitorwater.org/ World Water Monitoring Challenge] an international program managed by the [http://www.iwa-network.org/ International Water Association] and the [http://www.wef.org/ Water Environment Federation].<br />
<br><br />
Assembled and sold by Lamotte company as a “basic test kit,” each kit includes one set of hardware and enough reagents to conduct up to 50 rounds of testing for pH, dissolved oxygen, temperature, and turbidity. Included are:<br />
# [[media : English-Spanish_Instructions.pdf |Instruction booklet]]<br />
# Sample collection jar<br />
# PH test tube<br />
# Dissolved oxygen vial<br />
# Secchi disk decal<br />
# Temperature strips (14-40°C and 0-12°C)<br />
# 50 pH reagent tablets (enough for 50 tests)<br />
# 100 Dissolved oxygen reagent tablets (enough for 50 tests)<br />
# Color chart for determining DO, pH and turbidity test results<br />
<br><br />
<br />
[[file:Eca_check_easygel_guide.pg1.jpg|thumb|right|400px|Visualizing organisms with ECA Check source: ECA Easygel guide]]<br />
==== Microbiological Analyses ====<br />
Presence and quantity of E.coli, other coli forms, Salmonella and Aeromonas will be tested using [http://www.micrologylabs.com/products/3/ECA-Check-Easygel ECA Check Easygel]. Easygel was first approved for [http://www.usawaterquality.org/ Water Watch] volunteer monitoring programs in the USA in 1999. A study released in 2009 compared the results of “Easygel” and “3M Petrifilm” used by volunteers to the results of laboratory analysis. Both methods had an overall accuracy rate above 80%. One big benefit of the Easygel format is that environmental samples of up to 5ml can be readily plated, with no worries about having to melt (and cool down!) agarose as used in standard microbial plates.(7)(8)(10)(14)<br><br />
<br />
Members of the Hackuarium laboratory have used “Easygel” in previous educational activities, thus facilitating the training of hammedirt staff and volunteers.<br />
<br />
=== Sampling Methods ===<br />
<br />
'''Water samples will be taken just below the surface (0.5m) and collected in sterile containers with a secure, air-tight lid.'''<br><br />
<br />
'''Advantage:''' simple and inexpensive, an important consideration to a program on a budget. It also does not require any special sampling apparatus. The volunteer holds a sampling container under the surface of the water, expells visible air bubbles, and closes the container under the water (to avoids losing dissolved gasses, particularly important if testing for volatile analytes).<br><br />
<br />
'''Disadvantage:''' vertical gradients of temperature, oxygen, nutrients, and algae may be missed in these near surface samples. Deep lakes have a thermal gradient in the summer, and Lac Leman has at least two thermal regions (and, possibly, at least two chemical regions as well). Even in shallow, usually well-mixed lakes, chemical gradients will develop during calm periods.<br><br />
<br />
Sampling methods by other CBEM projects : [[media:Stepenucketal2010.pdf | Stepenuck et all PDF]], [[media:Wfs-2005-01.pdf|Fact Sheet Volunteer Water Monitoring]], [[media : Moore_E_Coli.pdf | SOP Moore Creek E.coli sampling PDF]], [[media :Texasstream.pdf | Texas Sampling PDF]]<br />
<br />
==== Heavy Metals ====<br />
Two samples of 250ml will be taken and transported to the hackuarium for later analysis. One sample will be acidified to fix the heavy metals in solution.<br />
<br />
==== Turbidity, temp, DO and PH ====<br />
One sample will be taken using the container supplied with the testing kit and processed immediately. <br><br />
<br />
==== Microbiological samples ====<br />
'''Three independent samples will be taken from each designated site''' in 15ml conical tubes pre-labeled in the following manner:<br />
# Location<br />
# Date<br />
# Sample number for that day and location<br />
# Time of sample<br />
<br><br />
Once collected, the '''samples will be placed on ice and transported to the facility at Renens for plating on the ECA Check plates within 6 hours.''' Label information will be recorded in the field notes and the “KoboToolBox” for that sampling date and location.<br />
<br />
=== Processing samples and recording results ===<br />
==== Turbidity, temp, DO and PH ====<br />
The instructions provided with the kit will be followed and the results will be noted in the field manual and entered into the “KoboToolbox” form for that sampling date and location.<br />
<br />
==== Microbiologicals ====<br />
One petri dish per sample will be labeled in the same manner as the sample container with the addition of the quantity of sample added to the media. A 1-5ml of sample water will be mixed into the provided gel media solution, plated and incubated for about 18 hours at the Hackuarium facility in Renens.<br><br />
<br />
After incubation, plates will be scored, counting total colony forming units (CFU), and each identifiable species (E. coli CFUs will appear dark blue, other coliform CFUs will appear lighter blue-gray or blue-violet, Aeromonas spp. will appear as pink to very light pink, and Salmonella spp. will appear as light green colonies). Data will be reported as CFU/100ml of sample.<br><br />
<br />
With values from three independent samples at each site, means and standard errors can be used to test significance of the obtained data over the course of the sampling period.<br />
<br />
=== Locations ===<br />
[[File:tweet.jpg|thumb|right|600px |Sampling locations for biological and chemical analysis, source: Sampling and analysis plan MCBPII]]<br />
Three of the five locations are currently part of the MCBPII beach-litter-survey project. Point 4 will be added to the beach litter survey by using a net to catch visible pollutants on the water surface below the boat dock. Point 3 will only be monitored for chemistry and biologicals. Correlations of the test results with the physical location of the sampling will be of great interest.<br />
<br />
<br />
<br />
To see a map of the locations that benefit from regular water quality monitoring : [http://www.vd.ch/themes/environnement/eaux/eau-de-baignade/qualite-de-leau-des-plages-cartographie/ Eau de baignade]<br />
<br />
=== Testing Schedule ===<br />
==== Calendar from biodesign.cc to be embedded here ====<br />
key dates to be defined :<br />
# Training for sampling and plating<br />
# Event public demonstration of sampling and plating<br />
# Start date for chemical samples<br />
# Start date for microbiologicals<br />
# Event public discussion of results, improvements and future projects<br />
==== Microbiologicals ====<br />
Testing will begin about 20 June 2016, and weekly samples will be taken from locations 3, 4 and 5. A 'negative control' sample will also be obtained each week from a local drinking fountain (labelled 'eau potable'). A positive control from an urban river (like the Vuachère or other) is also possible.<br><br />
<br />
If a Tuesday afternoon testing protocol is followed over 7 weeks, the timeline would run from 21 June -2 August, require 21 sterile 15ml conical tubes for the water sampling, and 21 ECA Check EasyGel plates per site. After including a single 'negative control' for each sampling day, this will require 70 plates.<br><br />
<br />
In case there are too many bacteria to count (TMTC) from certain samples, samples will be saved at 4oC and further dilutions can be also plated and scored.<br><br />
<br />
==== Turbidity, temp, DO and PH ====<br />
Testing will begin on the Tuesday or Thursday the week the kits are received (late May). The kit contains enough reagents to conduct 50 tests, thus allowing us to monitor the locations for 10 weeks. Data will be carefully recorded, digitized and analyzed.<br><br />
<br />
==== Field Blanks ====<br />
Field blanks are used to assess potential contamination from sample handling, airborne materials, equipment, media, and other sources. A field blank usually consists of a sterile diluent sample of 2 mL that is taken to the site and poured into a properly labeled sample container during the first bacteria sampling event of that day. The blank sample is collected in the same type of container, labeled as a field blank, and handled and analyzed along with all the bacteria samples collected on that day. It is used to identify errors or contamination in sample collection and analysis.<br />
<br />
=== Data === <br />
==== Handling and storage ====<br />
The addition of water quality testing will require changes in our digital form and reporting methods. The form currently used by surveyors will change, thus separating the data in two sections, one section prior to WQT and one after. Data for the two sections will have to be merged prior to any analysis. The results of bacterial testing will be available 48-72 hours after sampling, thus adding another step to the survey. This should not, however, change the availability of the other survey results which is currently 24 hours after each survey.<br><br />
<br />
==== Data analysis and presentation ====<br />
<br />
The existing data set for MCBPII includes visible pollution surveys, hydrologic and meteorological data. With the addition of microbiological and basic water chemistry a more complete picture of the environmental status of the locations in question can be established.<br><br />
<br />
Two interpretations of the microbiological data will be used: the geometric mean and the 95th percentile. The geometric mean is in common use in North America and the 95th percentile method conforms to EU directive 2006/7/EC. Furthermore, any publicly available water quality data in the area will be presented and integrated where appropriate.<br><br />
<br />
The relationship between the results of WQT and the quantity and type of visible pollutants will be explored.<br><br />
<br />
'''How is the water currently monitored and evaluated ? '''Here is the source document from the Swiss Confederation [[media :Evaluation+des+eaux+de+baignade.pdf | Eaux de baignade]]<br />
<br />
== References ==<br />
<br />
=== Sampling and Analysis in Community Based Environmental Monitoring ===<br />
# Assessing the performance of volunteers in monitoring Streams. Fore, Leska, Paulsen, Kit and O'Laughlin, Kate. Bellvue, WA : Blackwell Science, 2001, Fresh Water Biology. [[media:Fore,2001.pdf|Fore et all pdf]]<br />
# Volunteer environmental monitoring and the role of the universities : The case of Citizens Environment Watch. Savan, Beth, Morgan, Alexis and Gore, Chritopher. Toronto : s.n., June 2003, Environmental Management, Vol. 31, pp. 561-568.[[media:Savan+2003.pdf | Savan et all PDF]]<br />
# Nicholson, Emily, Ryan, Jane and Hodgkins, David. Community Data – where does the value lie? Assessing confidence limits of community collected water quality data. Victoria : Waterwatch Victoria c/o Department of Natural Resources & Environment, 2002. [[media:NicholsonEmily.pdf|Nicholson et all PDF]]<br />
# A review of citizen science and community-based environmental monitoring: issues and opportunities. Conrad, Cathy and Hilchey, Krista. [ed.] Springer. Halifax, Nova Scotia : s.n., 2010, Environ Monit Assess, pp. 273-291. [[media :Conrad-hilchey-2011-review.pdf | Conrad & Hilchey PDF]] <br />
# World water monitoring challenge. Instructions. Geneva : World water montioring Challenge, 2015. Instructions for the water monitoring test kit provided by the world water monitoring challenge.[[media : English-Spanish_Instructions.pdf | Instructions for PH, DO, temp and turbidity PDF]]<br />
# World Health Organization. Guidelines for safe recreational water environments. Geneva : World HEalth Organization, 2003. Vol. 1 Coastal and Fresh Waters. [[media:WhoGuideLines.pdf|WHO Guide Lines]]<br />
# Texas Stream Team Volunteer Water Quality Monitoring. E.coli Monitoring and Analysis Procedures. 2010. [[media :Texasstream.pdf | Texas Sampling PDF]]<br />
# Stepenuk, Kristine, et al. Volunteer monitoring of E. coli in streams of the upper Midwestern United States: a comparison of methods. [ed.] University of Wisconsin—Extension. Madison : Springer, 2010.[[media:Stepenucketal2010.pdf | Stepenuck et all PDF]]<br />
# Myers, D.N., et al. Fecal indicator bacteria (ver. 2.1). [book auth.] U.S. Geological survey. U.S. Geological Survey Techniques of Water-Resources Investigations. 2014, Vol. book 9, chap. A7, section 7.1.[[media :Fecalindicators.pdf | Myers et all PDF]] <br />
# Iowa Department of Natural Resources, Geological Survey. Citizens Monitoring Bacteria. Iowa City : s.n., 2005. Vols. Water Fact Sheet 2005-1.[[media:Wfs-2005-01.pdf|Fact Sheet Volunteer Water Monitoring]]<br />
# Arizona Department of Environmental Quality Water Quality Improvement Grant Program. Writing Effective Monitoring Plans. s.l. : Arizona department of environmental quality, 2008. TM 08-04.[[media:Writing.pdf | Guide to writing a sampling plan PDF]]<br />
# USEPA REGION 9 LABORATORY. STANDARD OPERATING PROCEDURE FOR VOLUNTEER MONITORING OF SURFACE WATERS FOR BACTERIA. Richmond : United States Environmental Agency, 2007.[[media:SOPEPARICHMOND.pdf| SOP Volunteer monitoring PDF]]<br />
# U.S. Geological Survey. National Field Manual for the collection of water quality data. 2006. Vol. Book 9. http://water.usgs.gov/owq/FieldManual/<br />
# Wolfson, Dr. Lois. E. coli Monitoring – Effective Techniques and Test Kits for Volunteers. Michigan Clean Water Corps Conference. s.l. : Michigan State University, October 16, 2007.[[media:WolfsonPresentation.pdf | Test Kit Presentation PDF]]<br />
# Epstein, Charlotte. KNOWLEDGE AND POWER IN GLOBAL ENVIRONMENTAL ACTIVISM. s.l. : International Journal of Peace Studies, 2005.[[media:Epstein_101IJPS.pdf | Epstein PDF]]<br />
# CH. Loi fédérale sur la protection des eaux. [Online] juin 1, 2014. https://www.admin.ch/opc/fr/classified-compilation/19910022/index.html#a4.<br />
# Kleehammer, Katie and Sigler, Adam. Moore Creek Volunteer Monitoring for Escherichia coli - Sampling and analysis. Bozeman : MSU Extension Water Quality, 2012.[[media : Moore_E_Coli.pdf | SOP Moore Creek E.coli sampling PDF]]<br />
# Homogeneous Distribution of Escherichia coli Measured within the Vertical Water Column of Small, Freshwater Streams. Buckalew, David, et al. Farmville, VA : Scientific Research Publishing, March 24, 2014, Water Resource and Protection, pp. 410-421. [[media : Distirbutionofecoliwatercolumn.pdf | Buckalew et all PDF]]<br />
# Micrology LAboratories. Easy Gel Method Procedure. Goshen, Indiana : s.n., 2015. Recomended procedures for chromogeinc media.[[media:Easygel_method_procedure.pdf | Procedure Easygel PDF]]<br />
# Micrology Laboratories. ECA Check Easy guide. Goshen : Manufacturers color guide for chromogenic media.[[media : Eca_check_easygel_guide.pdf | ECA guide to determining bacteria PDF]]<br />
# DIRECTIVE 2006/7/EC concerning the management of bathing water quality. European Union. Strassbourg : s.n., 2006, Official Journal of the European Union.[[media:DIRECTIVE2006EC_.pdf | Directive 2006/7/EC]]<br />
# Canfield, Daniel; Hoyer, Mark; Volunteer Lake Monitoring : Testing the Reliability of Data Collected by the Florida LakeWatch Program: Lake and Reservoir Management-March 2002 [[media : Floridalakes.pdf | Reliability of volunteer data PDF]]<br />
<br />
=== Documents from hammerdirt Clean Beach Projects ===<br />
* [[ Media : Montreux_april_activity_opt.pdf | Activity report Nov 2015 - April 2016]]<br />
* [[ Media : Pilot_project_cbem_montreux.pdf | Pilot project CBEM May 2016]]<br />
* [[Media:Clean_beach_pro_2015.pdf | Hammerdirt Clean Beach Project 2 2015 Draft]]<br />
* [[ Media : CH_OSPAR._COMPARISON_OPT.pdf | Comparison of Lake Geneva beaches to other OSPAR regions]]<br />
* [[ Media : Citizenscience.pdf | Citizen Science and litter studies (french)]]<br />
* [[ Media : MCBP1.pdf | MCBPI 2014-2015 results (French)]]<br />
* [[ Media : Plagespropres_nov2014_aout2015_opt.pdf | MCBPI 2014-2015 results (English)]]<br />
<br />
=== Literature ===<br />
[[Media:07_phytoplancton_camp.2014.pdf | 2014 Report on Leman biomass ]] <br><br />
[[Media:Rapports_Leman_2014.pdf | 2014 Physico-chemical Leman report]]<br />
<br />
=== Relevant Links ===<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253<br />
<br />
== Press ==<br />
== Background Information ==<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation can be found here:[[media : Hammerdirt.pdf | How can we work together ?]]<br />
<br><br><br />
<br />
[[Category:Projects]]<br />
[[Category:Work In Progress]]<br />
[[Category:Environment]]<br />
<br />
== Documentation and Collaboration Tools ==<br />
----<br />
Agree on documentation and collaboration tools<br />
* Internal communication - hackuarium slack <br />
* Calendar? - we have a biodesign google calendar<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
== Water Collection Protocols ==<br />
----<br />
<br><br><br />
<br />
=== Coliform Bacteria Counting ===<br />
----<br />
The presence of ''E. coli'' in natural waters is a direct indication of fecal contamination of water. Coliform bacteria and other bacterial species can also be found in public waters and contribute to human pathologies. There are several methods to distinguish ''E. coli'', coliform and other bacteria vs other microorganisms that may grow on an agar plate, of special interest 'chromogenic media' which contain substrates that form specific colors depending on enzymes produced by each species.<br />
==== Easy Gel ====<br />
Micrology Labs [http://www.micrologylabs.com/page/93/Coliscan-Easygel Coliscan Easygel]<br />
* Rachel asked for an offer including shipping and the 15% discount for the a coliform bacteria testing medium.<br />
* reminder request sent again 18 April to Jonathan Roth (CEO of Micrology Labs) and Doug Wengerd (who eventually answers notes to their 'info' address)<br />
[http://www.micrologylabs.com/page/95/Instructions Protocol] from the Micrology Labs<br><br />
* there have been some paying complications too, but their large scale order for 100 plates makes the 'per plate' cost half of another option <br><br />
<br />
<br />
To note: the Micrology Lab ECA Easygel plates are somewhat expensive, but can assay up to 5ml of sampled water per plate for ready scoring and disposal. Another currently proposed plate media would not only be less discriminating, but require more equipment for the sterile setup and final cleanup, and probably only allow 0.5ml to be assayed/plate. The Micrology plates are also used in other 'citizen science' campaigns and approved by regulatory bodies...<br />
<br />
==== Other Media ====<br />
* [https://en.wikipedia.org/wiki/Endo_agar Endo agar] where gram negatives are favored to grow. Fermentation of lactose in the medium by coliform bacteria gives metallic green sheen to those colonies.<br />
* [https://en.wikipedia.org/wiki/MacConkey_agar MacConkey agar] - also contains lactose and neutral red as a pH indicator, bile salts to inhibit gram-positive bacteria growth<br />
* [https://en.wikipedia.org/wiki/Sorbitol-MacConkey_agar MacConkey agar with sorbitol] is used to isolate E. coli O157, a pathogenic enteric bacteria<br />
* [https://en.wikipedia.org/wiki/Eosin_methylene_blue Eosin Methylene Blue agar] - Lactose fermenting bacteria turn a dark color, gram positive bacteria also inhibited<br />
<br />
<br />
<br><br />
==== DIY protocol ====<br />
<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br />
==== Other Methods ====<br />
* Good "travaux pratique" [http://www.bioutils.ch/protocoles/13-analyse-de-leau protocol] for bacterial counting and salts concentration from Bioutils, UNIGE <br><br />
* Other [[Media:Bacterial_counts.pdf | protocol]] proposing several direct and indirect methods <br><br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
----<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br />
<br />
=== Water Multi-meter ===<br />
----<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br></div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=7099Micro to Macro Water Pollution2016-05-23T11:13:43Z<p>Sachiko: /* Background Information */</p>
<hr />
<div>Community based environmental monitoring has been proven effective in a variety of fields, water quality monitoring by volunteers is in wide practice across North America. Four Swiss nonprofit associations use visible pollution inventories, microbiological monitoring and chemical analysis by combining classic laboratory techniques and the use of innovative bio-reporters to expand the capabilities of community based environmental monitoring.<br><br />
<br />
[[file:Sortingdebris.jpg|thumb|500px|right| hammerdirt team sorting debris at Vevey, Jan 2016. Source: MCBPII]]<br />
[[file : Pierrier.jpg |thumb|500px|right| Sorted debris Plage du Pierrier, Mar 2016. Source: MCBPII]]<br />
== Aims ==<br />
To effectively integrate more advanced and innovative water quality monitoring techniques to classic community based environmental monitoring activites.<br />
<br><br><br />
<br />
== Brainstorm Results ==<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* Microbial testing - distinguish fecal contaminants and others with selective plates<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
== Collaboration Defined ==<br />
{| class="wikitable"<br />
! Partner<br />
! Role<br />
|-<br />
| [http://www.genomicintegrity.org/ ACTION FOR GENOMIC INTEGRITY THROUGH RESEARCH!] <br />
| Technical oversight for the microbial assays, training of hammerdirt staff, quality control of laboratory operations and of sample processing and analyses.<br />
|-<br />
| [http://www.hackuarium.ch/fr/ HACKUARIUM]<br />
| Laboratory infrastructure and security, testing equipment and supplies for biologicals<br />
|-<br />
| [http://www.hammerdirt.ch/ HAMMERDIRT]<br />
| Collection and processing of samples, data storage and administration. Communication of analyses and results.<br />
|-<br />
| [https://biodesign.cc/ BIODESIGN.CC]<br />
| Analysis of samples for mercury, Cadmium Zinc, Alkanes and arsenic using the bio-reporters<br />
|}<br />
<br />
== Water Quality and Analysis ==<br />
=== Spring and Summer 2016 ===<br />
[[File:noswimming.jpg|thumb|right|400px|Location 5, Montreux rive gauche source : MCBPI July 2014]]<br />
==== Introduction ====<br />
<br />
One of the benefits of a “Community Based Environmental Monitoring” (CBEM) project is to expand the monitoring capacity of government agencies and engage the public in environmental stewardship. In response to questions from the public and our own professional curiosity we have decided to initiate a limited CBEM project (1) (2) .<br><br />
<br />
As part of the Montreux Clean Beach Project II(MCBPII), a water quality testing (WQT) program is being initiated at selected sites of the MCBPII. Symptoms reported by members and frequent bathers in the lake during previous summer seasons have sometimes been attributed to low bathing water quality, influenced by increased anthropogenic pressure of lakefront activities during certain times of the year. This year's WQT aims to gather microbiological data over a six week period in order to test this hypothesis.<br><br />
<br />
<br />
Meetings at “La Maison de la Rivière” and the “Institut National de Recherche Agronomique” support the idea that the WQT information proposed is not regularly collected at the Haut-Lac locations covered by the MCBPII.<br><br />
<br><br />
<br />
==== Objectives ====<br />
CBEM programs are designed to educate the public, involve local citizens in environmental stewardship and provide reliable data for government and other interested organizations. In this regard the MCBPII CBEM program is no different than that of any other existing project. (2)(3)(4)(5)(6)<br><br />
<br />
Specifically, the goals for this project are to:<br />
# Collect reliable water quality data as defined by the World Water Monitoring Challenge <br />
# Collect and enumerate the quantity of key bacteriological indicators, in particular those related to fecal contamination <br />
# Increase the skills of hammerdirt staff in regards to collecting and processing water samples.<br />
# Make the obtained data free and open to use for all concerned <br />
# Inform the public about affordable and simple water monitoring techniques<br />
# Inform the public of community based resources designed to advance scientific literacy<br />
<br><br />
More information [http://cbemn.ca/ CBEM Network]<br />
<br />
==== Deliverables ====<br />
[[File:Montreux_april_activity_opt_short-2.jpg|thumb|400px|right|Source: MCBPII Activity Report Nov 2015 - April 2016]]<br />
The objectives of a CBEM are designed to increase the monitoring capacity of current public systems and provide reliable, accessible data for the public and other government researchers. Data gathered from this project will be reported with our regular activity reports and the raw data will be available for download within 72 hours of the testing date from our repository on [https://github.com/hammerdirt/beachLitterSurveys Github] or through the KoboToolbox for the location in question. This document along with sampling protocols and all other supporting documents will be available on the wiki.<br />
<br><br><br />
Weekly results will be furnished to the CIPEL, SIGE and INRA:<br />
:# Location and number of tests<br />
:# Results of tests completed for the week<br />
An end of project report will be published in PDF format, available for interested parties, and include:<br />
:# Summary statistics and findings<br />
:# Graphs/plots<br />
:# Map overlay with densities and values<br />
:# Comparison with government supplied data (if available)<br />
:# Discussion of limitations and possible improvements to future CBEM projects<br />
<br />
More information [http://www.kobotoolbox.org/ KoboToolbox]<br />
<br />
=== Testing Materials ===<br />
==== Heavy Metals ====<br />
Bioreporters, designed and fabricated by biodesign.cc will be used to test for Alkanes, Arsenic, Mercury and Cadmium/Zinc. <br><br />
<br />
What are bioreporters ? Get some background information [http://wiki.biodesign.cc/wiki/Bioreporters_in_Pollutant_Detection here]<br />
<br />
==== Turbidity, temp, DO and PH ====<br />
Testing materials and supplies will be procured from the [http://www.monitorwater.org/ World Water Monitoring Challenge] an international program managed by the [http://www.iwa-network.org/ International Water Association] and the [http://www.wef.org/ Water Environment Federation].<br />
<br><br />
Assembled and sold by Lamotte company as a “basic test kit,” each kit includes one set of hardware and enough reagents to conduct up to 50 rounds of testing for pH, dissolved oxygen, temperature, and turbidity. Included are:<br />
# [[media : English-Spanish_Instructions.pdf |Instruction booklet]]<br />
# Sample collection jar<br />
# PH test tube<br />
# Dissolved oxygen vial<br />
# Secchi disk decal<br />
# Temperature strips (14-40°C and 0-12°C)<br />
# 50 pH reagent tablets (enough for 50 tests)<br />
# 100 Dissolved oxygen reagent tablets (enough for 50 tests)<br />
# Color chart for determining DO, pH and turbidity test results<br />
<br><br />
<br />
[[file:Eca_check_easygel_guide.pg1.jpg|thumb|right|400px|Visualizing organisms with ECA Check source: ECA Easygel guide]]<br />
==== Microbiological Analyses ====<br />
Presence and quantity of E.coli, other coli forms, Salmonella and Aeromonas will be tested using [http://www.micrologylabs.com/products/3/ECA-Check-Easygel ECA Check Easygel]. Easygel was first approved for [http://www.usawaterquality.org/ Water Watch] volunteer monitoring programs in the USA in 1999. A study released in 2009 compared the results of “Easygel” and “3M Petrifilm” used by volunteers to the results of laboratory analysis. Both methods had an overall accuracy rate above 80%. One big benefit of the Easygel format is that environmental samples of up to 5ml can be readily plated, with no worries about having to melt (and cool down!) agarose as used in standard microbial plates.(7)(8)(10)(14)<br><br />
<br />
Members of the Hackuarium laboratory have used “Easygel” in previous educational activities, thus facilitating the training of hammedirt staff and volunteers.<br />
<br />
=== Sampling Methods ===<br />
<br />
'''Water samples will be taken just below the surface (0.5m) and collected in sterile containers with a secure, air-tight lid.'''<br><br />
<br />
'''Advantage:''' simple and inexpensive, an important consideration to a program on a budget. It also does not require any special sampling apparatus. The volunteer holds a sampling container under the surface of the water, expells visible air bubbles, and closes the container under the water (to avoids losing dissolved gasses, particularly important if testing for volatile analytes).<br><br />
<br />
'''Disadvantage:''' vertical gradients of temperature, oxygen, nutrients, and algae may be missed in these near surface samples. Deep lakes have a thermal gradient in the summer, and Lac Leman has at least two thermal regions (and, possibly, at least two chemical regions as well). Even in shallow, usually well-mixed lakes, chemical gradients will develop during calm periods.<br><br />
<br />
Sampling methods by other CBEM projects : [[media:Stepenucketal2010.pdf | Stepenuck et all PDF]], [[media:Wfs-2005-01.pdf|Fact Sheet Volunteer Water Monitoring]], [[media : Moore_E_Coli.pdf | SOP Moore Creek E.coli sampling PDF]], [[media :Texasstream.pdf | Texas Sampling PDF]]<br />
<br />
==== Heavy Metals ====<br />
Two samples of 250ml will be taken and transported to the hackuarium for later analysis. One sample will be acidified to fix the heavy metals in solution.<br />
<br />
==== Turbidity, temp, DO and PH ====<br />
One sample will be taken using the container supplied with the testing kit and processed immediately. <br><br />
<br />
==== Microbiological samples ====<br />
'''Three independent samples will be taken from each designated site''' in 15ml conical tubes pre-labeled in the following manner:<br />
# Location<br />
# Date<br />
# Sample number for that day and location<br />
# Time of sample<br />
<br><br />
Once collected, the '''samples will be placed on ice and transported to the facility at Renens for plating on the ECA Check plates within 6 hours.''' Label information will be recorded in the field notes and the “KoboToolBox” for that sampling date and location.<br />
<br />
=== Processing samples and recording results ===<br />
==== Turbidity, temp, DO and PH ====<br />
The instructions provided with the kit will be followed and the results will be noted in the field manual and entered into the “KoboToolbox” form for that sampling date and location.<br />
<br />
==== Microbiologicals ====<br />
One petri dish per sample will be labeled in the same manner as the sample container with the addition of the quantity of sample added to the media. A 1-5ml of sample water will be mixed into the provided gel media solution, plated and incubated for about 18 hours at the Hackuarium facility in Renens.<br><br />
<br />
After incubation, plates will be scored, counting total colony forming units (CFU), and each identifiable species (E. coli CFUs will appear dark blue, other coliform CFUs will appear lighter blue-gray or blue-violet, Aeromonas spp. will appear as pink to very light pink, and Salmonella spp. will appear as light green colonies). Data will be reported as CFU/100ml of sample.<br><br />
<br />
With values from three independent samples at each site, means and standard errors can be used to test significance of the obtained data over the course of the sampling period.<br />
<br />
=== Locations ===<br />
[[File:tweet.jpg|thumb|right|600px |Sampling locations for biological and chemical analysis, source: Sampling and analysis plan MCBPII]]<br />
Three of the five locations are currently part of the MCBPII beach-litter-survey project. Point 4 will be added to the beach litter survey by using a net to catch visible pollutants on the water surface below the boat dock. Point 3 will only be monitored for chemistry and biologicals. Correlations of the test results with the physical location of the sampling will be of great interest.<br />
<br />
<br />
<br />
To see a map of the locations that benefit from regular water quality monitoring : [http://www.vd.ch/themes/environnement/eaux/eau-de-baignade/qualite-de-leau-des-plages-cartographie/ Eau de baignade]<br />
<br />
=== Testing Schedule ===<br />
==== Calendar from biodesign.cc to be embedded here ====<br />
key dates to be defined :<br />
# Training for sampling and plating<br />
# Event public demonstration of sampling and plating<br />
# Start date for chemical samples<br />
# Start date for microbiologicals<br />
# Event public discussion of results, improvements and future projects<br />
==== Microbiologicals ====<br />
Testing will begin about 20 June 2016, and weekly samples will be taken from locations 3, 4 and 5. A 'negative control' sample will also be obtained each week from a local drinking fountain (labelled 'eau potable'). A positive control from an urban river (like the Vuachère or other) is also possible.<br><br />
<br />
If a Tuesday afternoon testing protocol is followed over 7 weeks, the timeline would run from 21 June -2 August, require 21 sterile 15ml conical tubes for the water sampling, and 21 ECA Check EasyGel plates per site. After including a single 'negative control' for each sampling day, this will require 70 plates.<br><br />
<br />
In case there are too many bacteria to count (TMTC) from certain samples, samples will be saved at 4oC and further dilutions can be also plated and scored.<br><br />
<br />
==== Turbidity, temp, DO and PH ====<br />
Testing will begin on the Tuesday or Thursday the week the kits are received (late May). The kit contains enough reagents to conduct 50 tests, thus allowing us to monitor the locations for 10 weeks. Data will be carefully recorded, digitized and analyzed.<br><br />
<br />
==== Field Blanks ====<br />
Field blanks are used to assess potential contamination from sample handling, airborne materials, equipment, media, and other sources. A field blank usually consists of a sterile diluent sample of 2 mL that is taken to the site and poured into a properly labeled sample container during the first bacteria sampling event of that day. The blank sample is collected in the same type of container, labeled as a field blank, and handled and analyzed along with all the bacteria samples collected on that day. It is used to identify errors or contamination in sample collection and analysis.<br />
<br />
=== Data === <br />
==== Handling and storage ====<br />
The addition of water quality testing will require changes in our digital form and reporting methods. The form currently used by surveyors will change, thus separating the data in two sections, one section prior to WQT and one after. Data for the two sections will have to be merged prior to any analysis. The results of bacterial testing will be available 48-72 hours after sampling, thus adding another step to the survey. This should not, however, change the availability of the other survey results which is currently 24 hours after each survey.<br><br />
<br />
==== Data analysis and presentation ====<br />
<br />
The existing data set for MCBPII includes visible pollution surveys, hydrologic and meteorological data. With the addition of microbiological and basic water chemistry a more complete picture of the environmental status of the locations in question can be established.<br><br />
<br />
Two interpretations of the microbiological data will be used: the geometric mean and the 95th percentile. The geometric mean is in common use in North America and the 95th percentile method conforms to EU directive 2006/7/EC. Furthermore, any publicly available water quality data in the area will be presented and integrated where appropriate.<br><br />
<br />
The relationship between the results of WQT and the quantity and type of visible pollutants will be explored.<br><br />
<br />
'''How is the water currently monitored and evaluated ? '''Here is the source document from the Swiss Confederation [[media :Evaluation+des+eaux+de+baignade.pdf | Eaux de baignade]]<br />
<br />
== References ==<br />
<br />
=== Sampling and Analysis in Community Based Environmental Monitoring ===<br />
# Assessing the performance of volunteers in monitoring Streams. Fore, Leska, Paulsen, Kit and O'Laughlin, Kate. Bellvue, WA : Blackwell Science, 2001, Fresh Water Biology. [[media:Fore,2001.pdf|Fore et all pdf]]<br />
# Volunteer environmental monitoring and the role of the universities : The case of Citizens Environment Watch. Savan, Beth, Morgan, Alexis and Gore, Chritopher. Toronto : s.n., June 2003, Environmental Management, Vol. 31, pp. 561-568.[[media:Savan+2003.pdf | Savan et all PDF]]<br />
# Nicholson, Emily, Ryan, Jane and Hodgkins, David. Community Data – where does the value lie? Assessing confidence limits of community collected water quality data. Victoria : Waterwatch Victoria c/o Department of Natural Resources & Environment, 2002. [[media:NicholsonEmily.pdf|Nicholson et all PDF]]<br />
# A review of citizen science and community-based environmental monitoring: issues and opportunities. Conrad, Cathy and Hilchey, Krista. [ed.] Springer. Halifax, Nova Scotia : s.n., 2010, Environ Monit Assess, pp. 273-291. [[media :Conrad-hilchey-2011-review.pdf | Conrad & Hilchey PDF]] <br />
# World water monitoring challenge. Instructions. Geneva : World water montioring Challenge, 2015. Instructions for the water monitoring test kit provided by the world water monitoring challenge.[[media : English-Spanish_Instructions.pdf | Instructions for PH, DO, temp and turbidity PDF]]<br />
# World Health Organization. Guidelines for safe recreational water environments. Geneva : World HEalth Organization, 2003. Vol. 1 Coastal and Fresh Waters. [[media:WhoGuideLines.pdf|WHO Guide Lines]]<br />
# Texas Stream Team Volunteer Water Quality Monitoring. E.coli Monitoring and Analysis Procedures. 2010. [[media :Texasstream.pdf | Texas Sampling PDF]]<br />
# Stepenuk, Kristine, et al. Volunteer monitoring of E. coli in streams of the upper Midwestern United States: a comparison of methods. [ed.] University of Wisconsin—Extension. Madison : Springer, 2010.[[media:Stepenucketal2010.pdf | Stepenuck et all PDF]]<br />
# Myers, D.N., et al. Fecal indicator bacteria (ver. 2.1). [book auth.] U.S. Geological survey. U.S. Geological Survey Techniques of Water-Resources Investigations. 2014, Vol. book 9, chap. A7, section 7.1.[[media :Fecalindicators.pdf | Myers et all PDF]] <br />
# Iowa Department of Natural Resources, Geological Survey. Citizens Monitoring Bacteria. Iowa City : s.n., 2005. Vols. Water Fact Sheet 2005-1.[[media:Wfs-2005-01.pdf|Fact Sheet Volunteer Water Monitoring]]<br />
# Arizona Department of Environmental Quality Water Quality Improvement Grant Program. Writing Effective Monitoring Plans. s.l. : Arizona department of environmental quality, 2008. TM 08-04.[[media:Writing.pdf | Guide to writing a sampling plan PDF]]<br />
# USEPA REGION 9 LABORATORY. STANDARD OPERATING PROCEDURE FOR VOLUNTEER MONITORING OF SURFACE WATERS FOR BACTERIA. Richmond : United States Environmental Agency, 2007.[[media:SOPEPARICHMOND.pdf| SOP Volunteer monitoring PDF]]<br />
# U.S. Geological Survey. National Field Manual for the collection of water quality data. 2006. Vol. Book 9. http://water.usgs.gov/owq/FieldManual/<br />
# Wolfson, Dr. Lois. E. coli Monitoring – Effective Techniques and Test Kits for Volunteers. Michigan Clean Water Corps Conference. s.l. : Michigan State University, October 16, 2007.[[media:WolfsonPresentation.pdf | Test Kit Presentation PDF]]<br />
# Epstein, Charlotte. KNOWLEDGE AND POWER IN GLOBAL ENVIRONMENTAL ACTIVISM. s.l. : International Journal of Peace Studies, 2005.[[media:Epstein_101IJPS.pdf | Epstein PDF]]<br />
# CH. Loi fédérale sur la protection des eaux. [Online] juin 1, 2014. https://www.admin.ch/opc/fr/classified-compilation/19910022/index.html#a4.<br />
# Kleehammer, Katie and Sigler, Adam. Moore Creek Volunteer Monitoring for Escherichia coli - Sampling and analysis. Bozeman : MSU Extension Water Quality, 2012.[[media : Moore_E_Coli.pdf | SOP Moore Creek E.coli sampling PDF]]<br />
# Homogeneous Distribution of Escherichia coli Measured within the Vertical Water Column of Small, Freshwater Streams. Buckalew, David, et al. Farmville, VA : Scientific Research Publishing, March 24, 2014, Water Resource and Protection, pp. 410-421. [[media : Distirbutionofecoliwatercolumn.pdf | Buckalew et all PDF]]<br />
# Micrology LAboratories. Easy Gel Method Procedure. Goshen, Indiana : s.n., 2015. Recomended procedures for chromogeinc media.[[media:Easygel_method_procedure.pdf | Procedure Easygel PDF]]<br />
# Micrology Laboratories. ECA Check Easy guide. Goshen : Manufacturers color guide for chromogenic media.[[media : Eca_check_easygel_guide.pdf | ECA guide to determining bacteria PDF]]<br />
# DIRECTIVE 2006/7/EC concerning the management of bathing water quality. European Union. Strassbourg : s.n., 2006, Official Journal of the European Union.[[media:DIRECTIVE2006EC_.pdf | Directive 2006/7/EC]]<br />
# Canfield, Daniel; Hoyer, Mark; Volunteer Lake Monitoring : Testing the Reliability of Data Collected by the Florida LakeWatch Program: Lake and Reservoir Management-March 2002 [[media : Floridalakes.pdf | Reliability of volunteer data PDF]]<br />
<br />
=== Documents from hammerdirt Clean Beach Projects ===<br />
* [[ Media : Montreux_april_activity_opt.pdf | Activity report Nov 2015 - April 2016]]<br />
* [[ Media : Pilot_project_cbem_montreux.pdf | Pilot project CBEM May 2016]]<br />
* [[Media:Clean_beach_pro_2015.pdf | Hammerdirt Clean Beach Project 2 2015 Draft]]<br />
* [[ Media : CH_OSPAR._COMPARISON_OPT.pdf | Comparison of Lake Geneva beaches to other OSPAR regions]]<br />
* [[ Media : Citizenscience.pdf | Citizen Science and litter studies (french)]]<br />
* [[ Media : MCBP1.pdf | MCBPI 2014-2015 results (French)]]<br />
* [[ Media : Plagespropres_nov2014_aout2015_opt.pdf | MCBPI 2014-2015 results (English)]]<br />
<br />
=== Literature ===<br />
[[Media:07_phytoplancton_camp.2014.pdf | 2014 Report on Leman biomass ]] <br><br />
[[Media:Rapports_Leman_2014.pdf | 2014 Physico-chemical Leman report]]<br />
<br />
=== Relevant Links ===<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253<br />
<br />
== Press ==<br />
<br />
[[Category:Projects]]<br />
[[Category:Work In Progress]]<br />
[[Category:Environment]]<br />
<br />
== Documentation and Collaboration Tools ==<br />
----<br />
Agree on documentation and collaboration tools<br />
* Internal communication - hackuarium slack <br />
* Calendar? - we have a biodesign google calendar<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
== Water Collection Protocols ==<br />
----<br />
<br><br><br />
<br />
=== Coliform Bacteria Counting ===<br />
----<br />
The presence of ''E. coli'' in natural waters is a direct indication of fecal contamination of water. Coliform bacteria and other bacterial species can also be found in public waters and contribute to human pathologies. There are several methods to distinguish ''E. coli'', coliform and other bacteria vs other microorganisms that may grow on an agar plate, of special interest 'chromogenic media' which contain substrates that form specific colors depending on enzymes produced by each species.<br />
==== Easy Gel ====<br />
Micrology Labs [http://www.micrologylabs.com/page/93/Coliscan-Easygel Coliscan Easygel]<br />
* Rachel asked for an offer including shipping and the 15% discount for the a coliform bacteria testing medium.<br />
* reminder request sent again 18 April to Jonathan Roth (CEO of Micrology Labs) and Doug Wengerd (who eventually answers notes to their 'info' address)<br />
[http://www.micrologylabs.com/page/95/Instructions Protocol] from the Micrology Labs<br><br />
* there have been some paying complications too, but their large scale order for 100 plates makes the 'per plate' cost half of another option <br><br />
<br />
<br />
To note: the Micrology Lab ECA Easygel plates are somewhat expensive, but can assay up to 5ml of sampled water per plate for ready scoring and disposal. Another currently proposed plate media would not only be less discriminating, but require more equipment for the sterile setup and final cleanup, and probably only allow 0.5ml to be assayed/plate. The Micrology plates are also used in other 'citizen science' campaigns and approved by regulatory bodies...<br />
<br />
==== Other Media ====<br />
* [https://en.wikipedia.org/wiki/Endo_agar Endo agar] where gram negatives are favored to grow. Fermentation of lactose in the medium by coliform bacteria gives metallic green sheen to those colonies.<br />
* [https://en.wikipedia.org/wiki/MacConkey_agar MacConkey agar] - also contains lactose and neutral red as a pH indicator, bile salts to inhibit gram-positive bacteria growth<br />
* [https://en.wikipedia.org/wiki/Sorbitol-MacConkey_agar MacConkey agar with sorbitol] is used to isolate E. coli O157, a pathogenic enteric bacteria<br />
* [https://en.wikipedia.org/wiki/Eosin_methylene_blue Eosin Methylene Blue agar] - Lactose fermenting bacteria turn a dark color, gram positive bacteria also inhibited<br />
<br />
<br />
<br><br />
==== DIY protocol ====<br />
<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br />
==== Other Methods ====<br />
* Good "travaux pratique" [http://www.bioutils.ch/protocoles/13-analyse-de-leau protocol] for bacterial counting and salts concentration from Bioutils, UNIGE <br><br />
* Other [[Media:Bacterial_counts.pdf | protocol]] proposing several direct and indirect methods <br><br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
----<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br />
<br />
=== Water Multi-meter ===<br />
----<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br></div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Unmapping&diff=6857Unmapping2016-04-26T18:00:36Z<p>Sachiko: /* WHO */</p>
<hr />
<div><span style="font-family:Georgia;"><br />
<big>"It is not down in any map; true places never are."</big><br><br />
:::::::::<small>- Herman Melville, ''Moby Dick'', 1888</small><br><br><br />
<big>MAP PIECE</big><br><br />
<big>Draw a map to get lost.</big><br><br />
:::::::::<small>- 1964 spring y.o.</small><br><br><br />
</span><br />
<br><br />
=WHAT=<br />
Inspired by the conversations of the first D+arty Monkeys [[Darty_Monkeys#Virtual_roundtable_09.2F10.01.16 Global Virtual Hangouts]] on 9 January 2016, we found a common thread. UN-MAPPING.<br><br />
While mapping immediately conjures associations (matrix operations, physical maps, cartography, GPS tracking, ...) we would like to turn mapping around to ask what it can be.<br><br />
<br />
<br><br />
These are the beginnings of brainstorms. More soon...<br />
<br><br><br />
<br />
=WHO=<br />
* Vanessa - explore digital media to unfold information otherwise from nature and environment.<br />
* Sachiko - to deconstruct the ideas of [http://biodesign.cc/2014/05/05/mapping-in-yogyakarta/ mapping] around the BIODESIGN for the REAL WORLD project, more here: [http://wiki.biodesign.cc/wiki/Visualizing_the_State_of_Our_Waters Visualizing the State of Our Waters]<br />
<br><br />
<br />
=HOW=<br />
This is a process to define what unmapping as a process could be<br><br />
Some directional questions in our minds: <br><br />
* how could mapping be if we removed the anthropocentric perspective?<br />
* what if north is not north?<br />
* what is a map if it comes from rememberance?<br />
* how is a map embodied?<br />
<br><br />
<br />
=Inspirations=<br />
===Unconference===<br />
* 24 hrs. The Unconference PARENTHESIS - An Unconference organized by SARN :: Swiss Artistic Research Network [https://vimeo.com/122789999]<br />
<br />
===Remembrance===<br />
* Tega Brain Kilowatt-Hours [http://tegabrain.com/KiloWatt-Hours]: "Over time, the work forgets"<br />
<br />
* [http://www.tessmartinart.com/breda-on-my-mind/ Breda on my Mind]: a project by artist Tess Martin where people are invited to draw a map of their city from memory. ([https://vimeo.com/85241916 short clip on the making of])<br />
<br />
* [http://sensorymaps.com Sensory Maps]: the site of Kate McLean, an artist and designer, creator of smellmaps. "alternative sensory modes for individual and shared interpretation of place" ([http://sensorymaps.blogspot.ch her blog]).<br />
<br />
* [http://singaporerivermap.blogspot.ch/2010/09/documentation-shape-of-singapore-river.html Shape of Singapore River]: artist/archivist/cartographer Debbie Ding's 20 illustrations based on collected sketches made by people and what they think the shape of the Singapore River looks like, without making reference to anything else.<br />
<br />
* "Converging, layered ecologies" - an art&science field laboratory about converging ecologies Fieldnotes Hybridmatters [http://fieldnotes.hybridmatters.net/]<br />
<br />
* World Day of Water: In 2016, the theme is "Water and Jobs," [http://www.unwater.org/campaigns/world-water-day/en/]<br />
<br />
===Interactivity===<br />
* Waterwheel is an interactive, collaborative platform for sharing media, knowledge, ideas, performances and presentations about or inspired by water. [http://water-wheel.net/]<br />
* Interactive topography sand box [https://www.facebook.com/video.php?v=1420726251558170]<br />
<br />
===Conjuring beyond 2D===<br />
<br />
* Adrien Siegal's Mollata Meander [http://www.adriensegal.com/#!molalla-meander/c1wj6]: alluvial flows over 15 years of a section of the Molalla River in the Cascade Range of Clackamas County in NW Oregon<br />
<br />
* Luke Jerram's Tōhoku Japanese Earthquake [http://www.lukejerram.com/tohoku-japanese-earthquake/]: sculpture seismogram of the 2011 earthquake<br />
<br />
* Crime Reports by information designer Sha [http://postarchitectural.com/Crime-Reports]<br />
<br />
* Trash collages - Your junk is beautiful [https://youtu.be/eEfKXCbi154]<br />
<br />
* Hard Data by R. Luke DuBois string quartet and website, 2009 [http://archive.turbulence.org/Works/harddata/]: "open-source “information score” of the U.S.- led war in Iraq, taking economic, social (including casualty), political, and cultural statistics from both Iraq and the United States over the course of the war and placing them on a timeline."<br />
<br />
* The Center for Genomic Gastronomy 2011 [http://genomicgastronomy.com/work/2011-2/smog-tasting/ Smog Tasting] - uses egg foams to harvest air pollution. Smog from different locations can be tasted and compared. and a subsequent sonification 2015: [http://genomicgastronomy.com/work/2015-2/smog-synthesizer/ Smog Synthesizer]<br />
<br />
* "White clothing becomes grey after a few hours" Environmental science: Pollution patrol by Kat Austen, Nature 2015[http://www.nature.com/news/environmental-science-pollution-patrol-1.16654]<br />
<br />
* 3D map as a music player [https://youtu.be/XdE_L-cOwM0 Citymusic project] by Akko Goldenbeld<br />
<br />
<br />
<br><br></div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Unmapping&diff=6856Unmapping2016-04-26T17:59:27Z<p>Sachiko: /* HOW */</p>
<hr />
<div><span style="font-family:Georgia;"><br />
<big>"It is not down in any map; true places never are."</big><br><br />
:::::::::<small>- Herman Melville, ''Moby Dick'', 1888</small><br><br><br />
<big>MAP PIECE</big><br><br />
<big>Draw a map to get lost.</big><br><br />
:::::::::<small>- 1964 spring y.o.</small><br><br><br />
</span><br />
<br><br />
=WHAT=<br />
Inspired by the conversations of the first D+arty Monkeys [[Darty_Monkeys#Virtual_roundtable_09.2F10.01.16 Global Virtual Hangouts]] on 9 January 2016, we found a common thread. UN-MAPPING.<br><br />
While mapping immediately conjures associations (matrix operations, physical maps, cartography, GPS tracking, ...) we would like to turn mapping around to ask what it can be.<br><br />
<br />
<br><br />
These are the beginnings of brainstorms. More soon...<br />
<br><br><br />
<br />
=WHO=<br />
* Vanessa - explore digital media to unfold information otherwise from nature and environment.<br />
* Sachiko - my interest is to deconstruct the ideas of [http://biodesign.cc/2014/05/05/mapping-in-yogyakarta/ mapping] around the BIODESIGN for the REAL WORLD project<br />
<br><br />
<br />
=HOW=<br />
This is a process to define what unmapping as a process could be<br><br />
Some directional questions in our minds: <br><br />
* how could mapping be if we removed the anthropocentric perspective?<br />
* what if north is not north?<br />
* what is a map if it comes from rememberance?<br />
* how is a map embodied?<br />
<br><br />
<br />
=Inspirations=<br />
===Unconference===<br />
* 24 hrs. The Unconference PARENTHESIS - An Unconference organized by SARN :: Swiss Artistic Research Network [https://vimeo.com/122789999]<br />
<br />
===Remembrance===<br />
* Tega Brain Kilowatt-Hours [http://tegabrain.com/KiloWatt-Hours]: "Over time, the work forgets"<br />
<br />
* [http://www.tessmartinart.com/breda-on-my-mind/ Breda on my Mind]: a project by artist Tess Martin where people are invited to draw a map of their city from memory. ([https://vimeo.com/85241916 short clip on the making of])<br />
<br />
* [http://sensorymaps.com Sensory Maps]: the site of Kate McLean, an artist and designer, creator of smellmaps. "alternative sensory modes for individual and shared interpretation of place" ([http://sensorymaps.blogspot.ch her blog]).<br />
<br />
* [http://singaporerivermap.blogspot.ch/2010/09/documentation-shape-of-singapore-river.html Shape of Singapore River]: artist/archivist/cartographer Debbie Ding's 20 illustrations based on collected sketches made by people and what they think the shape of the Singapore River looks like, without making reference to anything else.<br />
<br />
* "Converging, layered ecologies" - an art&science field laboratory about converging ecologies Fieldnotes Hybridmatters [http://fieldnotes.hybridmatters.net/]<br />
<br />
* World Day of Water: In 2016, the theme is "Water and Jobs," [http://www.unwater.org/campaigns/world-water-day/en/]<br />
<br />
===Interactivity===<br />
* Waterwheel is an interactive, collaborative platform for sharing media, knowledge, ideas, performances and presentations about or inspired by water. [http://water-wheel.net/]<br />
* Interactive topography sand box [https://www.facebook.com/video.php?v=1420726251558170]<br />
<br />
===Conjuring beyond 2D===<br />
<br />
* Adrien Siegal's Mollata Meander [http://www.adriensegal.com/#!molalla-meander/c1wj6]: alluvial flows over 15 years of a section of the Molalla River in the Cascade Range of Clackamas County in NW Oregon<br />
<br />
* Luke Jerram's Tōhoku Japanese Earthquake [http://www.lukejerram.com/tohoku-japanese-earthquake/]: sculpture seismogram of the 2011 earthquake<br />
<br />
* Crime Reports by information designer Sha [http://postarchitectural.com/Crime-Reports]<br />
<br />
* Trash collages - Your junk is beautiful [https://youtu.be/eEfKXCbi154]<br />
<br />
* Hard Data by R. Luke DuBois string quartet and website, 2009 [http://archive.turbulence.org/Works/harddata/]: "open-source “information score” of the U.S.- led war in Iraq, taking economic, social (including casualty), political, and cultural statistics from both Iraq and the United States over the course of the war and placing them on a timeline."<br />
<br />
* The Center for Genomic Gastronomy 2011 [http://genomicgastronomy.com/work/2011-2/smog-tasting/ Smog Tasting] - uses egg foams to harvest air pollution. Smog from different locations can be tasted and compared. and a subsequent sonification 2015: [http://genomicgastronomy.com/work/2015-2/smog-synthesizer/ Smog Synthesizer]<br />
<br />
* "White clothing becomes grey after a few hours" Environmental science: Pollution patrol by Kat Austen, Nature 2015[http://www.nature.com/news/environmental-science-pollution-patrol-1.16654]<br />
<br />
* 3D map as a music player [https://youtu.be/XdE_L-cOwM0 Citymusic project] by Akko Goldenbeld<br />
<br />
<br />
<br><br></div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Unmapping&diff=6855Unmapping2016-04-26T17:08:42Z<p>Sachiko: </p>
<hr />
<div><span style="font-family:Georgia;"><br />
<big>"It is not down in any map; true places never are."</big><br><br />
:::::::::<small>- Herman Melville, ''Moby Dick'', 1888</small><br><br><br />
<big>MAP PIECE</big><br><br />
<big>Draw a map to get lost.</big><br><br />
:::::::::<small>- 1964 spring y.o.</small><br><br><br />
</span><br />
<br><br />
=WHAT=<br />
Inspired by the conversations of the first D+arty Monkeys [[Darty_Monkeys#Virtual_roundtable_09.2F10.01.16 Global Virtual Hangouts]] on 9 January 2016, we found a common thread. UN-MAPPING.<br><br />
While mapping immediately conjures associations (matrix operations, physical maps, cartography, GPS tracking, ...) we would like to turn mapping around to ask what it can be.<br><br />
<br />
<br><br />
These are the beginnings of brainstorms. More soon...<br />
<br><br><br />
<br />
=WHO=<br />
* Vanessa - explore digital media to unfold information otherwise from nature and environment.<br />
* Sachiko - my interest is to deconstruct the ideas of [http://biodesign.cc/2014/05/05/mapping-in-yogyakarta/ mapping] around the BIODESIGN for the REAL WORLD project<br />
<br><br />
<br />
=HOW=<br />
This is a process to define what unmapping as a process could be<br><br />
Some directional questions in our minds: <br><br />
* how could mapping be if we removed the anthropocentric perspective?<br />
* what if north is not north?<br />
* what is a map if it comes from rememberance?<br />
<br><br />
<br />
=Inspirations=<br />
===Unconference===<br />
* 24 hrs. The Unconference PARENTHESIS - An Unconference organized by SARN :: Swiss Artistic Research Network [https://vimeo.com/122789999]<br />
<br />
===Remembrance===<br />
* Tega Brain Kilowatt-Hours [http://tegabrain.com/KiloWatt-Hours]: "Over time, the work forgets"<br />
<br />
* [http://www.tessmartinart.com/breda-on-my-mind/ Breda on my Mind]: a project by artist Tess Martin where people are invited to draw a map of their city from memory. ([https://vimeo.com/85241916 short clip on the making of])<br />
<br />
* [http://sensorymaps.com Sensory Maps]: the site of Kate McLean, an artist and designer, creator of smellmaps. "alternative sensory modes for individual and shared interpretation of place" ([http://sensorymaps.blogspot.ch her blog]).<br />
<br />
* [http://singaporerivermap.blogspot.ch/2010/09/documentation-shape-of-singapore-river.html Shape of Singapore River]: artist/archivist/cartographer Debbie Ding's 20 illustrations based on collected sketches made by people and what they think the shape of the Singapore River looks like, without making reference to anything else.<br />
<br />
* "Converging, layered ecologies" - an art&science field laboratory about converging ecologies Fieldnotes Hybridmatters [http://fieldnotes.hybridmatters.net/]<br />
<br />
* World Day of Water: In 2016, the theme is "Water and Jobs," [http://www.unwater.org/campaigns/world-water-day/en/]<br />
<br />
===Interactivity===<br />
* Waterwheel is an interactive, collaborative platform for sharing media, knowledge, ideas, performances and presentations about or inspired by water. [http://water-wheel.net/]<br />
* Interactive topography sand box [https://www.facebook.com/video.php?v=1420726251558170]<br />
<br />
===Conjuring beyond 2D===<br />
<br />
* Adrien Siegal's Mollata Meander [http://www.adriensegal.com/#!molalla-meander/c1wj6]: alluvial flows over 15 years of a section of the Molalla River in the Cascade Range of Clackamas County in NW Oregon<br />
<br />
* Luke Jerram's Tōhoku Japanese Earthquake [http://www.lukejerram.com/tohoku-japanese-earthquake/]: sculpture seismogram of the 2011 earthquake<br />
<br />
* Crime Reports by information designer Sha [http://postarchitectural.com/Crime-Reports]<br />
<br />
* Trash collages - Your junk is beautiful [https://youtu.be/eEfKXCbi154]<br />
<br />
* Hard Data by R. Luke DuBois string quartet and website, 2009 [http://archive.turbulence.org/Works/harddata/]: "open-source “information score” of the U.S.- led war in Iraq, taking economic, social (including casualty), political, and cultural statistics from both Iraq and the United States over the course of the war and placing them on a timeline."<br />
<br />
* The Center for Genomic Gastronomy 2011 [http://genomicgastronomy.com/work/2011-2/smog-tasting/ Smog Tasting] - uses egg foams to harvest air pollution. Smog from different locations can be tasted and compared. and a subsequent sonification 2015: [http://genomicgastronomy.com/work/2015-2/smog-synthesizer/ Smog Synthesizer]<br />
<br />
* "White clothing becomes grey after a few hours" Environmental science: Pollution patrol by Kat Austen, Nature 2015[http://www.nature.com/news/environmental-science-pollution-patrol-1.16654]<br />
<br />
* 3D map as a music player [https://youtu.be/XdE_L-cOwM0 Citymusic project] by Akko Goldenbeld<br />
<br />
<br />
<br><br></div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Unmapping&diff=6854Unmapping2016-04-26T17:07:15Z<p>Sachiko: </p>
<hr />
<div><span style="font-family:Georgia;"><br />
<big>"It is not down in any map; true places never are."</big><br><br />
:::::::::<small>- Herman Melville, ''Moby Dick'', 1888</small><br><br><br />
<big>MAP PIECE</big><br><br />
<big>Draw a map to get lost.</big><br><br />
:::::::::<small>- 1964 spring y.o.</small><br><br />
</span><br />
<br><br />
=WHAT=<br />
Inspired by the conversations of the first D+arty Monkeys [[Darty_Monkeys#Virtual_roundtable_09.2F10.01.16 Global Virtual Hangouts]] on 9 January 2016, we found a common thread. UN-MAPPING.<br><br />
While mapping immediately conjures associations (matrix operations, physical maps, cartography, GPS tracking, ...) we would like to turn mapping around to ask what it can be.<br><br />
<br />
<br><br />
These are the beginnings of brainstorms. More soon...<br />
<br><br><br />
<br />
=WHO=<br />
* Vanessa - explore digital media to unfold information otherwise from nature and environment.<br />
* Sachiko - my interest is to deconstruct the ideas of [http://biodesign.cc/2014/05/05/mapping-in-yogyakarta/ mapping] around the BIODESIGN for the REAL WORLD project<br />
<br><br />
<br />
=HOW=<br />
This is a process to define what unmapping as a process could be<br><br />
Some directional questions in our minds: <br><br />
* how could mapping be if we removed the anthropocentric perspective?<br />
* what if north is not north?<br />
* what is a map if it comes from rememberance?<br />
<br><br />
<br />
=Inspirations=<br />
===Unconference===<br />
* 24 hrs. The Unconference PARENTHESIS - An Unconference organized by SARN :: Swiss Artistic Research Network [https://vimeo.com/122789999]<br />
<br />
===Remembrance===<br />
* Tega Brain Kilowatt-Hours [http://tegabrain.com/KiloWatt-Hours]: "Over time, the work forgets"<br />
<br />
* [http://www.tessmartinart.com/breda-on-my-mind/ Breda on my Mind]: a project by artist Tess Martin where people are invited to draw a map of their city from memory. ([https://vimeo.com/85241916 short clip on the making of])<br />
<br />
* [http://sensorymaps.com Sensory Maps]: the site of Kate McLean, an artist and designer, creator of smellmaps. "alternative sensory modes for individual and shared interpretation of place" ([http://sensorymaps.blogspot.ch her blog]).<br />
<br />
* [http://singaporerivermap.blogspot.ch/2010/09/documentation-shape-of-singapore-river.html Shape of Singapore River]: artist/archivist/cartographer Debbie Ding's 20 illustrations based on collected sketches made by people and what they think the shape of the Singapore River looks like, without making reference to anything else.<br />
<br />
* "Converging, layered ecologies" - an art&science field laboratory about converging ecologies Fieldnotes Hybridmatters [http://fieldnotes.hybridmatters.net/]<br />
<br />
* World Day of Water: In 2016, the theme is "Water and Jobs," [http://www.unwater.org/campaigns/world-water-day/en/]<br />
<br />
===Interactivity===<br />
* Waterwheel is an interactive, collaborative platform for sharing media, knowledge, ideas, performances and presentations about or inspired by water. [http://water-wheel.net/]<br />
* Interactive topography sand box [https://www.facebook.com/video.php?v=1420726251558170]<br />
<br />
===Conjuring beyond 2D===<br />
<br />
* Adrien Siegal's Mollata Meander [http://www.adriensegal.com/#!molalla-meander/c1wj6]: alluvial flows over 15 years of a section of the Molalla River in the Cascade Range of Clackamas County in NW Oregon<br />
<br />
* Luke Jerram's Tōhoku Japanese Earthquake [http://www.lukejerram.com/tohoku-japanese-earthquake/]: sculpture seismogram of the 2011 earthquake<br />
<br />
* Crime Reports by information designer Sha [http://postarchitectural.com/Crime-Reports]<br />
<br />
* Trash collages - Your junk is beautiful [https://youtu.be/eEfKXCbi154]<br />
<br />
* Hard Data by R. Luke DuBois string quartet and website, 2009 [http://archive.turbulence.org/Works/harddata/]: "open-source “information score” of the U.S.- led war in Iraq, taking economic, social (including casualty), political, and cultural statistics from both Iraq and the United States over the course of the war and placing them on a timeline."<br />
<br />
* The Center for Genomic Gastronomy 2011 [http://genomicgastronomy.com/work/2011-2/smog-tasting/ Smog Tasting] - uses egg foams to harvest air pollution. Smog from different locations can be tasted and compared. and a subsequent sonification 2015: [http://genomicgastronomy.com/work/2015-2/smog-synthesizer/ Smog Synthesizer]<br />
<br />
* "White clothing becomes grey after a few hours" Environmental science: Pollution patrol by Kat Austen, Nature 2015[http://www.nature.com/news/environmental-science-pollution-patrol-1.16654]<br />
<br />
* 3D map as a music player [https://youtu.be/XdE_L-cOwM0 Citymusic project] by Akko Goldenbeld<br />
<br />
<br />
<br><br></div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=6847Micro to Macro Water Pollution2016-04-21T10:39:13Z<p>Sachiko: /* Coliform Bacteria Counting */</p>
<hr />
<div>== Background Information ==<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation can be found here:[http://www.slideshare.net/RogerErismann/hammerdirt-project-iii How we can work together]<br />
<br><br><br />
<br />
== Aims ==<br />
To answer: Does the presence of macropollutants on the shores of Lac Leman correlate with micropollutants (biological, chemical, particulate, etc.) in the lake water?<br />
<br><br><br />
<br />
== Brainstorm Results ==<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
<br />
== Collaboration Defined ==<br />
The collaboration between Hammerdirt and BIO-DESIGN for the REAL WORLD as of 2016<br><br />
1st stage:<br><br />
* water collection protocols appropriate for each read-out<br />
* coliform bacteria counting<br />
::* easygel<br />
::* DIY version<br />
* community bioreporter kit field version for Switzerland<br />
::* robust hardware<br />
::* easy to manipulate wetware (remove possibility of error in the protocol - including standard curve generation, etc.)<br />
* a water multimeter<br />
::* pH, conductivity, dissolved O2, temperature<br />
<br><br><br />
<br />
== Action Plans ==<br />
* Hammerdirt collects baseline and routine water samples for testing<br />
* Research what other relevant datasets are out there and document it<br />
<br><br><br />
=== Documentation and Collaboration Tools ===<br />
----<br />
Agree on documentation and collaboration tools<br />
* Internal communication - hackuarium slack<br />
* Calendar? - we have a biodesign google calendar<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
=== Water Collection Protocols ===<br />
----<br />
<br><br><br />
<br />
=== Coliform Bacteria Counting ===<br />
----<br />
Coliform bacteria is an indirect indication of fecal contamination of the waters. There are several methods to distinguish coliform bacteria vs other microorganisms that may grow on an agar plate.<br />
==== Easy Gel ====<br />
Micrology Labs [http://www.micrologylabs.com/page/93/Coliscan-Easygel Coliscan Easygel]<br />
* Rachel asked for an offer including shipping and the 15% discount for the a coliform bacteria testing medium.<br />
* reminder request sent again 18 April to Jonathan Roth (CEO of Micrology Labs) and Doug Wengerd (who eventually answers notes to their 'info' address)<br />
[http://www.micrologylabs.com/page/95/Instructions Protocol] from the Micrology Labs<br><br />
<br />
<br />
To note: the Micrology Lab ECA Easygel plates are more expensive, but can assay up to 5ml of sampled water per plate for ready scoring and disposal. Another currently proposed plate media would not only be less discriminating, but require more equipment for the sterile setup and final cleanup, and probably only allow 0.5ml to be assayed/plate.<br />
<br />
==== Other Media ====<br />
* [https://en.wikipedia.org/wiki/Endo_agar Endo agar] where gram negatives are favored to grow. Fermentation of lactose in the medium by coliform bacteria gives metallic green sheen to those colonies.<br />
* [https://en.wikipedia.org/wiki/MacConkey_agar MacConkey agar] - also contains lactose and neutral red as a pH indicator, bile salts to inhibit gram-positive bacteria growth<br />
* [https://en.wikipedia.org/wiki/Sorbitol-MacConkey_agar MacConkey agar with sorbitol] is used to isolate E. coli O157, a pathogenic enteric bacteria<br />
* [https://en.wikipedia.org/wiki/Eosin_methylene_blue Eosin Methylene Blue agar] - Lactose fermenting bacteria turn a dark color, gram positive bacteria also inhibited<br />
<br />
<br />
<br><br />
==== DIY protocol ====<br />
<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br />
==== Other Methods ====<br />
* Good "travaux pratique" [http://www.bioutils.ch/protocoles/13-analyse-de-leau protocol] for bacterial counting and salts concentration from Bioutils, UNIGE <br><br />
* Other [[Media:Bacterial_counts.pdf | protocol]] proposing several direct and indirect methods <br><br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
----<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br />
<br />
=== Water Multi-meter ===<br />
----<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br><br />
<br />
== References ==<br />
=== Previous documents ===<br />
* [[Media:Clean_beach_pro_2015.pdf | Clean Beach Project 2015 Draft]]<br />
<br />
=== Literature ===<br />
[[Media:07_phytoplancton_camp.2014.pdf | 2014 Report on Leman biomass ]] <br><br />
[[Media:Rapports_Leman_2014.pdf | 2014 Physico-chemical Leman report]]<br />
<br />
=== Relevant Links ===<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=6846Micro to Macro Water Pollution2016-04-21T10:29:30Z<p>Sachiko: /* DIY protocol */</p>
<hr />
<div>== Background Information ==<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation can be found here:[http://www.slideshare.net/RogerErismann/hammerdirt-project-iii How we can work together]<br />
<br><br><br />
<br />
== Aims ==<br />
To answer: Does the presence of macropollutants on the shores of Lac Leman correlate with micropollutants (biological, chemical, particulate, etc.) in the lake water?<br />
<br><br><br />
<br />
== Brainstorm Results ==<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
<br />
== Collaboration Defined ==<br />
The collaboration between Hammerdirt and BIO-DESIGN for the REAL WORLD as of 2016<br><br />
1st stage:<br><br />
* water collection protocols appropriate for each read-out<br />
* coliform bacteria counting<br />
::* easygel<br />
::* DIY version<br />
* community bioreporter kit field version for Switzerland<br />
::* robust hardware<br />
::* easy to manipulate wetware (remove possibility of error in the protocol - including standard curve generation, etc.)<br />
* a water multimeter<br />
::* pH, conductivity, dissolved O2, temperature<br />
<br><br><br />
<br />
== Action Plans ==<br />
* Hammerdirt collects baseline and routine water samples for testing<br />
* Research what other relevant datasets are out there and document it<br />
<br><br><br />
=== Documentation and Collaboration Tools ===<br />
----<br />
Agree on documentation and collaboration tools<br />
* Internal communication - hackuarium slack<br />
* Calendar? - we have a biodesign google calendar<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
=== Water Collection Protocols ===<br />
----<br />
<br><br><br />
<br />
=== Coliform Bacteria Counting ===<br />
----<br />
Coliform bacteria is an indirect indication of fecal contamination of the waters. There are several methods to distinguish coliform bacteria vs other microorganisms that may grow on an agar plate.<br />
==== Easy Gel ====<br />
Micrology Labs [http://www.micrologylabs.com/page/93/Coliscan-Easygel Coliscan Easygel]<br />
* Rachel asked for an offer including shipping and the 15% discount for the a coliform bacteria testing medium.<br />
* reminder request sent again 18 April to Jonathan Roth (CEO of Micrology Labs) and Doug Wengerd (who eventually answers notes to their 'info' address)<br />
[http://www.micrologylabs.com/page/95/Instructions Protocol] from the Micrology Labs<br><br />
<br />
<br />
To note: the Micrology Lab ECA Easygel plates are more expensive, but can assay up to 5ml of sampled water per plate for ready scoring and disposal. Another currently proposed plate media would not only be less discriminating, but require more equipment for the sterile setup and final cleanup, and probably only allow 0.5ml to be assayed/plate.<br />
<br />
==== Other Media ====<br />
* [https://en.wikipedia.org/wiki/Endo_agar Endo agar] where gram negatives are favored to grow. Fermentation of lactose in the medium by coliform bacteria gives metallic green sheen to those colonies.<br />
<br><br />
==== DIY protocol ====<br />
<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br />
==== Other Methods ====<br />
* Good "travaux pratique" [http://www.bioutils.ch/protocoles/13-analyse-de-leau protocol] for bacterial counting and salts concentration from Bioutils, UNIGE <br><br />
* Other [[Media:Bacterial_counts.pdf | protocol]] proposing several direct and indirect methods <br><br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
----<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br />
<br />
=== Water Multi-meter ===<br />
----<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br><br />
<br />
== References ==<br />
=== Previous documents ===<br />
* [[Media:Clean_beach_pro_2015.pdf | Clean Beach Project 2015 Draft]]<br />
<br />
=== Literature ===<br />
[[Media:07_phytoplancton_camp.2014.pdf | 2014 Report on Leman biomass ]] <br><br />
[[Media:Rapports_Leman_2014.pdf | 2014 Physico-chemical Leman report]]<br />
<br />
=== Relevant Links ===<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Hackuarium&diff=6836Hackuarium2016-04-19T08:42:55Z<p>Sachiko: /* Evénements */</p>
<hr />
<div>Bienvenue sur le '''wiki''' de l'association [http://www.hackuarium.ch/ Hackuarium]<br />
<br />
<div><br />
''[[Main_Page | Click here to view the english version of this wiki.]]'' <br />
</div><br />
<br />
Notre communauté regroupe les curieux et les bricoleurs de la région Lausannoise dans un laboratoire ouvert et citoyen situé avec d'autres activités au sein de [[UniverCité]], à Renens, une ville de Suisse Romande.<br />
<br />
La matière vivante est de plus en plus facilement cultivable, modulable, modifiable. Entre science et design, innovation et création artistique, Hackuarium est une rencontre entre citoyens de la région lausannoise qui veulent promouvoir ou pratiquer la biologie DIY. Le laboratoire communautaire d'Hackuarium offre à chacun la possibilité de découvrir, d’expérimenter et de contribuer ses compétences dans le cadre de projets.<br />
<br />
Comme vous pouvez le voir, cette page est en chantier et a été construite pendant le [[1st_Ever_Hackuarium_Wiki_Sprint | 1er Hackuarium Wiki Sprint]] qui a eu lieu le 7 décembre 2014 à UniverCité.<br />
<br />
Le membre du [[Working Group | groupe de travail]] qui peut vous aider à commencer à contribuer en cas de besoin et la personne de contact du [[Board | comité]] pour nos outils en ligne est [[User:Sam | Sam]]. Tout le groupe de travail est joignable rapidement via [[Slack]] sur [#wg-doc].<br><br />
<br />
__TOC__<br />
<br />
== Qu'est que la biologie DIY? ==<br />
<br />
La biologie do-it-yourself (DIY) vise à démocratiser la recherche en biologie, et en particulier ses outils.<br />
<br />
La biologie DIY est parfois appelée "Biohacking" mais elle n'est en fait qu'une partie de ce mouvement qui applique les règle du hacking à la biotechnologie et la santé.<br />
<br />
Plus d'information sur [https://en.wikipedia.org/wiki/Do-it-yourself_biology Wikipedia] (en anglais).<br />
<br />
== L'Association Hackuarium ==<br />
Hackuarium est une communauté de bricoleurs passionnés constituée en association. L'assemblée constitutive a eu lieu le 13 août 2014.<br />
<br />
Nos membres pratiquent une science ouverte et participative, en dehors des institutions traditionnelles, dans le respect de la [http://diybio.org/codes/draft-diybio-code-of-ethics-from-european-congress/ charte éthique] du mouvement DIYbio EU. Nous favorisons par tous les moyens l'interdisciplinarité, et nos projets sont portés aussi bien par des scientifiques que par des citoyens architectes, designers, informaticiens, journalistes ou retraités.<br />
<br />
Nos projets préférés incluent la plupart du temps une approche à bas coût (low-cost) et la technologie la plus simple possible (low-tech). Nous nous inscrivons également dans une démarche d'upcycling de matériel mis au rebut par les laboratoires de la région.<br />
<br />
Notre laboratoire est ouvert à tous ceux qui partagent nos valeurs et se situe à Renens, au sein d'UniverCité, un lieu d'innovation inauguré le 26 mai 2014.<br><br />
<br />
== Qui sommes-nous? ==<br />
<br />
Notre communauté est le pilier de l'association Hackuarium. Nos membres, au passé varié et aux motivations multiples vivent à Lausanne et dans ses environs.<br><br />
<br />
=== Membres ===<br />
<br />
Nous encourageons les personnes intéressées à participer régulièrement aux activités de l'association à devenir membres.<br />
<br />
Etre membre permet d'avoir accès au laboratoire 24h/24, 7j/7, de bénéficier d'autres offres (rabais sur l'utilisation de l'atelier), de voter à l'assemblée générale et donc de participer activement à la vie de la communauté et aux prises de décisions.<br />
<br />
Etre membre de l'association Hackuarium implique payer une cotisation mensuelle de 20 francs suisses.<br><br />
<br />
=== Comité ===<br />
<br />
Le [[Board|comité de l'association]] Hackuarium est aujourd'hui composé de:<br><br />
* Président & Trésorier: [[User:luchenry | Luc Henry]]<br />
* Secrétaire: [[User:mmastern | Michal Masternak]]<br />
* Responsable laboratoire: [[User:hekkcess | Yann Pierson]]<br />
* Administrateur des outils web: [[User:Sam | Sam Sulaimanov]]<br />
* Art et Design: [[User:Vlorenzo | Vanessa Lorenzo]]<br />
* Talent scout and evangelist: [[User:Randogp | Gianpaolo Rando]]<br />
* Evènements: [[User:Alpittet | Anne-Laure Pittet]]<br />
* Membre: Ana Roldan<br />
<br />
L'agenda de la dernière assemblée générale est disponible [[20160120_General_Assembly | ici]] (20 janvier 2016).<br />
L'agenda de la dernière rencontre du comité est disponible [[20160329_Board_meeting | ici]] (29 mars 2016).<br />
<br />
=== Les amis d'Hackuarium ===<br />
<br />
::<li>[http://www.univercite.ch UniverCité]<br />
::<li>[[Exodes_Urbains | Exodes Urbains]]<br />
<br />
== Où travaillons-nous? ==<br />
Notre laboratoire communautaire se situe au Chemin du Closel 5 à Renens, en Suisse, dans une commune de la région lausannoise en plein développement.<br />
Hackuarium est situé dans le bâtiment IRL et fait partie d'[http://www.univercite.ch Univercité], un espace d'innovation abritant un espace de coworking, l'atelier [http://made.univercite.ch Made@UniverCité], plusieurs associations, des startups, etc.<br />
<br />
== Evénements ==<br />
<big>'''Evénements à venir'''</big><br />
<br><br />
::<li>'''Tous les mercredi, 19:00-23:00''' #OpenHackuarium: le laboratoire est ouvert au public.<br />
<br><br />
<br />
::<li>'''2016.06.14''' A vos agendas! Et venez participer à la [http://opendata.ch/2015/11/opendata-ch2016-am-14-juni-in-lausanne/ conference Opendata.ch/2016], Casino de Montbenon, Lausanne.<br />
::<li>'''2016.04.27''' Mercredi 19:30-21:00: [[Openhackuarium_vol._95 | Openhackuarium vol. 95]] Atelier impression T-shirt!<br />
::<li>'''2016.04.13''' Mercredi 19:30-21:00: [[Openhackuarium_vol._93 | Openhackuarium vol. 93]] 'Genomic integrity' and DIY 'comet assay' on cheek cells.<br />
<br />
Pour les evénements passés, cliquez [[past events|ici]].<br><br><br />
<br />
== [[Projects | Projets]] ==<br />
Hackuarium est une communauté rassemblée autour de différents projets. Si vous voulez en savoir plus, visitez les pages ci-dessous<br />
<br />
=== Projets Actifs ===<br />
<br />
* [[Open-Food-DNA |Open Food DNA]]<br />
* [[BeerDeCoded]]<br />
* [[Living Instruments]]<br />
* [[Bience | Bience (Bière et Science!)]]<br />
* [[APPS]]<br />
* [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Micro to Macro Water Pollution]] -avec [http://www.hammerdirt.ch/ Hammerdirt] et [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Spectro-pointer]]<br />
* [[Darty_Monkeys]]<br />
* [http://octanis.org/ Octanis]<br />
* [[Edible wall]]<br />
* [[ZéBU CH]]<br />
* [[Grow%26Mix_Bioink]]<br />
* [[unmapping]]<br />
<br />
=== Projets Archivés ===<br />
<br />
* [[Mycelium Structures]]<br />
* [[Projet Sylvan|Konkret Bacterien]] <br />
* [[Live Type]]<br />
* [[Projects:LivingLab Design|LivingLab Design]]<br />
* [[Projects:bioluminescence|Bioluminescence]]<br />
* [[Projects:Quantitative Anthropology|Quantitative Anthropology]]<br />
* [[Projects:Impression 3D|Impression 3D]]<br />
* [[Projects:Dépollution des stands de tirs Suisses]]<br />
* [[Incubateur bon marché]]<br />
* [[Space Seed]]<br />
* [[Reception d'images satellites]]<br />
<br />
== En pratique ==<br />
<br />
Sur [[ Media:Univercite map2-01.png | ce lien]] vous trouverez la carte montrant la vue d'ensemble d'Univercité.<br><br />
Sur [[ Media:map1.png | ce lien]] la carte montrant la vue d'ensemble d'Hackuarium détaillant ou se trouve la majorité du matériel.<br />
<br />
=== [[I m new | Je suis nouveau, je fais quoi ?]] ===<br />
Tu viens d'arriver? tu cherches tes repères? Alors commence alors par lire [[I m new | cette page ]].<br />
<br />
=== [[Life_Main | Règles de vie à Hackuarium]] ===<br />
[[Life_Main | Cette page ]] recense les codes de bonne conduite à adopter à Hackuarium ainsi que les quelques règles s'appliquant dans certains cas spécifiques.<br />
<br />
=== [[Protocols | Protocoles]] ===<br />
Tous les protocoles liés à Hackuarium se trouvent [[ BioP_Main | ici ]] (page en Anglais)<br />
Ils sont structurés et expliqués de façon à être axés sur les procédé de manipulation. L'idée est de donner les informations cruciales de manière à appliquer les techniques les plus communes appartenant à la boite à outils du biologiste. Les documents sont structurés comme suit:<br />
::<li> Un schéma décrivant le procédé<br />
::<li> Une explication brève du procédé et son utilité<br />
::<li> Un protocole décrivant les différentes procédures pour appliquer le procédé. Idéalement il y aurait une description pour le faire avec un kit commercial et un moyen DIY.<br />
::<li> Une partie détaillant les précautions à prendre pour travailler en toute sécurité.<br />
::<li> Des informations spécifiques à Hackuarium décrivant ou se trouve les instruments et comment les utiliser.<br />
<br />
=== [[Instru_Main | Instruments et leurs utilisation]] ===<br />
[[Instru_Main | Cette page ]](Anglais) recense tous les instruments disponibles sur le lieu, leur position ainsi que la manière dont ils doivent être utilisés.<br />
<br />
=== [https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing Liste à jour de nos besoins en matériel] ===<br />
Ce document présente le matériel dont nous avons besoin. Si il vous arrivait d'avoir une des pièce que nous recherchons faites nous le savoir, nous comptons sur vous! :-)<br />
<br />
=== [[Where we shop | Où faisons-nous nos achats]] ===<br />
<br />
=== [[Editing the wiki | Comment créer une nouvelle page de projet sur notre wiki]] ===<br />
<br />
== Bibliothèque et liste de lecture ==<br />
<br />
Notre espace contient une bibliothèque d'ouvrages de référence:<br />
<br />
- DELFANTI Alessandro, "Biohackers, The Politics of Open Science", 2013, London, Pluto Press<br />
<br />
- LALLEMENT Michel, "L'âge du faire. Hacking, travail, anarchie", 2015, Paris, Seuil<br />
<br />
Les liens suivants peuvent aussi vous intéresser:<br />
<br />
== Media and Press | Presse et média ==<br />
<br />
Si vous voulez des informations au sujet d'Hackuarium, n'hésitez pas à envoyer un email à hello[at]hackuarium[dot]ch.<br />
<br />
Vous trouverez dans le [[Press_kit | Press Kit]] tous les détails concernant notre passé médiatique. <br />
<br />
<br />
[[Category:Work In Progress]]</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Hackuarium&diff=6835Hackuarium2016-04-19T08:42:41Z<p>Sachiko: /* Evénements */</p>
<hr />
<div>Bienvenue sur le '''wiki''' de l'association [http://www.hackuarium.ch/ Hackuarium]<br />
<br />
<div><br />
''[[Main_Page | Click here to view the english version of this wiki.]]'' <br />
</div><br />
<br />
Notre communauté regroupe les curieux et les bricoleurs de la région Lausannoise dans un laboratoire ouvert et citoyen situé avec d'autres activités au sein de [[UniverCité]], à Renens, une ville de Suisse Romande.<br />
<br />
La matière vivante est de plus en plus facilement cultivable, modulable, modifiable. Entre science et design, innovation et création artistique, Hackuarium est une rencontre entre citoyens de la région lausannoise qui veulent promouvoir ou pratiquer la biologie DIY. Le laboratoire communautaire d'Hackuarium offre à chacun la possibilité de découvrir, d’expérimenter et de contribuer ses compétences dans le cadre de projets.<br />
<br />
Comme vous pouvez le voir, cette page est en chantier et a été construite pendant le [[1st_Ever_Hackuarium_Wiki_Sprint | 1er Hackuarium Wiki Sprint]] qui a eu lieu le 7 décembre 2014 à UniverCité.<br />
<br />
Le membre du [[Working Group | groupe de travail]] qui peut vous aider à commencer à contribuer en cas de besoin et la personne de contact du [[Board | comité]] pour nos outils en ligne est [[User:Sam | Sam]]. Tout le groupe de travail est joignable rapidement via [[Slack]] sur [#wg-doc].<br><br />
<br />
__TOC__<br />
<br />
== Qu'est que la biologie DIY? ==<br />
<br />
La biologie do-it-yourself (DIY) vise à démocratiser la recherche en biologie, et en particulier ses outils.<br />
<br />
La biologie DIY est parfois appelée "Biohacking" mais elle n'est en fait qu'une partie de ce mouvement qui applique les règle du hacking à la biotechnologie et la santé.<br />
<br />
Plus d'information sur [https://en.wikipedia.org/wiki/Do-it-yourself_biology Wikipedia] (en anglais).<br />
<br />
== L'Association Hackuarium ==<br />
Hackuarium est une communauté de bricoleurs passionnés constituée en association. L'assemblée constitutive a eu lieu le 13 août 2014.<br />
<br />
Nos membres pratiquent une science ouverte et participative, en dehors des institutions traditionnelles, dans le respect de la [http://diybio.org/codes/draft-diybio-code-of-ethics-from-european-congress/ charte éthique] du mouvement DIYbio EU. Nous favorisons par tous les moyens l'interdisciplinarité, et nos projets sont portés aussi bien par des scientifiques que par des citoyens architectes, designers, informaticiens, journalistes ou retraités.<br />
<br />
Nos projets préférés incluent la plupart du temps une approche à bas coût (low-cost) et la technologie la plus simple possible (low-tech). Nous nous inscrivons également dans une démarche d'upcycling de matériel mis au rebut par les laboratoires de la région.<br />
<br />
Notre laboratoire est ouvert à tous ceux qui partagent nos valeurs et se situe à Renens, au sein d'UniverCité, un lieu d'innovation inauguré le 26 mai 2014.<br><br />
<br />
== Qui sommes-nous? ==<br />
<br />
Notre communauté est le pilier de l'association Hackuarium. Nos membres, au passé varié et aux motivations multiples vivent à Lausanne et dans ses environs.<br><br />
<br />
=== Membres ===<br />
<br />
Nous encourageons les personnes intéressées à participer régulièrement aux activités de l'association à devenir membres.<br />
<br />
Etre membre permet d'avoir accès au laboratoire 24h/24, 7j/7, de bénéficier d'autres offres (rabais sur l'utilisation de l'atelier), de voter à l'assemblée générale et donc de participer activement à la vie de la communauté et aux prises de décisions.<br />
<br />
Etre membre de l'association Hackuarium implique payer une cotisation mensuelle de 20 francs suisses.<br><br />
<br />
=== Comité ===<br />
<br />
Le [[Board|comité de l'association]] Hackuarium est aujourd'hui composé de:<br><br />
* Président & Trésorier: [[User:luchenry | Luc Henry]]<br />
* Secrétaire: [[User:mmastern | Michal Masternak]]<br />
* Responsable laboratoire: [[User:hekkcess | Yann Pierson]]<br />
* Administrateur des outils web: [[User:Sam | Sam Sulaimanov]]<br />
* Art et Design: [[User:Vlorenzo | Vanessa Lorenzo]]<br />
* Talent scout and evangelist: [[User:Randogp | Gianpaolo Rando]]<br />
* Evènements: [[User:Alpittet | Anne-Laure Pittet]]<br />
* Membre: Ana Roldan<br />
<br />
L'agenda de la dernière assemblée générale est disponible [[20160120_General_Assembly | ici]] (20 janvier 2016).<br />
L'agenda de la dernière rencontre du comité est disponible [[20160329_Board_meeting | ici]] (29 mars 2016).<br />
<br />
=== Les amis d'Hackuarium ===<br />
<br />
::<li>[http://www.univercite.ch UniverCité]<br />
::<li>[[Exodes_Urbains | Exodes Urbains]]<br />
<br />
== Où travaillons-nous? ==<br />
Notre laboratoire communautaire se situe au Chemin du Closel 5 à Renens, en Suisse, dans une commune de la région lausannoise en plein développement.<br />
Hackuarium est situé dans le bâtiment IRL et fait partie d'[http://www.univercite.ch Univercité], un espace d'innovation abritant un espace de coworking, l'atelier [http://made.univercite.ch Made@UniverCité], plusieurs associations, des startups, etc.<br />
<br />
== Evénements ==<br />
<big>'''Evénements à venir'''</big><br />
<br><br />
::<li>'''Tous les mercredi, 19:00-23:00''' #OpenHackuarium: le laboratoire est ouvert au public.<br />
<br><br />
<br />
::<li>'''2016.06.14''' A vos agendas! Et venez participer à la [http://opendata.ch/2015/11/opendata-ch2016-am-14-juni-in-lausanne/ conference Opendata.ch/2016], Casino de Montbenon, Lausanne.<br />
::<li>'''2016.04.27''' Mercredi 19:30-21:00: [[Openhackuarium_vol._95 | Openhackuarium vol. 95]] Atelier impression T-shirt!<br />
::<li>'''2016.04.13''' Mercredi 19:30-21:00: [[Openhackuarium_vol._93 | Openhackuarium vol. 93]] 'Genomic integrity' and DIY 'comet assay' on cheek cells.<br />
<br />
Pour les evénements passés, cliquez [[past events|here]].<br><br><br />
<br />
== [[Projects | Projets]] ==<br />
Hackuarium est une communauté rassemblée autour de différents projets. Si vous voulez en savoir plus, visitez les pages ci-dessous<br />
<br />
=== Projets Actifs ===<br />
<br />
* [[Open-Food-DNA |Open Food DNA]]<br />
* [[BeerDeCoded]]<br />
* [[Living Instruments]]<br />
* [[Bience | Bience (Bière et Science!)]]<br />
* [[APPS]]<br />
* [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Micro to Macro Water Pollution]] -avec [http://www.hammerdirt.ch/ Hammerdirt] et [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Spectro-pointer]]<br />
* [[Darty_Monkeys]]<br />
* [http://octanis.org/ Octanis]<br />
* [[Edible wall]]<br />
* [[ZéBU CH]]<br />
* [[Grow%26Mix_Bioink]]<br />
* [[unmapping]]<br />
<br />
=== Projets Archivés ===<br />
<br />
* [[Mycelium Structures]]<br />
* [[Projet Sylvan|Konkret Bacterien]] <br />
* [[Live Type]]<br />
* [[Projects:LivingLab Design|LivingLab Design]]<br />
* [[Projects:bioluminescence|Bioluminescence]]<br />
* [[Projects:Quantitative Anthropology|Quantitative Anthropology]]<br />
* [[Projects:Impression 3D|Impression 3D]]<br />
* [[Projects:Dépollution des stands de tirs Suisses]]<br />
* [[Incubateur bon marché]]<br />
* [[Space Seed]]<br />
* [[Reception d'images satellites]]<br />
<br />
== En pratique ==<br />
<br />
Sur [[ Media:Univercite map2-01.png | ce lien]] vous trouverez la carte montrant la vue d'ensemble d'Univercité.<br><br />
Sur [[ Media:map1.png | ce lien]] la carte montrant la vue d'ensemble d'Hackuarium détaillant ou se trouve la majorité du matériel.<br />
<br />
=== [[I m new | Je suis nouveau, je fais quoi ?]] ===<br />
Tu viens d'arriver? tu cherches tes repères? Alors commence alors par lire [[I m new | cette page ]].<br />
<br />
=== [[Life_Main | Règles de vie à Hackuarium]] ===<br />
[[Life_Main | Cette page ]] recense les codes de bonne conduite à adopter à Hackuarium ainsi que les quelques règles s'appliquant dans certains cas spécifiques.<br />
<br />
=== [[Protocols | Protocoles]] ===<br />
Tous les protocoles liés à Hackuarium se trouvent [[ BioP_Main | ici ]] (page en Anglais)<br />
Ils sont structurés et expliqués de façon à être axés sur les procédé de manipulation. L'idée est de donner les informations cruciales de manière à appliquer les techniques les plus communes appartenant à la boite à outils du biologiste. Les documents sont structurés comme suit:<br />
::<li> Un schéma décrivant le procédé<br />
::<li> Une explication brève du procédé et son utilité<br />
::<li> Un protocole décrivant les différentes procédures pour appliquer le procédé. Idéalement il y aurait une description pour le faire avec un kit commercial et un moyen DIY.<br />
::<li> Une partie détaillant les précautions à prendre pour travailler en toute sécurité.<br />
::<li> Des informations spécifiques à Hackuarium décrivant ou se trouve les instruments et comment les utiliser.<br />
<br />
=== [[Instru_Main | Instruments et leurs utilisation]] ===<br />
[[Instru_Main | Cette page ]](Anglais) recense tous les instruments disponibles sur le lieu, leur position ainsi que la manière dont ils doivent être utilisés.<br />
<br />
=== [https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing Liste à jour de nos besoins en matériel] ===<br />
Ce document présente le matériel dont nous avons besoin. Si il vous arrivait d'avoir une des pièce que nous recherchons faites nous le savoir, nous comptons sur vous! :-)<br />
<br />
=== [[Where we shop | Où faisons-nous nos achats]] ===<br />
<br />
=== [[Editing the wiki | Comment créer une nouvelle page de projet sur notre wiki]] ===<br />
<br />
== Bibliothèque et liste de lecture ==<br />
<br />
Notre espace contient une bibliothèque d'ouvrages de référence:<br />
<br />
- DELFANTI Alessandro, "Biohackers, The Politics of Open Science", 2013, London, Pluto Press<br />
<br />
- LALLEMENT Michel, "L'âge du faire. Hacking, travail, anarchie", 2015, Paris, Seuil<br />
<br />
Les liens suivants peuvent aussi vous intéresser:<br />
<br />
== Media and Press | Presse et média ==<br />
<br />
Si vous voulez des informations au sujet d'Hackuarium, n'hésitez pas à envoyer un email à hello[at]hackuarium[dot]ch.<br />
<br />
Vous trouverez dans le [[Press_kit | Press Kit]] tous les détails concernant notre passé médiatique. <br />
<br />
<br />
[[Category:Work In Progress]]</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Main_Page&diff=6834Main Page2016-04-19T08:42:05Z<p>Sachiko: /* Committee */</p>
<hr />
<div>Welcome to the wiki of [http://www.hackuarium.ch/ Hackuarium] community.<br />
<br />
At Hackuarium, we want to bring biology (and biologists) to the world, and the real world back to biology. Our laboratory is an excuse to meet and discuss, build and develop ideas in a neutral, open, noncompetitive and not-for-profit environment.<br />
<br />
<div><br />
''[[Hackuarium | Cliquez ici pour accéder à la version française de ce wiki.]]'' <br />
</div><br />
<br />
This page was launched during our [[1st Ever Hackuarium Wiki Sprint]] that took place on 7 December 2014. As you might notice quickly, it is a work-in-progress.<br />
<br />
Scroll down and find out what this is all about!<br />
<br />
__TOC__<br />
<br />
=DIY Bio=<br />
<br />
==What is DIYbio?==<br />
<br />
DIYbio (Do-It-Yourself biology) is a movement that wants to free the practice of biological research and innovation from the institutional and industrial laboratories. Pursued both by amateurs and professional biologists, DIYbio is developing low-cost and low-tech solutions to problems identified by the community.<br />
<br />
The movement is characterised by an extremely diverse set of practices and participants. Some call themselves 'biohackers', in reference to the hacker culture.<br />
<br />
[http://DIYbio.org DIYbio.org] and [http://DIYbio.eu DIYbio.eu] are the portals of the international and european communities, respectively.<br />
<br />
For more information, visit the [http://www.wikipedia.org Wikipedia] page dedicated to [https://en.wikipedia.org/wiki/DIYbio DIYbio].<br />
<br><br />
<br />
=Hackuarium=<br />
<br />
Hackuarium is a not-for-profit association aiming at democratizing science through public engagement.<br />
<br><br />
<br />
Our laboratory in Renens (Switzerland) is open to anyone sharing the values of the association and who is dedicated to follow the [http://diybio.org/codes/draft-diybio-code-of-ethics-from-european-congress/ DIYbio Europe ethical guidelines].<br />
<br />
Our projects are initiated and carried out by scientists as well as non-scientists from a variety of background. They are passionate about tinkering with biology in particular, and technology in general. Some are engineers, architects, designers, IT and computer scientists or retired professionals, but others have no scientific education. They are mostly citizens interested in open and participatory research and innovation, outside the contrains of traditional institutions.<br />
<br />
Hackuarium members want to investigate new ways of carrying out interdisciplinary research and innovation, by making their results accessible (low-cost), simple and easily reproducible (low-tech) and by promoting an open source philosophy.<br />
<br />
Hackuarium is proudly using infrastructures provided by [http://www.univercite.ch UniverCité], an unconventional innovation hub opened in May 2014. Our equipment is mostly upcycled material from institutions and industries from western Switzerland.<br />
<br />
=Who we are=<br />
<br />
Renens is a hopping hub - and our members reflect the diversity that is in and around Lausanne/Renens.<br />
<br><br />
[[People | Check us out]], and find out what makes Hackuarium a good mix.<br />
<br><br />
<br />
==Committee==<br />
<br />
The current [[Board|committee]] is composed of the following people:<br />
<br />
* President & Treasurer: [[User:luchenry | Luc Henry]]<br />
* Secretary: [[User:mmastern | Michal Masternak]]<br />
* Lab Manager: [[User:hekkcess | Yann Pierson]]<br />
* Online tools administrator: [[User:Sam | Sam Sulaimanov]]<br />
* Art and Design coordinator: [[User:Vlorenzo | Vanessa Lorenzo]]<br />
* Talent scout and evangelist: [[User:Randogp | Gianpaolo Rando]]<br />
* Events and coordinator: [[User:Alpittet | Anne-Laure Pittet]]<br />
* Member: Ana Roldan<br />
<br />
The Agenda of the last board meeting can be found [[20151128_Board_Meeting | here]].<br><br><br />
<br />
==Members and Membership==<br />
<br />
Hackuarium operates on a membership basis at this current time.<br />
<br />
The monthly membership fee is 20 CHF. It gives 24/7 access to the lab.<br />
<br />
Please ask a member of the board if you want to join as a member.<br />
<br />
All events are open to anyone, including non-members.<br />
<br />
==Friends of Hackuarium==<br />
<br />
Spaces:<br />
::<li>[http://www.univercite.ch UniverCité]<br />
::<li>[http://lapaillasse.org La Paillasse, Paris]<br />
::<li>[https://lapaillassaone.wordpress.com Paillasse Saône, Lyon]<br />
<br><br />
<br />
Projects:<br />
::<li>[[Exodes_Urbains | Exodes Urbains]]<br />
::<li>[http://echopen.org/index.php?title=Main_Page EchOpen]<br />
<br><br />
<br />
==Where we are==<br />
Hackuarium is one of the association active at UniverCité, an innovation space under construction since May 2014 in the IRL building in Renens. We have documented our working environment as it has evolved.<br><br />
As of December 2015, UniverCité regroups a laboratory, a workshop and co-working space.<br><br />
<br><br />
<br />
=Events=<br />
<br />
<big>'''Upcoming Events'''</big><br />
<br><br />
'''Every Wednesday, 19:00-23:00''' #OpenHackuarium: our lab and space are open to the public. [mailto:hello@hackuarium.ch Get in touch!]<br />
<br><br />
:<li>'''2016.06.14''' Tuesday SAVE THE DATE [http://opendata.ch/2015/11/opendata-ch2016-am-14-juni-in-lausanne/ Opendata.ch/2016 Conference], Casino de Montbenon, Lausanne.<br />
:<li>'''2016.04.27''' Wednesday 19:30-21:00: [[Openhackuarium_vol._95 | Openhackuarium vol. 95]] T-shirt printing session!<br />
:<li>'''2016.04.13''' Wednesday 19:30-21:00: [[Openhackuarium_vol._93 | Openhackuarium vol. 93]] 'Genomic integrity' and DIY 'comet assay' on cheek cells.<br />
:<li>'''2016.04.06''' Wednesday 19:30-21:00: [http://wiki.hackuarium.ch/w/Openhackuarium_vol._92 Openhackuarium vol. 92] Darty Monkeys: 'Biofilia Night'.<br />
<br />
<br />
Please find the list of our [[past events]].<br><br><br />
<br />
=Projects=<br />
Here, you will find the projects going on in the Hackuarium.<br />
<br />
== Active Projects ==<br />
<br />
* [[Open-Food-DNA |Open-Food-DNA]]<br />
* [[BeerDeCoded]]<br />
* [[Living Instruments]]<br />
* [[Bience | Bience (Beer and Science!)]]<br />
* [[Protein purification systems]]<br />
* [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Micro to Macro Water Pollution]] - with [http://www.hammerdirt.ch/ Hammerdirt] and [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Spectro-pointer]]<br />
* [[Darty_Monkeys]]<br />
* [http://octanis.org/ Octanis]<br />
* [[Edible wall]]<br />
* [[ZéBU CH]]<br />
* [[Grow%26Mix_Bioink]]<br />
* [[unmapping]]<br />
* [[Compost Bacteria]]<br />
* [[AGiR! for genomic integrity]]<br />
<br />
== Archived Projects ==<br />
<br />
* [[Mycelium Structures]]<br />
* [[Live Type]]<br />
* [[Projects:LivingLab Design|LivingLab Design]]<br />
* [[Projects:bioluminescence|Bioluminescence]]<br />
* [[Projects:Quantitative Anthropology|Quantitative Anthropology]]<br />
* [[Projects:Impression 3D|Impression 3D]]<br />
* [[Projects:Dépollution des stands de tirs Suisses]]<br />
* [[Incubateur bon marché]]<br />
* [[Space Seed]]<br />
* [[Reception d'images satellites]]<br />
<br />
= Practical Informations =<br />
<br />
Following this [[ Media:Univercite map2-01.png | link]] you will find a general plan of Hackuarium.<br><br />
Following this [[ Media:map1.png | link]], you will find the plan of Hackuarium with the position of equipment.<br />
<br />
== [[Life_Main | Rules at Hackuarium]] ==<br />
[[Life_Main | This page ]] describe the code of conduct for Hackuarium members.<br />
<br />
== [[Protocols | Protocols]] ==<br />
All the protocols that we use at Hackuarium can be found [[ BioP_Main | here ]]<br />
They are detailed and structured so that the main focus is on applications. The idea is to give crucial information on how to apply the most common techniques of the Biology toolbox. The protocols are structured as follow:<br />
::<li> A scheme describing each <br />
::<li> A brief description of the protocol and its use<br />
::<li> A description of the different ways of carrying out the protocol. Ideally there should be a description of a commercial kit and a DIY kit.<br />
::<li> A description of the safety issues and best practice<br />
::<li> Information specific to Hackuarium and where to find the components, tools and reagents.<br />
<br />
== [[Instru_Main | Instruments available]] ==<br />
[[Instru_Main | This page ]] describes all the instruments available at Hackuarium (work in progress..), their location and how to use them.<br />
<br />
== [https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing Liste à jour de nos besoins en matériel] ==<br />
This document contains all the instruments and tools we need. If you happen to have a piece of equipment we are (or may be) looking for, [mailto:hello@hackuarium.ch contact us]!<br />
<br />
== [[Where we shop | Where we shop]] ==<br />
===Wetware===<br />
Consumables can be purchased from [http://www.huberlab.ch Huber Lab].<br />
<br />
Swiss-based [http://www.smiples.ch Smiples] has a very extensive listing of second hand laboratory and technical items. These can be bought from their online shop or from [https://www.ricardo.ch/online-shop/smiples/?SellerNickName=Smiples Ricardo].<br />
<br />
===Hardware===<br />
Options for electronic parts<br />
* [http://www.ebay.com Ebay] (international)<br />
* [http://www.aliexpress.com AliExpress] (China)<br />
* [https://www.adafruit.com Adafruit] (UK)<br />
<br><br />
* [http://www.seeedstudio.com/depot/ seeedstudio] (China)<br />
* [http://www.tmart.com/ Tmart] (Hong Kong)<br />
* [https://www.pi-shop.ch/ Rasberry pi shop] (Switzerland)<br />
* [http://www.distrelec.ch/ distrilec] (Switzerland)<br />
<br />
== Tools and Equipment found at Hackuarium ==<br />
<br />
::<li>[[Tools#Working_Equipment Working Equipment|Working Equipment]]<br />
::<li>[[Tools#Equipment_that_need_a_bit_of_fixing Needs Help|Equipment needing fixing]]<br />
::<li>[[Where we shop]]<br />
<br><br />
<br />
== [[Editing the wiki | How to built a new project page on our Wiki]] ==<br />
<br />
== Library and Reading List ==<br />
<br />
== Media and Press ==<br />
<br />
* Newsletter<br />
<br />
== Wanted ==<br />
Do you want to contribute to making Hackuarium a diverse and lively community? Check out our wanted lists:<br />
::<li>Skills<br />
::<li>Ideas<br />
::<li>[https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing Equipment]<br />
::<li>Materials<br />
<br><br></div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Past_events&diff=6833Past events2016-04-19T08:39:21Z<p>Sachiko: </p>
<hr />
<div>__TOC__<br />
== Past Events at Hackuarium ==<br />
<br><br />
::<li>'''2016.03.29''' Tuesday 19:30-21:00: [[20160329_Board_meeting | Board meeting]]<br />
::<li>'''2016.03.09''' Wednesday 19:30-21:30 Openhackuarium vol. 88 Presentation by and brainstorming with [http://www.hammerdirt.ch/current-project.html Hammerdirt]<br />
::<li>'''2016.03.08''' Tuesday 16:50 [[Events:Entre_Bière_Hackers_et_ADN_Café_Scientifique_au_Collège_Rousseau |Entre bière, hackers et ADN]] The [[BeerDeCoded| BeerDeCoded project]] on stage at the Café Scientifique of Collège Rousseau (Geneva).<br />
::<li>'''2016.03.04''' Friday 19:30-22:30 Visite of Hackuarium by participants of the [[GOSH_meeting | Gathering for Open Science Hardware]] (aka [http://openplant.org/oshwforscience/ GOSH!]).<br />
::<li>'''2016.02.12''' Friday 9:00-11:00: The [[Living_Instruments| Living Instruments]] project will be featured as part of the official [http://liftconference.com/lift16/workshops/living-organisms-musical-instruments-unprecedented-performance Lift Conference] program.<br />
::<li>'''2016.02.10''' Wednesday 19:30-21:00: School trip to the music venue [http://www.le-bourg.ch le Bourg] for an [http://www.wespoke.ch/les-concerts/le-bourg-2-hackuarium/ Openhackuarium vol. 84 special music] featuring the [[Living_Instruments| Living Instruments]] project.<br />
::<li>'''2016.02.04''' Thursday 19:30-20:30 [[20160204_Board_meeting | Board meeting]]<br />
::<li>'''2016.02.03''' Wednesday 19:30-21:00 Participants to the Biodesign.cc [http://wiki.biodesign.cc/wiki/Winter_School Winterschool] visit [[Openhackuarium_vol._83 | Openhackuarium vol. 83]].<br />
::<li>'''2016.01.23-24''' Saturday and Sunday 09:00-19:00 Another week-end dedicated to biomusical innovation with the [[Living_Instruments| Living Instruments]] project<br />
::<li>'''2016.01.20''' Wednesday 19:30-20:30: [[20160120_General_Assembly | General Assembly]] of the Hackuarium association. Please come, as a member, or as a friend!<br />
::<li>'''2015.12.09''' Wednesday 19:30-21:00: [[Openhackuarium_vol._75 | Openhackuarium vol. 75]] with a presentation of the project beMap.<br />
::<li>'''2015.12.02''' Wednesday 19:30-21:00: [[Openhackuarium_vol._74 | Openhackuarium vol. 74]] with presentations about open source projects in protein science and more!<br />
::<li>'''2015.11.28''' Saturday 9:30-15:30: [[DNA_Party_workchoppe_vol.2 | The real Beer DNA workshop]] Sign-up! Limited space available.<br />
::<li>'''2015.11.26''' Jeudi 19:30-21:00: [[20151128_Board_Meeting | Board Meeting]]<br />
::<li>'''2015.11.05''' Thursday 19:00-22:00: Lausanne Open Data vol. 3 [[Data_sharing_-_Lausanne_Open_Data_Meetup|Special meetup on Biomedical Data & Ethics]] ([http://www.meetup.com/Lausanne-Open-Data-Meetup/events/223791979/| more here])<br />
::<li>'''2015.10.28''' Wednesday 19:30-23:00: [[Openhackuarium_vol._69 |#OpenHackuarium vol. 60]] [http://hackteria.org Hackteria]: DIY bio in Indonesia and the Biology of cheese and wine. Part of a week-long experiment with [http://www.hesge.ch/head/en HEAD]: [http://hackteria.org/wiki/The_Art_of_BioHacking_-_HEAD The Art of BioHacking]<br />
::<li>'''2015.09.19-21''' A long week-end dedicated to biomusical innovation with the [[Living_Instruments| Living Instruments]] project<br />
::<li>'''2015.08.27''' Thursday 19:00-22:00: Lausanne Open Data vol. 1 ([http://www.meetup.com/Lausanne-Open-Data-Meetup/events/223762682/| more here])<br />
::<li>'''2015.08.26''' Wednesday 19:30-20:30: [[Openhackuarium_vol._60_%22Lac_Léman_Science_Hackathon%22_260815|#OpenHackuarium vol. 60: Do we need Lac Léman Science Hackathon?]]<br />
::<li>'''2015.08.20''' Thursday 19:00-22:00: Drone Racing 101<br />
::<li>'''2015.08.05''' Wednesday 19:30-20:30: [[Openhackuarium_vol._57_%22Bi%C3%A8re%22 | #OpenHackuarium vol. 57]] special Fermentation.<br />
::<li>'''2015.07.22''' Wednesday 19:30-20:30: [[Openhackuarium_vol._55_-_22.07.15 | #OpenHackuarium vol. 55]] special Urban/Vertical farming.<br />
::<li>'''2015.07.18''' Saturday 9:30-15:30: [[DNA_Party_workchoppe_vol.1 | A first DNA workshop/workchoppe]].<br />
::<li>'''2015.04.22''' Wednesday 19:30-20:30: General Assembly of Hackuarium association.<br />
::<li>'''2015.04.16''' Thursday 19:00-21:00: Discussion with Le Pansement, a medical students association.<br />
::<li>'''2015.04.15''' Wednesday 18:30-21:00: Practical Session "Garage Electrophoresis" with Le Pansement, a medical students association.<br />
::<li>'''2015.03.29''' Sunday 13:30-18:30: [[2nd_Hackuarium_Wiki_Sprint | Hackuarium Wiki Sprint #2]].<br />
::<li>'''2015.03.28''' Saturday 10:00-18:30: [[Open_DNA_Seq_Workshop | Open DNA Sequencing Workshop]].<br />
::<li>'''2015.02.18''' [[Visite_du_FlyLab_Paris_chez_nous| Drone night]] with Flylab Paris (part of La Paillasse) (FR).<br />
::<li>'''2014.12.07''' [[1st_Ever_Hackuarium_Wiki_Sprint | Hackuarium Wiki Sprint #1]].<br />
::<li>'''2014.11.27''' [[Events:BSNL_Roundtable | Roundtable at EPFL organised by BNSL]].<br />
::<li>'''2014.11.05''' [[Events:Bioart_NexTrends | NexTrends/ECAL Bioart conference]] at UniverCité.<br />
::<li>'''2014.10.22''' [[Events:Open_Access | Open Access conference]] at UniverCité.<br />
::<li>'''2014.10.09''' Conference by French artist [http://liagiraud.com Lia Giraud].<br />
::<li>'''2014.09.25-27''' [[Events:Design_Days_2014 | Design Days 2014]].<br />
::<li>'''2014.09.24''' Conference by [http://www.nicolasnova.net Nicolas Nova], co-fondateur du [http://nearfuturelaboratory.com Near Future Laboratory] et enseignant à la [http://www.hesge.ch/head/ HEAD], Genève.<br />
::<li>'''2014.08.27''' Introduction to [http://bricobio.org BricoBio] Montreal by Sarah Choukah.<br />
::<li>'''2014.08.20''' Introduction to [http://lapaillasse.org La Paillasse] Paris by Clément Epié and Nicolas Loubet.<br />
::<li>'''2014.06.06-07''' [http://hackteria.org/wiki/Tech4Dev Water Hackathon] organised by Hackteria.<br />
<br />
== Participation to External Events ==<br />
::<li>'''2014.11 - 2014.12''' [http://www.gasthauszumbaeren.ch//wire-lab/re-thinking-food- Re-Thinking Food], [http://www.gasthauszumbaeren.ch/de/home Gasthaus zum Bären], [http://www.thewire.ch/en/ W.I.R.E.], Zurich, Switzerland<br />
::<li>'''2014.09.25 - 2015.02.22''' [http://www.museedelamain.ch LAB/LIFE Exhibition], Musée de la Main, Lausanne, Switzerland</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Past_events&diff=6832Past events2016-04-19T08:39:03Z<p>Sachiko: </p>
<hr />
<div>__TOC__<br />
== Past Events ==<br />
<br><br />
::<li>'''2016.03.29''' Tuesday 19:30-21:00: [[20160329_Board_meeting | Board meeting]]<br />
::<li>'''2016.03.09''' Wednesday 19:30-21:30 Openhackuarium vol. 88 Presentation by and brainstorming with [http://www.hammerdirt.ch/current-project.html Hammerdirt]<br />
::<li>'''2016.03.08''' Tuesday 16:50 [[Events:Entre_Bière_Hackers_et_ADN_Café_Scientifique_au_Collège_Rousseau |Entre bière, hackers et ADN]] The [[BeerDeCoded| BeerDeCoded project]] on stage at the Café Scientifique of Collège Rousseau (Geneva).<br />
::<li>'''2016.03.04''' Friday 19:30-22:30 Visite of Hackuarium by participants of the [[GOSH_meeting | Gathering for Open Science Hardware]] (aka [http://openplant.org/oshwforscience/ GOSH!]).<br />
::<li>'''2016.02.12''' Friday 9:00-11:00: The [[Living_Instruments| Living Instruments]] project will be featured as part of the official [http://liftconference.com/lift16/workshops/living-organisms-musical-instruments-unprecedented-performance Lift Conference] program.<br />
::<li>'''2016.02.10''' Wednesday 19:30-21:00: School trip to the music venue [http://www.le-bourg.ch le Bourg] for an [http://www.wespoke.ch/les-concerts/le-bourg-2-hackuarium/ Openhackuarium vol. 84 special music] featuring the [[Living_Instruments| Living Instruments]] project.<br />
::<li>'''2016.02.04''' Thursday 19:30-20:30 [[20160204_Board_meeting | Board meeting]]<br />
::<li>'''2016.02.03''' Wednesday 19:30-21:00 Participants to the Biodesign.cc [http://wiki.biodesign.cc/wiki/Winter_School Winterschool] visit [[Openhackuarium_vol._83 | Openhackuarium vol. 83]].<br />
::<li>'''2016.01.23-24''' Saturday and Sunday 09:00-19:00 Another week-end dedicated to biomusical innovation with the [[Living_Instruments| Living Instruments]] project<br />
::<li>'''2016.01.20''' Wednesday 19:30-20:30: [[20160120_General_Assembly | General Assembly]] of the Hackuarium association. Please come, as a member, or as a friend!<br />
::<li>'''2015.12.09''' Wednesday 19:30-21:00: [[Openhackuarium_vol._75 | Openhackuarium vol. 75]] with a presentation of the project beMap.<br />
::<li>'''2015.12.02''' Wednesday 19:30-21:00: [[Openhackuarium_vol._74 | Openhackuarium vol. 74]] with presentations about open source projects in protein science and more!<br />
::<li>'''2015.11.28''' Saturday 9:30-15:30: [[DNA_Party_workchoppe_vol.2 | The real Beer DNA workshop]] Sign-up! Limited space available.<br />
::<li>'''2015.11.26''' Jeudi 19:30-21:00: [[20151128_Board_Meeting | Board Meeting]]<br />
::<li>'''2015.11.05''' Thursday 19:00-22:00: Lausanne Open Data vol. 3 [[Data_sharing_-_Lausanne_Open_Data_Meetup|Special meetup on Biomedical Data & Ethics]] ([http://www.meetup.com/Lausanne-Open-Data-Meetup/events/223791979/| more here])<br />
::<li>'''2015.10.28''' Wednesday 19:30-23:00: [[Openhackuarium_vol._69 |#OpenHackuarium vol. 60]] [http://hackteria.org Hackteria]: DIY bio in Indonesia and the Biology of cheese and wine. Part of a week-long experiment with [http://www.hesge.ch/head/en HEAD]: [http://hackteria.org/wiki/The_Art_of_BioHacking_-_HEAD The Art of BioHacking]<br />
::<li>'''2015.09.19-21''' A long week-end dedicated to biomusical innovation with the [[Living_Instruments| Living Instruments]] project<br />
::<li>'''2015.08.27''' Thursday 19:00-22:00: Lausanne Open Data vol. 1 ([http://www.meetup.com/Lausanne-Open-Data-Meetup/events/223762682/| more here])<br />
::<li>'''2015.08.26''' Wednesday 19:30-20:30: [[Openhackuarium_vol._60_%22Lac_Léman_Science_Hackathon%22_260815|#OpenHackuarium vol. 60: Do we need Lac Léman Science Hackathon?]]<br />
::<li>'''2015.08.20''' Thursday 19:00-22:00: Drone Racing 101<br />
::<li>'''2015.08.05''' Wednesday 19:30-20:30: [[Openhackuarium_vol._57_%22Bi%C3%A8re%22 | #OpenHackuarium vol. 57]] special Fermentation.<br />
::<li>'''2015.07.22''' Wednesday 19:30-20:30: [[Openhackuarium_vol._55_-_22.07.15 | #OpenHackuarium vol. 55]] special Urban/Vertical farming.<br />
::<li>'''2015.07.18''' Saturday 9:30-15:30: [[DNA_Party_workchoppe_vol.1 | A first DNA workshop/workchoppe]].<br />
::<li>'''2015.04.22''' Wednesday 19:30-20:30: General Assembly of Hackuarium association.<br />
::<li>'''2015.04.16''' Thursday 19:00-21:00: Discussion with Le Pansement, a medical students association.<br />
::<li>'''2015.04.15''' Wednesday 18:30-21:00: Practical Session "Garage Electrophoresis" with Le Pansement, a medical students association.<br />
::<li>'''2015.03.29''' Sunday 13:30-18:30: [[2nd_Hackuarium_Wiki_Sprint | Hackuarium Wiki Sprint #2]].<br />
::<li>'''2015.03.28''' Saturday 10:00-18:30: [[Open_DNA_Seq_Workshop | Open DNA Sequencing Workshop]].<br />
::<li>'''2015.02.18''' [[Visite_du_FlyLab_Paris_chez_nous| Drone night]] with Flylab Paris (part of La Paillasse) (FR).<br />
::<li>'''2014.12.07''' [[1st_Ever_Hackuarium_Wiki_Sprint | Hackuarium Wiki Sprint #1]].<br />
::<li>'''2014.11.27''' [[Events:BSNL_Roundtable | Roundtable at EPFL organised by BNSL]].<br />
::<li>'''2014.11.05''' [[Events:Bioart_NexTrends | NexTrends/ECAL Bioart conference]] at UniverCité.<br />
::<li>'''2014.10.22''' [[Events:Open_Access | Open Access conference]] at UniverCité.<br />
::<li>'''2014.10.09''' Conference by French artist [http://liagiraud.com Lia Giraud].<br />
::<li>'''2014.09.25-27''' [[Events:Design_Days_2014 | Design Days 2014]].<br />
::<li>'''2014.09.24''' Conference by [http://www.nicolasnova.net Nicolas Nova], co-fondateur du [http://nearfuturelaboratory.com Near Future Laboratory] et enseignant à la [http://www.hesge.ch/head/ HEAD], Genève.<br />
::<li>'''2014.08.27''' Introduction to [http://bricobio.org BricoBio] Montreal by Sarah Choukah.<br />
::<li>'''2014.08.20''' Introduction to [http://lapaillasse.org La Paillasse] Paris by Clément Epié and Nicolas Loubet.<br />
::<li>'''2014.06.06-07''' [http://hackteria.org/wiki/Tech4Dev Water Hackathon] organised by Hackteria.<br />
<br />
== Participation to External Events ==<br />
::<li>'''2014.11 - 2014.12''' [http://www.gasthauszumbaeren.ch//wire-lab/re-thinking-food- Re-Thinking Food], [http://www.gasthauszumbaeren.ch/de/home Gasthaus zum Bären], [http://www.thewire.ch/en/ W.I.R.E.], Zurich, Switzerland<br />
::<li>'''2014.09.25 - 2015.02.22''' [http://www.museedelamain.ch LAB/LIFE Exhibition], Musée de la Main, Lausanne, Switzerland</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Past_events&diff=6831Past events2016-04-19T08:38:43Z<p>Sachiko: /* Past Events */</p>
<hr />
<div>== Past Events ==<br />
__TOC__<br />
<br><br />
::<li>'''2016.03.29''' Tuesday 19:30-21:00: [[20160329_Board_meeting | Board meeting]]<br />
::<li>'''2016.03.09''' Wednesday 19:30-21:30 Openhackuarium vol. 88 Presentation by and brainstorming with [http://www.hammerdirt.ch/current-project.html Hammerdirt]<br />
::<li>'''2016.03.08''' Tuesday 16:50 [[Events:Entre_Bière_Hackers_et_ADN_Café_Scientifique_au_Collège_Rousseau |Entre bière, hackers et ADN]] The [[BeerDeCoded| BeerDeCoded project]] on stage at the Café Scientifique of Collège Rousseau (Geneva).<br />
::<li>'''2016.03.04''' Friday 19:30-22:30 Visite of Hackuarium by participants of the [[GOSH_meeting | Gathering for Open Science Hardware]] (aka [http://openplant.org/oshwforscience/ GOSH!]).<br />
::<li>'''2016.02.12''' Friday 9:00-11:00: The [[Living_Instruments| Living Instruments]] project will be featured as part of the official [http://liftconference.com/lift16/workshops/living-organisms-musical-instruments-unprecedented-performance Lift Conference] program.<br />
::<li>'''2016.02.10''' Wednesday 19:30-21:00: School trip to the music venue [http://www.le-bourg.ch le Bourg] for an [http://www.wespoke.ch/les-concerts/le-bourg-2-hackuarium/ Openhackuarium vol. 84 special music] featuring the [[Living_Instruments| Living Instruments]] project.<br />
::<li>'''2016.02.04''' Thursday 19:30-20:30 [[20160204_Board_meeting | Board meeting]]<br />
::<li>'''2016.02.03''' Wednesday 19:30-21:00 Participants to the Biodesign.cc [http://wiki.biodesign.cc/wiki/Winter_School Winterschool] visit [[Openhackuarium_vol._83 | Openhackuarium vol. 83]].<br />
::<li>'''2016.01.23-24''' Saturday and Sunday 09:00-19:00 Another week-end dedicated to biomusical innovation with the [[Living_Instruments| Living Instruments]] project<br />
::<li>'''2016.01.20''' Wednesday 19:30-20:30: [[20160120_General_Assembly | General Assembly]] of the Hackuarium association. Please come, as a member, or as a friend!<br />
::<li>'''2015.12.09''' Wednesday 19:30-21:00: [[Openhackuarium_vol._75 | Openhackuarium vol. 75]] with a presentation of the project beMap.<br />
::<li>'''2015.12.02''' Wednesday 19:30-21:00: [[Openhackuarium_vol._74 | Openhackuarium vol. 74]] with presentations about open source projects in protein science and more!<br />
::<li>'''2015.11.28''' Saturday 9:30-15:30: [[DNA_Party_workchoppe_vol.2 | The real Beer DNA workshop]] Sign-up! Limited space available.<br />
::<li>'''2015.11.26''' Jeudi 19:30-21:00: [[20151128_Board_Meeting | Board Meeting]]<br />
::<li>'''2015.11.05''' Thursday 19:00-22:00: Lausanne Open Data vol. 3 [[Data_sharing_-_Lausanne_Open_Data_Meetup|Special meetup on Biomedical Data & Ethics]] ([http://www.meetup.com/Lausanne-Open-Data-Meetup/events/223791979/| more here])<br />
::<li>'''2015.10.28''' Wednesday 19:30-23:00: [[Openhackuarium_vol._69 |#OpenHackuarium vol. 60]] [http://hackteria.org Hackteria]: DIY bio in Indonesia and the Biology of cheese and wine. Part of a week-long experiment with [http://www.hesge.ch/head/en HEAD]: [http://hackteria.org/wiki/The_Art_of_BioHacking_-_HEAD The Art of BioHacking]<br />
::<li>'''2015.09.19-21''' A long week-end dedicated to biomusical innovation with the [[Living_Instruments| Living Instruments]] project<br />
::<li>'''2015.08.27''' Thursday 19:00-22:00: Lausanne Open Data vol. 1 ([http://www.meetup.com/Lausanne-Open-Data-Meetup/events/223762682/| more here])<br />
::<li>'''2015.08.26''' Wednesday 19:30-20:30: [[Openhackuarium_vol._60_%22Lac_Léman_Science_Hackathon%22_260815|#OpenHackuarium vol. 60: Do we need Lac Léman Science Hackathon?]]<br />
::<li>'''2015.08.20''' Thursday 19:00-22:00: Drone Racing 101<br />
::<li>'''2015.08.05''' Wednesday 19:30-20:30: [[Openhackuarium_vol._57_%22Bi%C3%A8re%22 | #OpenHackuarium vol. 57]] special Fermentation.<br />
::<li>'''2015.07.22''' Wednesday 19:30-20:30: [[Openhackuarium_vol._55_-_22.07.15 | #OpenHackuarium vol. 55]] special Urban/Vertical farming.<br />
::<li>'''2015.07.18''' Saturday 9:30-15:30: [[DNA_Party_workchoppe_vol.1 | A first DNA workshop/workchoppe]].<br />
::<li>'''2015.04.22''' Wednesday 19:30-20:30: General Assembly of Hackuarium association.<br />
::<li>'''2015.04.16''' Thursday 19:00-21:00: Discussion with Le Pansement, a medical students association.<br />
::<li>'''2015.04.15''' Wednesday 18:30-21:00: Practical Session "Garage Electrophoresis" with Le Pansement, a medical students association.<br />
::<li>'''2015.03.29''' Sunday 13:30-18:30: [[2nd_Hackuarium_Wiki_Sprint | Hackuarium Wiki Sprint #2]].<br />
::<li>'''2015.03.28''' Saturday 10:00-18:30: [[Open_DNA_Seq_Workshop | Open DNA Sequencing Workshop]].<br />
::<li>'''2015.02.18''' [[Visite_du_FlyLab_Paris_chez_nous| Drone night]] with Flylab Paris (part of La Paillasse) (FR).<br />
::<li>'''2014.12.07''' [[1st_Ever_Hackuarium_Wiki_Sprint | Hackuarium Wiki Sprint #1]].<br />
::<li>'''2014.11.27''' [[Events:BSNL_Roundtable | Roundtable at EPFL organised by BNSL]].<br />
::<li>'''2014.11.05''' [[Events:Bioart_NexTrends | NexTrends/ECAL Bioart conference]] at UniverCité.<br />
::<li>'''2014.10.22''' [[Events:Open_Access | Open Access conference]] at UniverCité.<br />
::<li>'''2014.10.09''' Conference by French artist [http://liagiraud.com Lia Giraud].<br />
::<li>'''2014.09.25-27''' [[Events:Design_Days_2014 | Design Days 2014]].<br />
::<li>'''2014.09.24''' Conference by [http://www.nicolasnova.net Nicolas Nova], co-fondateur du [http://nearfuturelaboratory.com Near Future Laboratory] et enseignant à la [http://www.hesge.ch/head/ HEAD], Genève.<br />
::<li>'''2014.08.27''' Introduction to [http://bricobio.org BricoBio] Montreal by Sarah Choukah.<br />
::<li>'''2014.08.20''' Introduction to [http://lapaillasse.org La Paillasse] Paris by Clément Epié and Nicolas Loubet.<br />
::<li>'''2014.06.06-07''' [http://hackteria.org/wiki/Tech4Dev Water Hackathon] organised by Hackteria.<br />
<br />
== Participation to External Events ==<br />
::<li>'''2014.11 - 2014.12''' [http://www.gasthauszumbaeren.ch//wire-lab/re-thinking-food- Re-Thinking Food], [http://www.gasthauszumbaeren.ch/de/home Gasthaus zum Bären], [http://www.thewire.ch/en/ W.I.R.E.], Zurich, Switzerland<br />
::<li>'''2014.09.25 - 2015.02.22''' [http://www.museedelamain.ch LAB/LIFE Exhibition], Musée de la Main, Lausanne, Switzerland</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Past_events&diff=6830Past events2016-04-19T08:38:32Z<p>Sachiko: </p>
<hr />
<div>== Past Events ==<br />
___TOC___<br />
<br><br />
::<li>'''2016.03.29''' Tuesday 19:30-21:00: [[20160329_Board_meeting | Board meeting]]<br />
::<li>'''2016.03.09''' Wednesday 19:30-21:30 Openhackuarium vol. 88 Presentation by and brainstorming with [http://www.hammerdirt.ch/current-project.html Hammerdirt]<br />
::<li>'''2016.03.08''' Tuesday 16:50 [[Events:Entre_Bière_Hackers_et_ADN_Café_Scientifique_au_Collège_Rousseau |Entre bière, hackers et ADN]] The [[BeerDeCoded| BeerDeCoded project]] on stage at the Café Scientifique of Collège Rousseau (Geneva).<br />
::<li>'''2016.03.04''' Friday 19:30-22:30 Visite of Hackuarium by participants of the [[GOSH_meeting | Gathering for Open Science Hardware]] (aka [http://openplant.org/oshwforscience/ GOSH!]).<br />
::<li>'''2016.02.12''' Friday 9:00-11:00: The [[Living_Instruments| Living Instruments]] project will be featured as part of the official [http://liftconference.com/lift16/workshops/living-organisms-musical-instruments-unprecedented-performance Lift Conference] program.<br />
::<li>'''2016.02.10''' Wednesday 19:30-21:00: School trip to the music venue [http://www.le-bourg.ch le Bourg] for an [http://www.wespoke.ch/les-concerts/le-bourg-2-hackuarium/ Openhackuarium vol. 84 special music] featuring the [[Living_Instruments| Living Instruments]] project.<br />
::<li>'''2016.02.04''' Thursday 19:30-20:30 [[20160204_Board_meeting | Board meeting]]<br />
::<li>'''2016.02.03''' Wednesday 19:30-21:00 Participants to the Biodesign.cc [http://wiki.biodesign.cc/wiki/Winter_School Winterschool] visit [[Openhackuarium_vol._83 | Openhackuarium vol. 83]].<br />
::<li>'''2016.01.23-24''' Saturday and Sunday 09:00-19:00 Another week-end dedicated to biomusical innovation with the [[Living_Instruments| Living Instruments]] project<br />
::<li>'''2016.01.20''' Wednesday 19:30-20:30: [[20160120_General_Assembly | General Assembly]] of the Hackuarium association. Please come, as a member, or as a friend!<br />
::<li>'''2015.12.09''' Wednesday 19:30-21:00: [[Openhackuarium_vol._75 | Openhackuarium vol. 75]] with a presentation of the project beMap.<br />
::<li>'''2015.12.02''' Wednesday 19:30-21:00: [[Openhackuarium_vol._74 | Openhackuarium vol. 74]] with presentations about open source projects in protein science and more!<br />
::<li>'''2015.11.28''' Saturday 9:30-15:30: [[DNA_Party_workchoppe_vol.2 | The real Beer DNA workshop]] Sign-up! Limited space available.<br />
::<li>'''2015.11.26''' Jeudi 19:30-21:00: [[20151128_Board_Meeting | Board Meeting]]<br />
::<li>'''2015.11.05''' Thursday 19:00-22:00: Lausanne Open Data vol. 3 [[Data_sharing_-_Lausanne_Open_Data_Meetup|Special meetup on Biomedical Data & Ethics]] ([http://www.meetup.com/Lausanne-Open-Data-Meetup/events/223791979/| more here])<br />
::<li>'''2015.10.28''' Wednesday 19:30-23:00: [[Openhackuarium_vol._69 |#OpenHackuarium vol. 60]] [http://hackteria.org Hackteria]: DIY bio in Indonesia and the Biology of cheese and wine. Part of a week-long experiment with [http://www.hesge.ch/head/en HEAD]: [http://hackteria.org/wiki/The_Art_of_BioHacking_-_HEAD The Art of BioHacking]<br />
::<li>'''2015.09.19-21''' A long week-end dedicated to biomusical innovation with the [[Living_Instruments| Living Instruments]] project<br />
::<li>'''2015.08.27''' Thursday 19:00-22:00: Lausanne Open Data vol. 1 ([http://www.meetup.com/Lausanne-Open-Data-Meetup/events/223762682/| more here])<br />
::<li>'''2015.08.26''' Wednesday 19:30-20:30: [[Openhackuarium_vol._60_%22Lac_Léman_Science_Hackathon%22_260815|#OpenHackuarium vol. 60: Do we need Lac Léman Science Hackathon?]]<br />
::<li>'''2015.08.20''' Thursday 19:00-22:00: Drone Racing 101<br />
::<li>'''2015.08.05''' Wednesday 19:30-20:30: [[Openhackuarium_vol._57_%22Bi%C3%A8re%22 | #OpenHackuarium vol. 57]] special Fermentation.<br />
::<li>'''2015.07.22''' Wednesday 19:30-20:30: [[Openhackuarium_vol._55_-_22.07.15 | #OpenHackuarium vol. 55]] special Urban/Vertical farming.<br />
::<li>'''2015.07.18''' Saturday 9:30-15:30: [[DNA_Party_workchoppe_vol.1 | A first DNA workshop/workchoppe]].<br />
::<li>'''2015.04.22''' Wednesday 19:30-20:30: General Assembly of Hackuarium association.<br />
::<li>'''2015.04.16''' Thursday 19:00-21:00: Discussion with Le Pansement, a medical students association.<br />
::<li>'''2015.04.15''' Wednesday 18:30-21:00: Practical Session "Garage Electrophoresis" with Le Pansement, a medical students association.<br />
::<li>'''2015.03.29''' Sunday 13:30-18:30: [[2nd_Hackuarium_Wiki_Sprint | Hackuarium Wiki Sprint #2]].<br />
::<li>'''2015.03.28''' Saturday 10:00-18:30: [[Open_DNA_Seq_Workshop | Open DNA Sequencing Workshop]].<br />
::<li>'''2015.02.18''' [[Visite_du_FlyLab_Paris_chez_nous| Drone night]] with Flylab Paris (part of La Paillasse) (FR).<br />
::<li>'''2014.12.07''' [[1st_Ever_Hackuarium_Wiki_Sprint | Hackuarium Wiki Sprint #1]].<br />
::<li>'''2014.11.27''' [[Events:BSNL_Roundtable | Roundtable at EPFL organised by BNSL]].<br />
::<li>'''2014.11.05''' [[Events:Bioart_NexTrends | NexTrends/ECAL Bioart conference]] at UniverCité.<br />
::<li>'''2014.10.22''' [[Events:Open_Access | Open Access conference]] at UniverCité.<br />
::<li>'''2014.10.09''' Conference by French artist [http://liagiraud.com Lia Giraud].<br />
::<li>'''2014.09.25-27''' [[Events:Design_Days_2014 | Design Days 2014]].<br />
::<li>'''2014.09.24''' Conference by [http://www.nicolasnova.net Nicolas Nova], co-fondateur du [http://nearfuturelaboratory.com Near Future Laboratory] et enseignant à la [http://www.hesge.ch/head/ HEAD], Genève.<br />
::<li>'''2014.08.27''' Introduction to [http://bricobio.org BricoBio] Montreal by Sarah Choukah.<br />
::<li>'''2014.08.20''' Introduction to [http://lapaillasse.org La Paillasse] Paris by Clément Epié and Nicolas Loubet.<br />
::<li>'''2014.06.06-07''' [http://hackteria.org/wiki/Tech4Dev Water Hackathon] organised by Hackteria.<br />
<br />
== Participation to External Events ==<br />
::<li>'''2014.11 - 2014.12''' [http://www.gasthauszumbaeren.ch//wire-lab/re-thinking-food- Re-Thinking Food], [http://www.gasthauszumbaeren.ch/de/home Gasthaus zum Bären], [http://www.thewire.ch/en/ W.I.R.E.], Zurich, Switzerland<br />
::<li>'''2014.09.25 - 2015.02.22''' [http://www.museedelamain.ch LAB/LIFE Exhibition], Musée de la Main, Lausanne, Switzerland</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Hackuarium&diff=6829Hackuarium2016-04-19T08:37:40Z<p>Sachiko: /* Evénements */</p>
<hr />
<div>Bienvenue sur le '''wiki''' de l'association [http://www.hackuarium.ch/ Hackuarium]<br />
<br />
<div><br />
''[[Main_Page | Click here to view the english version of this wiki.]]'' <br />
</div><br />
<br />
Notre communauté regroupe les curieux et les bricoleurs de la région Lausannoise dans un laboratoire ouvert et citoyen situé avec d'autres activités au sein de [[UniverCité]], à Renens, une ville de Suisse Romande.<br />
<br />
La matière vivante est de plus en plus facilement cultivable, modulable, modifiable. Entre science et design, innovation et création artistique, Hackuarium est une rencontre entre citoyens de la région lausannoise qui veulent promouvoir ou pratiquer la biologie DIY. Le laboratoire communautaire d'Hackuarium offre à chacun la possibilité de découvrir, d’expérimenter et de contribuer ses compétences dans le cadre de projets.<br />
<br />
Comme vous pouvez le voir, cette page est en chantier et a été construite pendant le [[1st_Ever_Hackuarium_Wiki_Sprint | 1er Hackuarium Wiki Sprint]] qui a eu lieu le 7 décembre 2014 à UniverCité.<br />
<br />
Le membre du [[Working Group | groupe de travail]] qui peut vous aider à commencer à contribuer en cas de besoin et la personne de contact du [[Board | comité]] pour nos outils en ligne est [[User:Sam | Sam]]. Tout le groupe de travail est joignable rapidement via [[Slack]] sur [#wg-doc].<br><br />
<br />
__TOC__<br />
<br />
== Qu'est que la biologie DIY? ==<br />
<br />
La biologie do-it-yourself (DIY) vise à démocratiser la recherche en biologie, et en particulier ses outils.<br />
<br />
La biologie DIY est parfois appelée "Biohacking" mais elle n'est en fait qu'une partie de ce mouvement qui applique les règle du hacking à la biotechnologie et la santé.<br />
<br />
Plus d'information sur [https://en.wikipedia.org/wiki/Do-it-yourself_biology Wikipedia] (en anglais).<br />
<br />
== L'Association Hackuarium ==<br />
Hackuarium est une communauté de bricoleurs passionnés constituée en association. L'assemblée constitutive a eu lieu le 13 août 2014.<br />
<br />
Nos membres pratiquent une science ouverte et participative, en dehors des institutions traditionnelles, dans le respect de la [http://diybio.org/codes/draft-diybio-code-of-ethics-from-european-congress/ charte éthique] du mouvement DIYbio EU. Nous favorisons par tous les moyens l'interdisciplinarité, et nos projets sont portés aussi bien par des scientifiques que par des citoyens architectes, designers, informaticiens, journalistes ou retraités.<br />
<br />
Nos projets préférés incluent la plupart du temps une approche à bas coût (low-cost) et la technologie la plus simple possible (low-tech). Nous nous inscrivons également dans une démarche d'upcycling de matériel mis au rebut par les laboratoires de la région.<br />
<br />
Notre laboratoire est ouvert à tous ceux qui partagent nos valeurs et se situe à Renens, au sein d'UniverCité, un lieu d'innovation inauguré le 26 mai 2014.<br><br />
<br />
== Qui sommes-nous? ==<br />
<br />
Notre communauté est le pilier de l'association Hackuarium. Nos membres, au passé varié et aux motivations multiples vivent à Lausanne et dans ses environs.<br><br />
<br />
=== Membres ===<br />
<br />
Nous encourageons les personnes intéressées à participer régulièrement aux activités de l'association à devenir membres.<br />
<br />
Etre membre permet d'avoir accès au laboratoire 24h/24, 7j/7, de bénéficier d'autres offres (rabais sur l'utilisation de l'atelier), de voter à l'assemblée générale et donc de participer activement à la vie de la communauté et aux prises de décisions.<br />
<br />
Etre membre de l'association Hackuarium implique payer une cotisation mensuelle de 20 francs suisses.<br><br />
<br />
=== Comité ===<br />
<br />
Le [[Board|comité de l'association]] Hackuarium est aujourd'hui composé de:<br><br />
* Président & Trésorier: [[User:luchenry | Luc Henry]]<br />
* Secrétaire: [[User:mmastern | Michal Masternak]]<br />
* Responsable laboratoire: [[User:hekkcess | Yann Pierson]]<br />
* Administrateur des outils web: [[User:Sam | Sam Sulaimanov]]<br />
* Art et Design: [[User:Vlorenzo | Vanessa Lorenzo]]<br />
* Talent scout and evangelist: [[User:Randogp | Gianpaolo Rando]]<br />
* Evènements: [[User:Alpittet | Anne-Laure Pittet]]<br />
* Membre: Ana Roldan<br />
<br />
L'agenda de la dernière assemblée générale est disponible [[20160120_General_Assembly | ici]] (20 janvier 2016).<br />
L'agenda de la dernière rencontre du comité est disponible [[20160329_Board_meeting | ici]] (29 mars 2016).<br />
<br />
=== Les amis d'Hackuarium ===<br />
<br />
::<li>[http://www.univercite.ch UniverCité]<br />
::<li>[[Exodes_Urbains | Exodes Urbains]]<br />
<br />
== Où travaillons-nous? ==<br />
Notre laboratoire communautaire se situe au Chemin du Closel 5 à Renens, en Suisse, dans une commune de la région lausannoise en plein développement.<br />
Hackuarium est situé dans le bâtiment IRL et fait partie d'[http://www.univercite.ch Univercité], un espace d'innovation abritant un espace de coworking, l'atelier [http://made.univercite.ch Made@UniverCité], plusieurs associations, des startups, etc.<br />
<br />
== Evénements ==<br />
<big>'''Evénements à venir'''</big><br />
<br><br />
::<li>'''Tous les mercredi, 19:00-23:00''' #OpenHackuarium: le laboratoire est ouvert au public.<br />
<br><br />
<br />
::<li>'''2016.06.14''' A vos agendas! Et venez participer à la [http://opendata.ch/2015/11/opendata-ch2016-am-14-juni-in-lausanne/ conference Opendata.ch/2016], Casino de Montbenon, Lausanne.<br />
::<li>'''2016.04.27''' Mercredi 19:30-21:00: [[Openhackuarium_vol._95 | Openhackuarium vol. 95]] Atelier impression T-shirt!<br />
::<li>'''2016.04.13''' Mercredi 19:30-21:00: [[Openhackuarium_vol._93 | Openhackuarium vol. 93]] 'Genomic integrity' and DIY 'comet assay' on cheek cells.<br />
<br />
Pour les evénements passés, cliquez [[past events]].<br><br><br />
<br />
== [[Projects | Projets]] ==<br />
Hackuarium est une communauté rassemblée autour de différents projets. Si vous voulez en savoir plus, visitez les pages ci-dessous<br />
<br />
=== Projets Actifs ===<br />
<br />
* [[Open-Food-DNA |Open Food DNA]]<br />
* [[BeerDeCoded]]<br />
* [[Living Instruments]]<br />
* [[Bience | Bience (Bière et Science!)]]<br />
* [[APPS]]<br />
* [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Micro to Macro Water Pollution]] -avec [http://www.hammerdirt.ch/ Hammerdirt] et [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Spectro-pointer]]<br />
* [[Darty_Monkeys]]<br />
* [http://octanis.org/ Octanis]<br />
* [[Edible wall]]<br />
* [[ZéBU CH]]<br />
* [[Grow%26Mix_Bioink]]<br />
* [[unmapping]]<br />
<br />
=== Projets Archivés ===<br />
<br />
* [[Mycelium Structures]]<br />
* [[Projet Sylvan|Konkret Bacterien]] <br />
* [[Live Type]]<br />
* [[Projects:LivingLab Design|LivingLab Design]]<br />
* [[Projects:bioluminescence|Bioluminescence]]<br />
* [[Projects:Quantitative Anthropology|Quantitative Anthropology]]<br />
* [[Projects:Impression 3D|Impression 3D]]<br />
* [[Projects:Dépollution des stands de tirs Suisses]]<br />
* [[Incubateur bon marché]]<br />
* [[Space Seed]]<br />
* [[Reception d'images satellites]]<br />
<br />
== En pratique ==<br />
<br />
Sur [[ Media:Univercite map2-01.png | ce lien]] vous trouverez la carte montrant la vue d'ensemble d'Univercité.<br><br />
Sur [[ Media:map1.png | ce lien]] la carte montrant la vue d'ensemble d'Hackuarium détaillant ou se trouve la majorité du matériel.<br />
<br />
=== [[I m new | Je suis nouveau, je fais quoi ?]] ===<br />
Tu viens d'arriver? tu cherches tes repères? Alors commence alors par lire [[I m new | cette page ]].<br />
<br />
=== [[Life_Main | Règles de vie à Hackuarium]] ===<br />
[[Life_Main | Cette page ]] recense les codes de bonne conduite à adopter à Hackuarium ainsi que les quelques règles s'appliquant dans certains cas spécifiques.<br />
<br />
=== [[Protocols | Protocoles]] ===<br />
Tous les protocoles liés à Hackuarium se trouvent [[ BioP_Main | ici ]] (page en Anglais)<br />
Ils sont structurés et expliqués de façon à être axés sur les procédé de manipulation. L'idée est de donner les informations cruciales de manière à appliquer les techniques les plus communes appartenant à la boite à outils du biologiste. Les documents sont structurés comme suit:<br />
::<li> Un schéma décrivant le procédé<br />
::<li> Une explication brève du procédé et son utilité<br />
::<li> Un protocole décrivant les différentes procédures pour appliquer le procédé. Idéalement il y aurait une description pour le faire avec un kit commercial et un moyen DIY.<br />
::<li> Une partie détaillant les précautions à prendre pour travailler en toute sécurité.<br />
::<li> Des informations spécifiques à Hackuarium décrivant ou se trouve les instruments et comment les utiliser.<br />
<br />
=== [[Instru_Main | Instruments et leurs utilisation]] ===<br />
[[Instru_Main | Cette page ]](Anglais) recense tous les instruments disponibles sur le lieu, leur position ainsi que la manière dont ils doivent être utilisés.<br />
<br />
=== [https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing Liste à jour de nos besoins en matériel] ===<br />
Ce document présente le matériel dont nous avons besoin. Si il vous arrivait d'avoir une des pièce que nous recherchons faites nous le savoir, nous comptons sur vous! :-)<br />
<br />
=== [[Where we shop | Où faisons-nous nos achats]] ===<br />
<br />
=== [[Editing the wiki | Comment créer une nouvelle page de projet sur notre wiki]] ===<br />
<br />
== Bibliothèque et liste de lecture ==<br />
<br />
Notre espace contient une bibliothèque d'ouvrages de référence:<br />
<br />
- DELFANTI Alessandro, "Biohackers, The Politics of Open Science", 2013, London, Pluto Press<br />
<br />
- LALLEMENT Michel, "L'âge du faire. Hacking, travail, anarchie", 2015, Paris, Seuil<br />
<br />
Les liens suivants peuvent aussi vous intéresser:<br />
<br />
== Media and Press | Presse et média ==<br />
<br />
Si vous voulez des informations au sujet d'Hackuarium, n'hésitez pas à envoyer un email à hello[at]hackuarium[dot]ch.<br />
<br />
Vous trouverez dans le [[Press_kit | Press Kit]] tous les détails concernant notre passé médiatique. <br />
<br />
<br />
[[Category:Work In Progress]]</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Hackuarium&diff=6828Hackuarium2016-04-19T08:36:28Z<p>Sachiko: /* Evénements */</p>
<hr />
<div>Bienvenue sur le '''wiki''' de l'association [http://www.hackuarium.ch/ Hackuarium]<br />
<br />
<div><br />
''[[Main_Page | Click here to view the english version of this wiki.]]'' <br />
</div><br />
<br />
Notre communauté regroupe les curieux et les bricoleurs de la région Lausannoise dans un laboratoire ouvert et citoyen situé avec d'autres activités au sein de [[UniverCité]], à Renens, une ville de Suisse Romande.<br />
<br />
La matière vivante est de plus en plus facilement cultivable, modulable, modifiable. Entre science et design, innovation et création artistique, Hackuarium est une rencontre entre citoyens de la région lausannoise qui veulent promouvoir ou pratiquer la biologie DIY. Le laboratoire communautaire d'Hackuarium offre à chacun la possibilité de découvrir, d’expérimenter et de contribuer ses compétences dans le cadre de projets.<br />
<br />
Comme vous pouvez le voir, cette page est en chantier et a été construite pendant le [[1st_Ever_Hackuarium_Wiki_Sprint | 1er Hackuarium Wiki Sprint]] qui a eu lieu le 7 décembre 2014 à UniverCité.<br />
<br />
Le membre du [[Working Group | groupe de travail]] qui peut vous aider à commencer à contribuer en cas de besoin et la personne de contact du [[Board | comité]] pour nos outils en ligne est [[User:Sam | Sam]]. Tout le groupe de travail est joignable rapidement via [[Slack]] sur [#wg-doc].<br><br />
<br />
__TOC__<br />
<br />
== Qu'est que la biologie DIY? ==<br />
<br />
La biologie do-it-yourself (DIY) vise à démocratiser la recherche en biologie, et en particulier ses outils.<br />
<br />
La biologie DIY est parfois appelée "Biohacking" mais elle n'est en fait qu'une partie de ce mouvement qui applique les règle du hacking à la biotechnologie et la santé.<br />
<br />
Plus d'information sur [https://en.wikipedia.org/wiki/Do-it-yourself_biology Wikipedia] (en anglais).<br />
<br />
== L'Association Hackuarium ==<br />
Hackuarium est une communauté de bricoleurs passionnés constituée en association. L'assemblée constitutive a eu lieu le 13 août 2014.<br />
<br />
Nos membres pratiquent une science ouverte et participative, en dehors des institutions traditionnelles, dans le respect de la [http://diybio.org/codes/draft-diybio-code-of-ethics-from-european-congress/ charte éthique] du mouvement DIYbio EU. Nous favorisons par tous les moyens l'interdisciplinarité, et nos projets sont portés aussi bien par des scientifiques que par des citoyens architectes, designers, informaticiens, journalistes ou retraités.<br />
<br />
Nos projets préférés incluent la plupart du temps une approche à bas coût (low-cost) et la technologie la plus simple possible (low-tech). Nous nous inscrivons également dans une démarche d'upcycling de matériel mis au rebut par les laboratoires de la région.<br />
<br />
Notre laboratoire est ouvert à tous ceux qui partagent nos valeurs et se situe à Renens, au sein d'UniverCité, un lieu d'innovation inauguré le 26 mai 2014.<br><br />
<br />
== Qui sommes-nous? ==<br />
<br />
Notre communauté est le pilier de l'association Hackuarium. Nos membres, au passé varié et aux motivations multiples vivent à Lausanne et dans ses environs.<br><br />
<br />
=== Membres ===<br />
<br />
Nous encourageons les personnes intéressées à participer régulièrement aux activités de l'association à devenir membres.<br />
<br />
Etre membre permet d'avoir accès au laboratoire 24h/24, 7j/7, de bénéficier d'autres offres (rabais sur l'utilisation de l'atelier), de voter à l'assemblée générale et donc de participer activement à la vie de la communauté et aux prises de décisions.<br />
<br />
Etre membre de l'association Hackuarium implique payer une cotisation mensuelle de 20 francs suisses.<br><br />
<br />
=== Comité ===<br />
<br />
Le [[Board|comité de l'association]] Hackuarium est aujourd'hui composé de:<br><br />
* Président & Trésorier: [[User:luchenry | Luc Henry]]<br />
* Secrétaire: [[User:mmastern | Michal Masternak]]<br />
* Responsable laboratoire: [[User:hekkcess | Yann Pierson]]<br />
* Administrateur des outils web: [[User:Sam | Sam Sulaimanov]]<br />
* Art et Design: [[User:Vlorenzo | Vanessa Lorenzo]]<br />
* Talent scout and evangelist: [[User:Randogp | Gianpaolo Rando]]<br />
* Evènements: [[User:Alpittet | Anne-Laure Pittet]]<br />
* Membre: Ana Roldan<br />
<br />
L'agenda de la dernière assemblée générale est disponible [[20160120_General_Assembly | ici]] (20 janvier 2016).<br />
L'agenda de la dernière rencontre du comité est disponible [[20160329_Board_meeting | ici]] (29 mars 2016).<br />
<br />
=== Les amis d'Hackuarium ===<br />
<br />
::<li>[http://www.univercite.ch UniverCité]<br />
::<li>[[Exodes_Urbains | Exodes Urbains]]<br />
<br />
== Où travaillons-nous? ==<br />
Notre laboratoire communautaire se situe au Chemin du Closel 5 à Renens, en Suisse, dans une commune de la région lausannoise en plein développement.<br />
Hackuarium est situé dans le bâtiment IRL et fait partie d'[http://www.univercite.ch Univercité], un espace d'innovation abritant un espace de coworking, l'atelier [http://made.univercite.ch Made@UniverCité], plusieurs associations, des startups, etc.<br />
<br />
== Evénements ==<br />
<big>'''Evénements à venir'''</big><br />
<br><br />
::<li>'''Tous les mercredi, 19:00-23:00''' #OpenHackuarium: le laboratoire est ouvert au public.<br />
<br><br />
<br />
::<li>'''2016.06.14''' A vos agendas! Et venez participer à la [http://opendata.ch/2015/11/opendata-ch2016-am-14-juni-in-lausanne/ conference Opendata.ch/2016], Casino de Montbenon, Lausanne.<br />
::<li>'''2016.04.27''' Mercredi 19:30-21:00: [[Openhackuarium_vol._95 | Openhackuarium vol. 95]] Atelier impression T-shirt!<br />
::<li>'''2016.04.13''' Mercredi 19:30-21:00: [[Openhackuarium_vol._93 | Openhackuarium vol. 93]] 'Genomic integrity' and DIY 'comet assay' on cheek cells.<br />
<br />
Pour les evénements passés, cliquez [[Past Events]].<br><br><br />
<br />
== [[Projects | Projets]] ==<br />
Hackuarium est une communauté rassemblée autour de différents projets. Si vous voulez en savoir plus, visitez les pages ci-dessous<br />
<br />
=== Projets Actifs ===<br />
<br />
* [[Open-Food-DNA |Open Food DNA]]<br />
* [[BeerDeCoded]]<br />
* [[Living Instruments]]<br />
* [[Bience | Bience (Bière et Science!)]]<br />
* [[APPS]]<br />
* [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Micro to Macro Water Pollution]] -avec [http://www.hammerdirt.ch/ Hammerdirt] et [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Spectro-pointer]]<br />
* [[Darty_Monkeys]]<br />
* [http://octanis.org/ Octanis]<br />
* [[Edible wall]]<br />
* [[ZéBU CH]]<br />
* [[Grow%26Mix_Bioink]]<br />
* [[unmapping]]<br />
<br />
=== Projets Archivés ===<br />
<br />
* [[Mycelium Structures]]<br />
* [[Projet Sylvan|Konkret Bacterien]] <br />
* [[Live Type]]<br />
* [[Projects:LivingLab Design|LivingLab Design]]<br />
* [[Projects:bioluminescence|Bioluminescence]]<br />
* [[Projects:Quantitative Anthropology|Quantitative Anthropology]]<br />
* [[Projects:Impression 3D|Impression 3D]]<br />
* [[Projects:Dépollution des stands de tirs Suisses]]<br />
* [[Incubateur bon marché]]<br />
* [[Space Seed]]<br />
* [[Reception d'images satellites]]<br />
<br />
== En pratique ==<br />
<br />
Sur [[ Media:Univercite map2-01.png | ce lien]] vous trouverez la carte montrant la vue d'ensemble d'Univercité.<br><br />
Sur [[ Media:map1.png | ce lien]] la carte montrant la vue d'ensemble d'Hackuarium détaillant ou se trouve la majorité du matériel.<br />
<br />
=== [[I m new | Je suis nouveau, je fais quoi ?]] ===<br />
Tu viens d'arriver? tu cherches tes repères? Alors commence alors par lire [[I m new | cette page ]].<br />
<br />
=== [[Life_Main | Règles de vie à Hackuarium]] ===<br />
[[Life_Main | Cette page ]] recense les codes de bonne conduite à adopter à Hackuarium ainsi que les quelques règles s'appliquant dans certains cas spécifiques.<br />
<br />
=== [[Protocols | Protocoles]] ===<br />
Tous les protocoles liés à Hackuarium se trouvent [[ BioP_Main | ici ]] (page en Anglais)<br />
Ils sont structurés et expliqués de façon à être axés sur les procédé de manipulation. L'idée est de donner les informations cruciales de manière à appliquer les techniques les plus communes appartenant à la boite à outils du biologiste. Les documents sont structurés comme suit:<br />
::<li> Un schéma décrivant le procédé<br />
::<li> Une explication brève du procédé et son utilité<br />
::<li> Un protocole décrivant les différentes procédures pour appliquer le procédé. Idéalement il y aurait une description pour le faire avec un kit commercial et un moyen DIY.<br />
::<li> Une partie détaillant les précautions à prendre pour travailler en toute sécurité.<br />
::<li> Des informations spécifiques à Hackuarium décrivant ou se trouve les instruments et comment les utiliser.<br />
<br />
=== [[Instru_Main | Instruments et leurs utilisation]] ===<br />
[[Instru_Main | Cette page ]](Anglais) recense tous les instruments disponibles sur le lieu, leur position ainsi que la manière dont ils doivent être utilisés.<br />
<br />
=== [https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing Liste à jour de nos besoins en matériel] ===<br />
Ce document présente le matériel dont nous avons besoin. Si il vous arrivait d'avoir une des pièce que nous recherchons faites nous le savoir, nous comptons sur vous! :-)<br />
<br />
=== [[Where we shop | Où faisons-nous nos achats]] ===<br />
<br />
=== [[Editing the wiki | Comment créer une nouvelle page de projet sur notre wiki]] ===<br />
<br />
== Bibliothèque et liste de lecture ==<br />
<br />
Notre espace contient une bibliothèque d'ouvrages de référence:<br />
<br />
- DELFANTI Alessandro, "Biohackers, The Politics of Open Science", 2013, London, Pluto Press<br />
<br />
- LALLEMENT Michel, "L'âge du faire. Hacking, travail, anarchie", 2015, Paris, Seuil<br />
<br />
Les liens suivants peuvent aussi vous intéresser:<br />
<br />
== Media and Press | Presse et média ==<br />
<br />
Si vous voulez des informations au sujet d'Hackuarium, n'hésitez pas à envoyer un email à hello[at]hackuarium[dot]ch.<br />
<br />
Vous trouverez dans le [[Press_kit | Press Kit]] tous les détails concernant notre passé médiatique. <br />
<br />
<br />
[[Category:Work In Progress]]</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Main_Page&diff=6827Main Page2016-04-19T08:33:31Z<p>Sachiko: /* Events */</p>
<hr />
<div>Welcome to the wiki of [http://www.hackuarium.ch/ Hackuarium] community.<br />
<br />
At Hackuarium, we want to bring biology (and biologists) to the world, and the real world back to biology. Our laboratory is an excuse to meet and discuss, build and develop ideas in a neutral, open, noncompetitive and not-for-profit environment.<br />
<br />
<div><br />
''[[Hackuarium | Cliquez ici pour accéder à la version française de ce wiki.]]'' <br />
</div><br />
<br />
This page was launched during our [[1st Ever Hackuarium Wiki Sprint]] that took place on 7 December 2014. As you might notice quickly, it is a work-in-progress.<br />
<br />
Scroll down and find out what this is all about!<br />
<br />
__TOC__<br />
<br />
=DIY Bio=<br />
<br />
==What is DIYbio?==<br />
<br />
DIYbio (Do-It-Yourself biology) is a movement that wants to free the practice of biological research and innovation from the institutional and industrial laboratories. Pursued both by amateurs and professional biologists, DIYbio is developing low-cost and low-tech solutions to problems identified by the community.<br />
<br />
The movement is characterised by an extremely diverse set of practices and participants. Some call themselves 'biohackers', in reference to the hacker culture.<br />
<br />
[http://DIYbio.org DIYbio.org] and [http://DIYbio.eu DIYbio.eu] are the portals of the international and european communities, respectively.<br />
<br />
For more information, visit the [http://www.wikipedia.org Wikipedia] page dedicated to [https://en.wikipedia.org/wiki/DIYbio DIYbio].<br />
<br><br />
<br />
=Hackuarium=<br />
<br />
Hackuarium is a not-for-profit association aiming at democratizing science through public engagement.<br />
<br><br />
<br />
Our laboratory in Renens (Switzerland) is open to anyone sharing the values of the association and who is dedicated to follow the [http://diybio.org/codes/draft-diybio-code-of-ethics-from-european-congress/ DIYbio Europe ethical guidelines].<br />
<br />
Our projects are initiated and carried out by scientists as well as non-scientists from a variety of background. They are passionate about tinkering with biology in particular, and technology in general. Some are engineers, architects, designers, IT and computer scientists or retired professionals, but others have no scientific education. They are mostly citizens interested in open and participatory research and innovation, outside the contrains of traditional institutions.<br />
<br />
Hackuarium members want to investigate new ways of carrying out interdisciplinary research and innovation, by making their results accessible (low-cost), simple and easily reproducible (low-tech) and by promoting an open source philosophy.<br />
<br />
Hackuarium is proudly using infrastructures provided by [http://www.univercite.ch UniverCité], an unconventional innovation hub opened in May 2014. Our equipment is mostly upcycled material from institutions and industries from western Switzerland.<br />
<br />
=Who we are=<br />
<br />
Renens is a hopping hub - and our members reflect the diversity that is in and around Lausanne/Renens.<br />
<br><br />
[[People | Check us out]], and find out what makes Hackuarium a good mix.<br />
<br><br />
<br />
==Committee==<br />
<br />
The current [[Board|committee]] is composed of the following people:<br />
<br />
* President & Treasurer: [[User:luchenry | Luc Henry]]<br />
* Secretary: [[User:mmastern | Michal Masternak]]<br />
* Lab Manager: [[User:hekkcess | Yann Pierson]]<br />
* Online tools administrator: [[User:Sam | Sam Sulaimanov]]<br />
* Art and Design coordinator: [[User:Vlorenzo | Vanessa Lorenzo]]<br />
* Talent scout and evangelist: [[User:Randogp | Gianpaolo Rando]]<br />
* Events and coordinator: [[User:Alpittet | Anne-Laure Pittet]]<br />
* Member: Ana Roldan<br />
<br />
The Agenda of the last board meeting can be found [[20151128_Board_Meeting | here]].<br />
<br />
==Members and Membership==<br />
<br />
Hackuarium operates on a membership basis at this current time.<br />
<br />
The monthly membership fee is 20 CHF. It gives 24/7 access to the lab.<br />
<br />
Please ask a member of the board if you want to join as a member.<br />
<br />
All events are open to anyone, including non-members.<br />
<br />
==Friends of Hackuarium==<br />
<br />
Spaces:<br />
::<li>[http://www.univercite.ch UniverCité]<br />
::<li>[http://lapaillasse.org La Paillasse, Paris]<br />
::<li>[https://lapaillassaone.wordpress.com Paillasse Saône, Lyon]<br />
<br><br />
<br />
Projects:<br />
::<li>[[Exodes_Urbains | Exodes Urbains]]<br />
::<li>[http://echopen.org/index.php?title=Main_Page EchOpen]<br />
<br><br />
<br />
==Where we are==<br />
Hackuarium is one of the association active at UniverCité, an innovation space under construction since May 2014 in the IRL building in Renens. We have documented our working environment as it has evolved.<br><br />
As of December 2015, UniverCité regroups a laboratory, a workshop and co-working space.<br><br />
<br><br />
<br />
=Events=<br />
<br />
<big>'''Upcoming Events'''</big><br />
<br><br />
'''Every Wednesday, 19:00-23:00''' #OpenHackuarium: our lab and space are open to the public. [mailto:hello@hackuarium.ch Get in touch!]<br />
<br><br />
:<li>'''2016.06.14''' Tuesday SAVE THE DATE [http://opendata.ch/2015/11/opendata-ch2016-am-14-juni-in-lausanne/ Opendata.ch/2016 Conference], Casino de Montbenon, Lausanne.<br />
:<li>'''2016.04.27''' Wednesday 19:30-21:00: [[Openhackuarium_vol._95 | Openhackuarium vol. 95]] T-shirt printing session!<br />
:<li>'''2016.04.13''' Wednesday 19:30-21:00: [[Openhackuarium_vol._93 | Openhackuarium vol. 93]] 'Genomic integrity' and DIY 'comet assay' on cheek cells.<br />
:<li>'''2016.04.06''' Wednesday 19:30-21:00: [http://wiki.hackuarium.ch/w/Openhackuarium_vol._92 Openhackuarium vol. 92] Darty Monkeys: 'Biofilia Night'.<br />
<br />
<br />
Please find the list of our [[past events]].<br><br><br />
<br />
=Projects=<br />
Here, you will find the projects going on in the Hackuarium.<br />
<br />
== Active Projects ==<br />
<br />
* [[Open-Food-DNA |Open-Food-DNA]]<br />
* [[BeerDeCoded]]<br />
* [[Living Instruments]]<br />
* [[Bience | Bience (Beer and Science!)]]<br />
* [[Protein purification systems]]<br />
* [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Micro to Macro Water Pollution]] - with [http://www.hammerdirt.ch/ Hammerdirt] and [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Spectro-pointer]]<br />
* [[Darty_Monkeys]]<br />
* [http://octanis.org/ Octanis]<br />
* [[Edible wall]]<br />
* [[ZéBU CH]]<br />
* [[Grow%26Mix_Bioink]]<br />
* [[unmapping]]<br />
* [[Compost Bacteria]]<br />
* [[AGiR! for genomic integrity]]<br />
<br />
== Archived Projects ==<br />
<br />
* [[Mycelium Structures]]<br />
* [[Live Type]]<br />
* [[Projects:LivingLab Design|LivingLab Design]]<br />
* [[Projects:bioluminescence|Bioluminescence]]<br />
* [[Projects:Quantitative Anthropology|Quantitative Anthropology]]<br />
* [[Projects:Impression 3D|Impression 3D]]<br />
* [[Projects:Dépollution des stands de tirs Suisses]]<br />
* [[Incubateur bon marché]]<br />
* [[Space Seed]]<br />
* [[Reception d'images satellites]]<br />
<br />
= Practical Informations =<br />
<br />
Following this [[ Media:Univercite map2-01.png | link]] you will find a general plan of Hackuarium.<br><br />
Following this [[ Media:map1.png | link]], you will find the plan of Hackuarium with the position of equipment.<br />
<br />
== [[Life_Main | Rules at Hackuarium]] ==<br />
[[Life_Main | This page ]] describe the code of conduct for Hackuarium members.<br />
<br />
== [[Protocols | Protocols]] ==<br />
All the protocols that we use at Hackuarium can be found [[ BioP_Main | here ]]<br />
They are detailed and structured so that the main focus is on applications. The idea is to give crucial information on how to apply the most common techniques of the Biology toolbox. The protocols are structured as follow:<br />
::<li> A scheme describing each <br />
::<li> A brief description of the protocol and its use<br />
::<li> A description of the different ways of carrying out the protocol. Ideally there should be a description of a commercial kit and a DIY kit.<br />
::<li> A description of the safety issues and best practice<br />
::<li> Information specific to Hackuarium and where to find the components, tools and reagents.<br />
<br />
== [[Instru_Main | Instruments available]] ==<br />
[[Instru_Main | This page ]] describes all the instruments available at Hackuarium (work in progress..), their location and how to use them.<br />
<br />
== [https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing Liste à jour de nos besoins en matériel] ==<br />
This document contains all the instruments and tools we need. If you happen to have a piece of equipment we are (or may be) looking for, [mailto:hello@hackuarium.ch contact us]!<br />
<br />
== [[Where we shop | Where we shop]] ==<br />
===Wetware===<br />
Consumables can be purchased from [http://www.huberlab.ch Huber Lab].<br />
<br />
Swiss-based [http://www.smiples.ch Smiples] has a very extensive listing of second hand laboratory and technical items. These can be bought from their online shop or from [https://www.ricardo.ch/online-shop/smiples/?SellerNickName=Smiples Ricardo].<br />
<br />
===Hardware===<br />
Options for electronic parts<br />
* [http://www.ebay.com Ebay] (international)<br />
* [http://www.aliexpress.com AliExpress] (China)<br />
* [https://www.adafruit.com Adafruit] (UK)<br />
<br><br />
* [http://www.seeedstudio.com/depot/ seeedstudio] (China)<br />
* [http://www.tmart.com/ Tmart] (Hong Kong)<br />
* [https://www.pi-shop.ch/ Rasberry pi shop] (Switzerland)<br />
* [http://www.distrelec.ch/ distrilec] (Switzerland)<br />
<br />
== Tools and Equipment found at Hackuarium ==<br />
<br />
::<li>[[Tools#Working_Equipment Working Equipment|Working Equipment]]<br />
::<li>[[Tools#Equipment_that_need_a_bit_of_fixing Needs Help|Equipment needing fixing]]<br />
::<li>[[Where we shop]]<br />
<br><br />
<br />
== [[Editing the wiki | How to built a new project page on our Wiki]] ==<br />
<br />
== Library and Reading List ==<br />
<br />
== Media and Press ==<br />
<br />
* Newsletter<br />
<br />
== Wanted ==<br />
Do you want to contribute to making Hackuarium a diverse and lively community? Check out our wanted lists:<br />
::<li>Skills<br />
::<li>Ideas<br />
::<li>[https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing Equipment]<br />
::<li>Materials<br />
<br><br></div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Main_Page&diff=6826Main Page2016-04-19T08:33:05Z<p>Sachiko: /* Events */</p>
<hr />
<div>Welcome to the wiki of [http://www.hackuarium.ch/ Hackuarium] community.<br />
<br />
At Hackuarium, we want to bring biology (and biologists) to the world, and the real world back to biology. Our laboratory is an excuse to meet and discuss, build and develop ideas in a neutral, open, noncompetitive and not-for-profit environment.<br />
<br />
<div><br />
''[[Hackuarium | Cliquez ici pour accéder à la version française de ce wiki.]]'' <br />
</div><br />
<br />
This page was launched during our [[1st Ever Hackuarium Wiki Sprint]] that took place on 7 December 2014. As you might notice quickly, it is a work-in-progress.<br />
<br />
Scroll down and find out what this is all about!<br />
<br />
__TOC__<br />
<br />
=DIY Bio=<br />
<br />
==What is DIYbio?==<br />
<br />
DIYbio (Do-It-Yourself biology) is a movement that wants to free the practice of biological research and innovation from the institutional and industrial laboratories. Pursued both by amateurs and professional biologists, DIYbio is developing low-cost and low-tech solutions to problems identified by the community.<br />
<br />
The movement is characterised by an extremely diverse set of practices and participants. Some call themselves 'biohackers', in reference to the hacker culture.<br />
<br />
[http://DIYbio.org DIYbio.org] and [http://DIYbio.eu DIYbio.eu] are the portals of the international and european communities, respectively.<br />
<br />
For more information, visit the [http://www.wikipedia.org Wikipedia] page dedicated to [https://en.wikipedia.org/wiki/DIYbio DIYbio].<br />
<br><br />
<br />
=Hackuarium=<br />
<br />
Hackuarium is a not-for-profit association aiming at democratizing science through public engagement.<br />
<br><br />
<br />
Our laboratory in Renens (Switzerland) is open to anyone sharing the values of the association and who is dedicated to follow the [http://diybio.org/codes/draft-diybio-code-of-ethics-from-european-congress/ DIYbio Europe ethical guidelines].<br />
<br />
Our projects are initiated and carried out by scientists as well as non-scientists from a variety of background. They are passionate about tinkering with biology in particular, and technology in general. Some are engineers, architects, designers, IT and computer scientists or retired professionals, but others have no scientific education. They are mostly citizens interested in open and participatory research and innovation, outside the contrains of traditional institutions.<br />
<br />
Hackuarium members want to investigate new ways of carrying out interdisciplinary research and innovation, by making their results accessible (low-cost), simple and easily reproducible (low-tech) and by promoting an open source philosophy.<br />
<br />
Hackuarium is proudly using infrastructures provided by [http://www.univercite.ch UniverCité], an unconventional innovation hub opened in May 2014. Our equipment is mostly upcycled material from institutions and industries from western Switzerland.<br />
<br />
=Who we are=<br />
<br />
Renens is a hopping hub - and our members reflect the diversity that is in and around Lausanne/Renens.<br />
<br><br />
[[People | Check us out]], and find out what makes Hackuarium a good mix.<br />
<br><br />
<br />
==Committee==<br />
<br />
The current [[Board|committee]] is composed of the following people:<br />
<br />
* President & Treasurer: [[User:luchenry | Luc Henry]]<br />
* Secretary: [[User:mmastern | Michal Masternak]]<br />
* Lab Manager: [[User:hekkcess | Yann Pierson]]<br />
* Online tools administrator: [[User:Sam | Sam Sulaimanov]]<br />
* Art and Design coordinator: [[User:Vlorenzo | Vanessa Lorenzo]]<br />
* Talent scout and evangelist: [[User:Randogp | Gianpaolo Rando]]<br />
* Events and coordinator: [[User:Alpittet | Anne-Laure Pittet]]<br />
* Member: Ana Roldan<br />
<br />
The Agenda of the last board meeting can be found [[20151128_Board_Meeting | here]].<br />
<br />
==Members and Membership==<br />
<br />
Hackuarium operates on a membership basis at this current time.<br />
<br />
The monthly membership fee is 20 CHF. It gives 24/7 access to the lab.<br />
<br />
Please ask a member of the board if you want to join as a member.<br />
<br />
All events are open to anyone, including non-members.<br />
<br />
==Friends of Hackuarium==<br />
<br />
Spaces:<br />
::<li>[http://www.univercite.ch UniverCité]<br />
::<li>[http://lapaillasse.org La Paillasse, Paris]<br />
::<li>[https://lapaillassaone.wordpress.com Paillasse Saône, Lyon]<br />
<br><br />
<br />
Projects:<br />
::<li>[[Exodes_Urbains | Exodes Urbains]]<br />
::<li>[http://echopen.org/index.php?title=Main_Page EchOpen]<br />
<br><br />
<br />
==Where we are==<br />
Hackuarium is one of the association active at UniverCité, an innovation space under construction since May 2014 in the IRL building in Renens. We have documented our working environment as it has evolved.<br><br />
As of December 2015, UniverCité regroups a laboratory, a workshop and co-working space.<br><br />
<br><br />
<br />
=Events=<br />
<br />
<big>Upcoming Events</big><br />
<br><br />
'''Every Wednesday, 19:00-23:00''' #OpenHackuarium: our lab and space are open to the public. [mailto:hello@hackuarium.ch Get in touch!]<br />
<br><br />
:<li>'''2016.06.14''' Tuesday SAVE THE DATE [http://opendata.ch/2015/11/opendata-ch2016-am-14-juni-in-lausanne/ Opendata.ch/2016 Conference], Casino de Montbenon, Lausanne.<br />
:<li>'''2016.04.27''' Wednesday 19:30-21:00: [[Openhackuarium_vol._95 | Openhackuarium vol. 95]] T-shirt printing session!<br />
:<li>'''2016.04.13''' Wednesday 19:30-21:00: [[Openhackuarium_vol._93 | Openhackuarium vol. 93]] 'Genomic integrity' and DIY 'comet assay' on cheek cells.<br />
:<li>'''2016.04.06''' Wednesday 19:30-21:00: [http://wiki.hackuarium.ch/w/Openhackuarium_vol._92 Openhackuarium vol. 92] Darty Monkeys: 'Biofilia Night'.<br />
<br />
<br />
Please find the list of our [[past events]].<br><br><br />
<br />
=Projects=<br />
Here, you will find the projects going on in the Hackuarium.<br />
<br />
== Active Projects ==<br />
<br />
* [[Open-Food-DNA |Open-Food-DNA]]<br />
* [[BeerDeCoded]]<br />
* [[Living Instruments]]<br />
* [[Bience | Bience (Beer and Science!)]]<br />
* [[Protein purification systems]]<br />
* [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Micro to Macro Water Pollution]] - with [http://www.hammerdirt.ch/ Hammerdirt] and [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Spectro-pointer]]<br />
* [[Darty_Monkeys]]<br />
* [http://octanis.org/ Octanis]<br />
* [[Edible wall]]<br />
* [[ZéBU CH]]<br />
* [[Grow%26Mix_Bioink]]<br />
* [[unmapping]]<br />
* [[Compost Bacteria]]<br />
* [[AGiR! for genomic integrity]]<br />
<br />
== Archived Projects ==<br />
<br />
* [[Mycelium Structures]]<br />
* [[Live Type]]<br />
* [[Projects:LivingLab Design|LivingLab Design]]<br />
* [[Projects:bioluminescence|Bioluminescence]]<br />
* [[Projects:Quantitative Anthropology|Quantitative Anthropology]]<br />
* [[Projects:Impression 3D|Impression 3D]]<br />
* [[Projects:Dépollution des stands de tirs Suisses]]<br />
* [[Incubateur bon marché]]<br />
* [[Space Seed]]<br />
* [[Reception d'images satellites]]<br />
<br />
= Practical Informations =<br />
<br />
Following this [[ Media:Univercite map2-01.png | link]] you will find a general plan of Hackuarium.<br><br />
Following this [[ Media:map1.png | link]], you will find the plan of Hackuarium with the position of equipment.<br />
<br />
== [[Life_Main | Rules at Hackuarium]] ==<br />
[[Life_Main | This page ]] describe the code of conduct for Hackuarium members.<br />
<br />
== [[Protocols | Protocols]] ==<br />
All the protocols that we use at Hackuarium can be found [[ BioP_Main | here ]]<br />
They are detailed and structured so that the main focus is on applications. The idea is to give crucial information on how to apply the most common techniques of the Biology toolbox. The protocols are structured as follow:<br />
::<li> A scheme describing each <br />
::<li> A brief description of the protocol and its use<br />
::<li> A description of the different ways of carrying out the protocol. Ideally there should be a description of a commercial kit and a DIY kit.<br />
::<li> A description of the safety issues and best practice<br />
::<li> Information specific to Hackuarium and where to find the components, tools and reagents.<br />
<br />
== [[Instru_Main | Instruments available]] ==<br />
[[Instru_Main | This page ]] describes all the instruments available at Hackuarium (work in progress..), their location and how to use them.<br />
<br />
== [https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing Liste à jour de nos besoins en matériel] ==<br />
This document contains all the instruments and tools we need. If you happen to have a piece of equipment we are (or may be) looking for, [mailto:hello@hackuarium.ch contact us]!<br />
<br />
== [[Where we shop | Where we shop]] ==<br />
===Wetware===<br />
Consumables can be purchased from [http://www.huberlab.ch Huber Lab].<br />
<br />
Swiss-based [http://www.smiples.ch Smiples] has a very extensive listing of second hand laboratory and technical items. These can be bought from their online shop or from [https://www.ricardo.ch/online-shop/smiples/?SellerNickName=Smiples Ricardo].<br />
<br />
===Hardware===<br />
Options for electronic parts<br />
* [http://www.ebay.com Ebay] (international)<br />
* [http://www.aliexpress.com AliExpress] (China)<br />
* [https://www.adafruit.com Adafruit] (UK)<br />
<br><br />
* [http://www.seeedstudio.com/depot/ seeedstudio] (China)<br />
* [http://www.tmart.com/ Tmart] (Hong Kong)<br />
* [https://www.pi-shop.ch/ Rasberry pi shop] (Switzerland)<br />
* [http://www.distrelec.ch/ distrilec] (Switzerland)<br />
<br />
== Tools and Equipment found at Hackuarium ==<br />
<br />
::<li>[[Tools#Working_Equipment Working Equipment|Working Equipment]]<br />
::<li>[[Tools#Equipment_that_need_a_bit_of_fixing Needs Help|Equipment needing fixing]]<br />
::<li>[[Where we shop]]<br />
<br><br />
<br />
== [[Editing the wiki | How to built a new project page on our Wiki]] ==<br />
<br />
== Library and Reading List ==<br />
<br />
== Media and Press ==<br />
<br />
* Newsletter<br />
<br />
== Wanted ==<br />
Do you want to contribute to making Hackuarium a diverse and lively community? Check out our wanted lists:<br />
::<li>Skills<br />
::<li>Ideas<br />
::<li>[https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing Equipment]<br />
::<li>Materials<br />
<br><br></div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Main_Page&diff=6825Main Page2016-04-19T08:32:27Z<p>Sachiko: /* Events */</p>
<hr />
<div>Welcome to the wiki of [http://www.hackuarium.ch/ Hackuarium] community.<br />
<br />
At Hackuarium, we want to bring biology (and biologists) to the world, and the real world back to biology. Our laboratory is an excuse to meet and discuss, build and develop ideas in a neutral, open, noncompetitive and not-for-profit environment.<br />
<br />
<div><br />
''[[Hackuarium | Cliquez ici pour accéder à la version française de ce wiki.]]'' <br />
</div><br />
<br />
This page was launched during our [[1st Ever Hackuarium Wiki Sprint]] that took place on 7 December 2014. As you might notice quickly, it is a work-in-progress.<br />
<br />
Scroll down and find out what this is all about!<br />
<br />
__TOC__<br />
<br />
=DIY Bio=<br />
<br />
==What is DIYbio?==<br />
<br />
DIYbio (Do-It-Yourself biology) is a movement that wants to free the practice of biological research and innovation from the institutional and industrial laboratories. Pursued both by amateurs and professional biologists, DIYbio is developing low-cost and low-tech solutions to problems identified by the community.<br />
<br />
The movement is characterised by an extremely diverse set of practices and participants. Some call themselves 'biohackers', in reference to the hacker culture.<br />
<br />
[http://DIYbio.org DIYbio.org] and [http://DIYbio.eu DIYbio.eu] are the portals of the international and european communities, respectively.<br />
<br />
For more information, visit the [http://www.wikipedia.org Wikipedia] page dedicated to [https://en.wikipedia.org/wiki/DIYbio DIYbio].<br />
<br><br />
<br />
=Hackuarium=<br />
<br />
Hackuarium is a not-for-profit association aiming at democratizing science through public engagement.<br />
<br><br />
<br />
Our laboratory in Renens (Switzerland) is open to anyone sharing the values of the association and who is dedicated to follow the [http://diybio.org/codes/draft-diybio-code-of-ethics-from-european-congress/ DIYbio Europe ethical guidelines].<br />
<br />
Our projects are initiated and carried out by scientists as well as non-scientists from a variety of background. They are passionate about tinkering with biology in particular, and technology in general. Some are engineers, architects, designers, IT and computer scientists or retired professionals, but others have no scientific education. They are mostly citizens interested in open and participatory research and innovation, outside the contrains of traditional institutions.<br />
<br />
Hackuarium members want to investigate new ways of carrying out interdisciplinary research and innovation, by making their results accessible (low-cost), simple and easily reproducible (low-tech) and by promoting an open source philosophy.<br />
<br />
Hackuarium is proudly using infrastructures provided by [http://www.univercite.ch UniverCité], an unconventional innovation hub opened in May 2014. Our equipment is mostly upcycled material from institutions and industries from western Switzerland.<br />
<br />
=Who we are=<br />
<br />
Renens is a hopping hub - and our members reflect the diversity that is in and around Lausanne/Renens.<br />
<br><br />
[[People | Check us out]], and find out what makes Hackuarium a good mix.<br />
<br><br />
<br />
==Committee==<br />
<br />
The current [[Board|committee]] is composed of the following people:<br />
<br />
* President & Treasurer: [[User:luchenry | Luc Henry]]<br />
* Secretary: [[User:mmastern | Michal Masternak]]<br />
* Lab Manager: [[User:hekkcess | Yann Pierson]]<br />
* Online tools administrator: [[User:Sam | Sam Sulaimanov]]<br />
* Art and Design coordinator: [[User:Vlorenzo | Vanessa Lorenzo]]<br />
* Talent scout and evangelist: [[User:Randogp | Gianpaolo Rando]]<br />
* Events and coordinator: [[User:Alpittet | Anne-Laure Pittet]]<br />
* Member: Ana Roldan<br />
<br />
The Agenda of the last board meeting can be found [[20151128_Board_Meeting | here]].<br />
<br />
==Members and Membership==<br />
<br />
Hackuarium operates on a membership basis at this current time.<br />
<br />
The monthly membership fee is 20 CHF. It gives 24/7 access to the lab.<br />
<br />
Please ask a member of the board if you want to join as a member.<br />
<br />
All events are open to anyone, including non-members.<br />
<br />
==Friends of Hackuarium==<br />
<br />
Spaces:<br />
::<li>[http://www.univercite.ch UniverCité]<br />
::<li>[http://lapaillasse.org La Paillasse, Paris]<br />
::<li>[https://lapaillassaone.wordpress.com Paillasse Saône, Lyon]<br />
<br><br />
<br />
Projects:<br />
::<li>[[Exodes_Urbains | Exodes Urbains]]<br />
::<li>[http://echopen.org/index.php?title=Main_Page EchOpen]<br />
<br><br />
<br />
==Where we are==<br />
Hackuarium is one of the association active at UniverCité, an innovation space under construction since May 2014 in the IRL building in Renens. We have documented our working environment as it has evolved.<br><br />
As of December 2015, UniverCité regroups a laboratory, a workshop and co-working space.<br><br />
<br><br />
<br />
=Events=<br />
<br />
Upcoming Events<br />
<br><br />
'''Every Wednesday, 19:00-23:00''' #OpenHackuarium: our lab and space are open to the public. [mailto:hello@hackuarium.ch Get in touch!]<br />
<br><br />
:<li>'''2016.06.14''' Tuesday SAVE THE DATE [http://opendata.ch/2015/11/opendata-ch2016-am-14-juni-in-lausanne/ Opendata.ch/2016 Conference], Casino de Montbenon, Lausanne.<br />
:<li>'''2016.04.27''' Wednesday 19:30-21:00: [[Openhackuarium_vol._95 | Openhackuarium vol. 95]] T-shirt printing session!<br />
:<li>'''2016.04.13''' Wednesday 19:30-21:00: [[Openhackuarium_vol._93 | Openhackuarium vol. 93]] 'Genomic integrity' and DIY 'comet assay' on cheek cells.<br />
:<li>'''2016.04.06''' Wednesday 19:30-21:00: [http://wiki.hackuarium.ch/w/Openhackuarium_vol._92 Openhackuarium vol. 92] Darty Monkeys: 'Biofilia Night'.<br />
<br />
<br />
Please find the list of our [[past events]].<br><br><br />
<br />
=Projects=<br />
Here, you will find the projects going on in the Hackuarium.<br />
<br />
== Active Projects ==<br />
<br />
* [[Open-Food-DNA |Open-Food-DNA]]<br />
* [[BeerDeCoded]]<br />
* [[Living Instruments]]<br />
* [[Bience | Bience (Beer and Science!)]]<br />
* [[Protein purification systems]]<br />
* [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Micro to Macro Water Pollution]] - with [http://www.hammerdirt.ch/ Hammerdirt] and [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Spectro-pointer]]<br />
* [[Darty_Monkeys]]<br />
* [http://octanis.org/ Octanis]<br />
* [[Edible wall]]<br />
* [[ZéBU CH]]<br />
* [[Grow%26Mix_Bioink]]<br />
* [[unmapping]]<br />
* [[Compost Bacteria]]<br />
* [[AGiR! for genomic integrity]]<br />
<br />
== Archived Projects ==<br />
<br />
* [[Mycelium Structures]]<br />
* [[Live Type]]<br />
* [[Projects:LivingLab Design|LivingLab Design]]<br />
* [[Projects:bioluminescence|Bioluminescence]]<br />
* [[Projects:Quantitative Anthropology|Quantitative Anthropology]]<br />
* [[Projects:Impression 3D|Impression 3D]]<br />
* [[Projects:Dépollution des stands de tirs Suisses]]<br />
* [[Incubateur bon marché]]<br />
* [[Space Seed]]<br />
* [[Reception d'images satellites]]<br />
<br />
= Practical Informations =<br />
<br />
Following this [[ Media:Univercite map2-01.png | link]] you will find a general plan of Hackuarium.<br><br />
Following this [[ Media:map1.png | link]], you will find the plan of Hackuarium with the position of equipment.<br />
<br />
== [[Life_Main | Rules at Hackuarium]] ==<br />
[[Life_Main | This page ]] describe the code of conduct for Hackuarium members.<br />
<br />
== [[Protocols | Protocols]] ==<br />
All the protocols that we use at Hackuarium can be found [[ BioP_Main | here ]]<br />
They are detailed and structured so that the main focus is on applications. The idea is to give crucial information on how to apply the most common techniques of the Biology toolbox. The protocols are structured as follow:<br />
::<li> A scheme describing each <br />
::<li> A brief description of the protocol and its use<br />
::<li> A description of the different ways of carrying out the protocol. Ideally there should be a description of a commercial kit and a DIY kit.<br />
::<li> A description of the safety issues and best practice<br />
::<li> Information specific to Hackuarium and where to find the components, tools and reagents.<br />
<br />
== [[Instru_Main | Instruments available]] ==<br />
[[Instru_Main | This page ]] describes all the instruments available at Hackuarium (work in progress..), their location and how to use them.<br />
<br />
== [https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing Liste à jour de nos besoins en matériel] ==<br />
This document contains all the instruments and tools we need. If you happen to have a piece of equipment we are (or may be) looking for, [mailto:hello@hackuarium.ch contact us]!<br />
<br />
== [[Where we shop | Where we shop]] ==<br />
===Wetware===<br />
Consumables can be purchased from [http://www.huberlab.ch Huber Lab].<br />
<br />
Swiss-based [http://www.smiples.ch Smiples] has a very extensive listing of second hand laboratory and technical items. These can be bought from their online shop or from [https://www.ricardo.ch/online-shop/smiples/?SellerNickName=Smiples Ricardo].<br />
<br />
===Hardware===<br />
Options for electronic parts<br />
* [http://www.ebay.com Ebay] (international)<br />
* [http://www.aliexpress.com AliExpress] (China)<br />
* [https://www.adafruit.com Adafruit] (UK)<br />
<br><br />
* [http://www.seeedstudio.com/depot/ seeedstudio] (China)<br />
* [http://www.tmart.com/ Tmart] (Hong Kong)<br />
* [https://www.pi-shop.ch/ Rasberry pi shop] (Switzerland)<br />
* [http://www.distrelec.ch/ distrilec] (Switzerland)<br />
<br />
== Tools and Equipment found at Hackuarium ==<br />
<br />
::<li>[[Tools#Working_Equipment Working Equipment|Working Equipment]]<br />
::<li>[[Tools#Equipment_that_need_a_bit_of_fixing Needs Help|Equipment needing fixing]]<br />
::<li>[[Where we shop]]<br />
<br><br />
<br />
== [[Editing the wiki | How to built a new project page on our Wiki]] ==<br />
<br />
== Library and Reading List ==<br />
<br />
== Media and Press ==<br />
<br />
* Newsletter<br />
<br />
== Wanted ==<br />
Do you want to contribute to making Hackuarium a diverse and lively community? Check out our wanted lists:<br />
::<li>Skills<br />
::<li>Ideas<br />
::<li>[https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing Equipment]<br />
::<li>Materials<br />
<br><br></div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Main_Page&diff=6824Main Page2016-04-19T08:31:30Z<p>Sachiko: /* Where we are */</p>
<hr />
<div>Welcome to the wiki of [http://www.hackuarium.ch/ Hackuarium] community.<br />
<br />
At Hackuarium, we want to bring biology (and biologists) to the world, and the real world back to biology. Our laboratory is an excuse to meet and discuss, build and develop ideas in a neutral, open, noncompetitive and not-for-profit environment.<br />
<br />
<div><br />
''[[Hackuarium | Cliquez ici pour accéder à la version française de ce wiki.]]'' <br />
</div><br />
<br />
This page was launched during our [[1st Ever Hackuarium Wiki Sprint]] that took place on 7 December 2014. As you might notice quickly, it is a work-in-progress.<br />
<br />
Scroll down and find out what this is all about!<br />
<br />
__TOC__<br />
<br />
=DIY Bio=<br />
<br />
==What is DIYbio?==<br />
<br />
DIYbio (Do-It-Yourself biology) is a movement that wants to free the practice of biological research and innovation from the institutional and industrial laboratories. Pursued both by amateurs and professional biologists, DIYbio is developing low-cost and low-tech solutions to problems identified by the community.<br />
<br />
The movement is characterised by an extremely diverse set of practices and participants. Some call themselves 'biohackers', in reference to the hacker culture.<br />
<br />
[http://DIYbio.org DIYbio.org] and [http://DIYbio.eu DIYbio.eu] are the portals of the international and european communities, respectively.<br />
<br />
For more information, visit the [http://www.wikipedia.org Wikipedia] page dedicated to [https://en.wikipedia.org/wiki/DIYbio DIYbio].<br />
<br><br />
<br />
=Hackuarium=<br />
<br />
Hackuarium is a not-for-profit association aiming at democratizing science through public engagement.<br />
<br><br />
<br />
Our laboratory in Renens (Switzerland) is open to anyone sharing the values of the association and who is dedicated to follow the [http://diybio.org/codes/draft-diybio-code-of-ethics-from-european-congress/ DIYbio Europe ethical guidelines].<br />
<br />
Our projects are initiated and carried out by scientists as well as non-scientists from a variety of background. They are passionate about tinkering with biology in particular, and technology in general. Some are engineers, architects, designers, IT and computer scientists or retired professionals, but others have no scientific education. They are mostly citizens interested in open and participatory research and innovation, outside the contrains of traditional institutions.<br />
<br />
Hackuarium members want to investigate new ways of carrying out interdisciplinary research and innovation, by making their results accessible (low-cost), simple and easily reproducible (low-tech) and by promoting an open source philosophy.<br />
<br />
Hackuarium is proudly using infrastructures provided by [http://www.univercite.ch UniverCité], an unconventional innovation hub opened in May 2014. Our equipment is mostly upcycled material from institutions and industries from western Switzerland.<br />
<br />
=Who we are=<br />
<br />
Renens is a hopping hub - and our members reflect the diversity that is in and around Lausanne/Renens.<br />
<br><br />
[[People | Check us out]], and find out what makes Hackuarium a good mix.<br />
<br><br />
<br />
==Committee==<br />
<br />
The current [[Board|committee]] is composed of the following people:<br />
<br />
* President & Treasurer: [[User:luchenry | Luc Henry]]<br />
* Secretary: [[User:mmastern | Michal Masternak]]<br />
* Lab Manager: [[User:hekkcess | Yann Pierson]]<br />
* Online tools administrator: [[User:Sam | Sam Sulaimanov]]<br />
* Art and Design coordinator: [[User:Vlorenzo | Vanessa Lorenzo]]<br />
* Talent scout and evangelist: [[User:Randogp | Gianpaolo Rando]]<br />
* Events and coordinator: [[User:Alpittet | Anne-Laure Pittet]]<br />
* Member: Ana Roldan<br />
<br />
The Agenda of the last board meeting can be found [[20151128_Board_Meeting | here]].<br />
<br />
==Members and Membership==<br />
<br />
Hackuarium operates on a membership basis at this current time.<br />
<br />
The monthly membership fee is 20 CHF. It gives 24/7 access to the lab.<br />
<br />
Please ask a member of the board if you want to join as a member.<br />
<br />
All events are open to anyone, including non-members.<br />
<br />
==Friends of Hackuarium==<br />
<br />
Spaces:<br />
::<li>[http://www.univercite.ch UniverCité]<br />
::<li>[http://lapaillasse.org La Paillasse, Paris]<br />
::<li>[https://lapaillassaone.wordpress.com Paillasse Saône, Lyon]<br />
<br><br />
<br />
Projects:<br />
::<li>[[Exodes_Urbains | Exodes Urbains]]<br />
::<li>[http://echopen.org/index.php?title=Main_Page EchOpen]<br />
<br><br />
<br />
==Where we are==<br />
Hackuarium is one of the association active at UniverCité, an innovation space under construction since May 2014 in the IRL building in Renens. We have documented our working environment as it has evolved.<br><br />
As of December 2015, UniverCité regroups a laboratory, a workshop and co-working space.<br><br />
<br><br />
<br />
=Events=<br />
<br />
== Upcoming Events ==<br />
<br><br />
'''Every Wednesday, 19:00-23:00''' #OpenHackuarium: our lab and space are open to the public. [mailto:hello@hackuarium.ch Get in touch!]<br />
<br><br />
:<li>'''2016.06.14''' Tuesday SAVE THE DATE [http://opendata.ch/2015/11/opendata-ch2016-am-14-juni-in-lausanne/ Opendata.ch/2016 Conference], Casino de Montbenon, Lausanne.<br />
:<li>'''2016.04.27''' Wednesday 19:30-21:00: [[Openhackuarium_vol._95 | Openhackuarium vol. 95]] T-shirt printing session!<br />
:<li>'''2016.04.13''' Wednesday 19:30-21:00: [[Openhackuarium_vol._93 | Openhackuarium vol. 93]] 'Genomic integrity' and DIY 'comet assay' on cheek cells.<br />
:<li>'''2016.04.06''' Wednesday 19:30-21:00: [http://wiki.hackuarium.ch/w/Openhackuarium_vol._92 Openhackuarium vol. 92] Darty Monkeys: 'Biofilia Night'.<br />
<br />
<br />
== Past Events ==<br />
<br><br />
Please find the list of our [[past events]].<br><br />
<br />
=Projects=<br />
Here, you will find the projects going on in the Hackuarium.<br />
<br />
== Active Projects ==<br />
<br />
* [[Open-Food-DNA |Open-Food-DNA]]<br />
* [[BeerDeCoded]]<br />
* [[Living Instruments]]<br />
* [[Bience | Bience (Beer and Science!)]]<br />
* [[Protein purification systems]]<br />
* [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Micro to Macro Water Pollution]] - with [http://www.hammerdirt.ch/ Hammerdirt] and [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Spectro-pointer]]<br />
* [[Darty_Monkeys]]<br />
* [http://octanis.org/ Octanis]<br />
* [[Edible wall]]<br />
* [[ZéBU CH]]<br />
* [[Grow%26Mix_Bioink]]<br />
* [[unmapping]]<br />
* [[Compost Bacteria]]<br />
* [[AGiR! for genomic integrity]]<br />
<br />
== Archived Projects ==<br />
<br />
* [[Mycelium Structures]]<br />
* [[Live Type]]<br />
* [[Projects:LivingLab Design|LivingLab Design]]<br />
* [[Projects:bioluminescence|Bioluminescence]]<br />
* [[Projects:Quantitative Anthropology|Quantitative Anthropology]]<br />
* [[Projects:Impression 3D|Impression 3D]]<br />
* [[Projects:Dépollution des stands de tirs Suisses]]<br />
* [[Incubateur bon marché]]<br />
* [[Space Seed]]<br />
* [[Reception d'images satellites]]<br />
<br />
= Practical Informations =<br />
<br />
Following this [[ Media:Univercite map2-01.png | link]] you will find a general plan of Hackuarium.<br><br />
Following this [[ Media:map1.png | link]], you will find the plan of Hackuarium with the position of equipment.<br />
<br />
== [[Life_Main | Rules at Hackuarium]] ==<br />
[[Life_Main | This page ]] describe the code of conduct for Hackuarium members.<br />
<br />
== [[Protocols | Protocols]] ==<br />
All the protocols that we use at Hackuarium can be found [[ BioP_Main | here ]]<br />
They are detailed and structured so that the main focus is on applications. The idea is to give crucial information on how to apply the most common techniques of the Biology toolbox. The protocols are structured as follow:<br />
::<li> A scheme describing each <br />
::<li> A brief description of the protocol and its use<br />
::<li> A description of the different ways of carrying out the protocol. Ideally there should be a description of a commercial kit and a DIY kit.<br />
::<li> A description of the safety issues and best practice<br />
::<li> Information specific to Hackuarium and where to find the components, tools and reagents.<br />
<br />
== [[Instru_Main | Instruments available]] ==<br />
[[Instru_Main | This page ]] describes all the instruments available at Hackuarium (work in progress..), their location and how to use them.<br />
<br />
== [https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing Liste à jour de nos besoins en matériel] ==<br />
This document contains all the instruments and tools we need. If you happen to have a piece of equipment we are (or may be) looking for, [mailto:hello@hackuarium.ch contact us]!<br />
<br />
== [[Where we shop | Where we shop]] ==<br />
===Wetware===<br />
Consumables can be purchased from [http://www.huberlab.ch Huber Lab].<br />
<br />
Swiss-based [http://www.smiples.ch Smiples] has a very extensive listing of second hand laboratory and technical items. These can be bought from their online shop or from [https://www.ricardo.ch/online-shop/smiples/?SellerNickName=Smiples Ricardo].<br />
<br />
===Hardware===<br />
Options for electronic parts<br />
* [http://www.ebay.com Ebay] (international)<br />
* [http://www.aliexpress.com AliExpress] (China)<br />
* [https://www.adafruit.com Adafruit] (UK)<br />
<br><br />
* [http://www.seeedstudio.com/depot/ seeedstudio] (China)<br />
* [http://www.tmart.com/ Tmart] (Hong Kong)<br />
* [https://www.pi-shop.ch/ Rasberry pi shop] (Switzerland)<br />
* [http://www.distrelec.ch/ distrilec] (Switzerland)<br />
<br />
== Tools and Equipment found at Hackuarium ==<br />
<br />
::<li>[[Tools#Working_Equipment Working Equipment|Working Equipment]]<br />
::<li>[[Tools#Equipment_that_need_a_bit_of_fixing Needs Help|Equipment needing fixing]]<br />
::<li>[[Where we shop]]<br />
<br><br />
<br />
== [[Editing the wiki | How to built a new project page on our Wiki]] ==<br />
<br />
== Library and Reading List ==<br />
<br />
== Media and Press ==<br />
<br />
* Newsletter<br />
<br />
== Wanted ==<br />
Do you want to contribute to making Hackuarium a diverse and lively community? Check out our wanted lists:<br />
::<li>Skills<br />
::<li>Ideas<br />
::<li>[https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing Equipment]<br />
::<li>Materials<br />
<br><br></div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Past_events&diff=6823Past events2016-04-19T08:28:41Z<p>Sachiko: Created page with "== Past Events == <br> ::<li>'''2016.03.29''' Tuesday 19:30-21:00: Board meeting ::<li>'''2016.03.09''' Wednesday 19:30-21:30 Openhackuarium vol...."</p>
<hr />
<div>== Past Events ==<br />
<br><br />
::<li>'''2016.03.29''' Tuesday 19:30-21:00: [[20160329_Board_meeting | Board meeting]]<br />
::<li>'''2016.03.09''' Wednesday 19:30-21:30 Openhackuarium vol. 88 Presentation by and brainstorming with [http://www.hammerdirt.ch/current-project.html Hammerdirt]<br />
::<li>'''2016.03.08''' Tuesday 16:50 [[Events:Entre_Bière_Hackers_et_ADN_Café_Scientifique_au_Collège_Rousseau |Entre bière, hackers et ADN]] The [[BeerDeCoded| BeerDeCoded project]] on stage at the Café Scientifique of Collège Rousseau (Geneva).<br />
::<li>'''2016.03.04''' Friday 19:30-22:30 Visite of Hackuarium by participants of the [[GOSH_meeting | Gathering for Open Science Hardware]] (aka [http://openplant.org/oshwforscience/ GOSH!]).<br />
::<li>'''2016.02.12''' Friday 9:00-11:00: The [[Living_Instruments| Living Instruments]] project will be featured as part of the official [http://liftconference.com/lift16/workshops/living-organisms-musical-instruments-unprecedented-performance Lift Conference] program.<br />
::<li>'''2016.02.10''' Wednesday 19:30-21:00: School trip to the music venue [http://www.le-bourg.ch le Bourg] for an [http://www.wespoke.ch/les-concerts/le-bourg-2-hackuarium/ Openhackuarium vol. 84 special music] featuring the [[Living_Instruments| Living Instruments]] project.<br />
::<li>'''2016.02.04''' Thursday 19:30-20:30 [[20160204_Board_meeting | Board meeting]]<br />
::<li>'''2016.02.03''' Wednesday 19:30-21:00 Participants to the Biodesign.cc [http://wiki.biodesign.cc/wiki/Winter_School Winterschool] visit [[Openhackuarium_vol._83 | Openhackuarium vol. 83]].<br />
::<li>'''2016.01.23-24''' Saturday and Sunday 09:00-19:00 Another week-end dedicated to biomusical innovation with the [[Living_Instruments| Living Instruments]] project<br />
::<li>'''2016.01.20''' Wednesday 19:30-20:30: [[20160120_General_Assembly | General Assembly]] of the Hackuarium association. Please come, as a member, or as a friend!<br />
::<li>'''2015.12.09''' Wednesday 19:30-21:00: [[Openhackuarium_vol._75 | Openhackuarium vol. 75]] with a presentation of the project beMap.<br />
::<li>'''2015.12.02''' Wednesday 19:30-21:00: [[Openhackuarium_vol._74 | Openhackuarium vol. 74]] with presentations about open source projects in protein science and more!<br />
::<li>'''2015.11.28''' Saturday 9:30-15:30: [[DNA_Party_workchoppe_vol.2 | The real Beer DNA workshop]] Sign-up! Limited space available.<br />
::<li>'''2015.11.26''' Jeudi 19:30-21:00: [[20151128_Board_Meeting | Board Meeting]]<br />
::<li>'''2015.11.05''' Thursday 19:00-22:00: Lausanne Open Data vol. 3 [[Data_sharing_-_Lausanne_Open_Data_Meetup|Special meetup on Biomedical Data & Ethics]] ([http://www.meetup.com/Lausanne-Open-Data-Meetup/events/223791979/| more here])<br />
::<li>'''2015.10.28''' Wednesday 19:30-23:00: [[Openhackuarium_vol._69 |#OpenHackuarium vol. 60]] [http://hackteria.org Hackteria]: DIY bio in Indonesia and the Biology of cheese and wine. Part of a week-long experiment with [http://www.hesge.ch/head/en HEAD]: [http://hackteria.org/wiki/The_Art_of_BioHacking_-_HEAD The Art of BioHacking]<br />
::<li>'''2015.09.19-21''' A long week-end dedicated to biomusical innovation with the [[Living_Instruments| Living Instruments]] project<br />
::<li>'''2015.08.27''' Thursday 19:00-22:00: Lausanne Open Data vol. 1 ([http://www.meetup.com/Lausanne-Open-Data-Meetup/events/223762682/| more here])<br />
::<li>'''2015.08.26''' Wednesday 19:30-20:30: [[Openhackuarium_vol._60_%22Lac_Léman_Science_Hackathon%22_260815|#OpenHackuarium vol. 60: Do we need Lac Léman Science Hackathon?]]<br />
::<li>'''2015.08.20''' Thursday 19:00-22:00: Drone Racing 101<br />
::<li>'''2015.08.05''' Wednesday 19:30-20:30: [[Openhackuarium_vol._57_%22Bi%C3%A8re%22 | #OpenHackuarium vol. 57]] special Fermentation.<br />
::<li>'''2015.07.22''' Wednesday 19:30-20:30: [[Openhackuarium_vol._55_-_22.07.15 | #OpenHackuarium vol. 55]] special Urban/Vertical farming.<br />
::<li>'''2015.07.18''' Saturday 9:30-15:30: [[DNA_Party_workchoppe_vol.1 | A first DNA workshop/workchoppe]].<br />
::<li>'''2015.04.22''' Wednesday 19:30-20:30: General Assembly of Hackuarium association.<br />
::<li>'''2015.04.16''' Thursday 19:00-21:00: Discussion with Le Pansement, a medical students association.<br />
::<li>'''2015.04.15''' Wednesday 18:30-21:00: Practical Session "Garage Electrophoresis" with Le Pansement, a medical students association.<br />
::<li>'''2015.03.29''' Sunday 13:30-18:30: [[2nd_Hackuarium_Wiki_Sprint | Hackuarium Wiki Sprint #2]].<br />
::<li>'''2015.03.28''' Saturday 10:00-18:30: [[Open_DNA_Seq_Workshop | Open DNA Sequencing Workshop]].<br />
::<li>'''2015.02.18''' [[Visite_du_FlyLab_Paris_chez_nous| Drone night]] with Flylab Paris (part of La Paillasse) (FR).<br />
::<li>'''2014.12.07''' [[1st_Ever_Hackuarium_Wiki_Sprint | Hackuarium Wiki Sprint #1]].<br />
::<li>'''2014.11.27''' [[Events:BSNL_Roundtable | Roundtable at EPFL organised by BNSL]].<br />
::<li>'''2014.11.05''' [[Events:Bioart_NexTrends | NexTrends/ECAL Bioart conference]] at UniverCité.<br />
::<li>'''2014.10.22''' [[Events:Open_Access | Open Access conference]] at UniverCité.<br />
::<li>'''2014.10.09''' Conference by French artist [http://liagiraud.com Lia Giraud].<br />
::<li>'''2014.09.25-27''' [[Events:Design_Days_2014 | Design Days 2014]].<br />
::<li>'''2014.09.24''' Conference by [http://www.nicolasnova.net Nicolas Nova], co-fondateur du [http://nearfuturelaboratory.com Near Future Laboratory] et enseignant à la [http://www.hesge.ch/head/ HEAD], Genève.<br />
::<li>'''2014.08.27''' Introduction to [http://bricobio.org BricoBio] Montreal by Sarah Choukah.<br />
::<li>'''2014.08.20''' Introduction to [http://lapaillasse.org La Paillasse] Paris by Clément Epié and Nicolas Loubet.<br />
::<li>'''2014.06.06-07''' [http://hackteria.org/wiki/Tech4Dev Water Hackathon] organised by Hackteria.<br />
<br />
== Participation to External Events ==<br />
::<li>'''2014.11 - 2014.12''' [http://www.gasthauszumbaeren.ch//wire-lab/re-thinking-food- Re-Thinking Food], [http://www.gasthauszumbaeren.ch/de/home Gasthaus zum Bären], [http://www.thewire.ch/en/ W.I.R.E.], Zurich, Switzerland<br />
::<li>'''2014.09.25 - 2015.02.22''' [http://www.museedelamain.ch LAB/LIFE Exhibition], Musée de la Main, Lausanne, Switzerland</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Main_Page&diff=6822Main Page2016-04-19T08:27:47Z<p>Sachiko: /* Events */</p>
<hr />
<div>Welcome to the wiki of [http://www.hackuarium.ch/ Hackuarium] community.<br />
<br />
At Hackuarium, we want to bring biology (and biologists) to the world, and the real world back to biology. Our laboratory is an excuse to meet and discuss, build and develop ideas in a neutral, open, noncompetitive and not-for-profit environment.<br />
<br />
<div><br />
''[[Hackuarium | Cliquez ici pour accéder à la version française de ce wiki.]]'' <br />
</div><br />
<br />
This page was launched during our [[1st Ever Hackuarium Wiki Sprint]] that took place on 7 December 2014. As you might notice quickly, it is a work-in-progress.<br />
<br />
Scroll down and find out what this is all about!<br />
<br />
__TOC__<br />
<br />
=DIY Bio=<br />
<br />
==What is DIYbio?==<br />
<br />
DIYbio (Do-It-Yourself biology) is a movement that wants to free the practice of biological research and innovation from the institutional and industrial laboratories. Pursued both by amateurs and professional biologists, DIYbio is developing low-cost and low-tech solutions to problems identified by the community.<br />
<br />
The movement is characterised by an extremely diverse set of practices and participants. Some call themselves 'biohackers', in reference to the hacker culture.<br />
<br />
[http://DIYbio.org DIYbio.org] and [http://DIYbio.eu DIYbio.eu] are the portals of the international and european communities, respectively.<br />
<br />
For more information, visit the [http://www.wikipedia.org Wikipedia] page dedicated to [https://en.wikipedia.org/wiki/DIYbio DIYbio].<br />
<br><br />
<br />
=Hackuarium=<br />
<br />
Hackuarium is a not-for-profit association aiming at democratizing science through public engagement.<br />
<br><br />
<br />
Our laboratory in Renens (Switzerland) is open to anyone sharing the values of the association and who is dedicated to follow the [http://diybio.org/codes/draft-diybio-code-of-ethics-from-european-congress/ DIYbio Europe ethical guidelines].<br />
<br />
Our projects are initiated and carried out by scientists as well as non-scientists from a variety of background. They are passionate about tinkering with biology in particular, and technology in general. Some are engineers, architects, designers, IT and computer scientists or retired professionals, but others have no scientific education. They are mostly citizens interested in open and participatory research and innovation, outside the contrains of traditional institutions.<br />
<br />
Hackuarium members want to investigate new ways of carrying out interdisciplinary research and innovation, by making their results accessible (low-cost), simple and easily reproducible (low-tech) and by promoting an open source philosophy.<br />
<br />
Hackuarium is proudly using infrastructures provided by [http://www.univercite.ch UniverCité], an unconventional innovation hub opened in May 2014. Our equipment is mostly upcycled material from institutions and industries from western Switzerland.<br />
<br />
=Who we are=<br />
<br />
Renens is a hopping hub - and our members reflect the diversity that is in and around Lausanne/Renens.<br />
<br><br />
[[People | Check us out]], and find out what makes Hackuarium a good mix.<br />
<br><br />
<br />
==Committee==<br />
<br />
The current [[Board|committee]] is composed of the following people:<br />
<br />
* President & Treasurer: [[User:luchenry | Luc Henry]]<br />
* Secretary: [[User:mmastern | Michal Masternak]]<br />
* Lab Manager: [[User:hekkcess | Yann Pierson]]<br />
* Online tools administrator: [[User:Sam | Sam Sulaimanov]]<br />
* Art and Design coordinator: [[User:Vlorenzo | Vanessa Lorenzo]]<br />
* Talent scout and evangelist: [[User:Randogp | Gianpaolo Rando]]<br />
* Events and coordinator: [[User:Alpittet | Anne-Laure Pittet]]<br />
* Member: Ana Roldan<br />
<br />
The Agenda of the last board meeting can be found [[20151128_Board_Meeting | here]].<br />
<br />
==Members and Membership==<br />
<br />
Hackuarium operates on a membership basis at this current time.<br />
<br />
The monthly membership fee is 20 CHF. It gives 24/7 access to the lab.<br />
<br />
Please ask a member of the board if you want to join as a member.<br />
<br />
All events are open to anyone, including non-members.<br />
<br />
==Friends of Hackuarium==<br />
<br />
Spaces:<br />
::<li>[http://www.univercite.ch UniverCité]<br />
::<li>[http://lapaillasse.org La Paillasse, Paris]<br />
::<li>[https://lapaillassaone.wordpress.com Paillasse Saône, Lyon]<br />
<br><br />
<br />
Projects:<br />
::<li>[[Exodes_Urbains | Exodes Urbains]]<br />
::<li>[http://echopen.org/index.php?title=Main_Page EchOpen]<br />
<br><br />
<br />
==Where we are==<br />
Hackuarium is one of the association active at UniverCité, an innovation space under construction since May 2014 in the IRL building in Renens. We have documented our working environment as it has evolved.<br><br />
As of December 2015, UniverCité regroups a laboratory, a workshop and co-working space.<br />
<br><br />
<br />
=Events=<br />
<br />
== Upcoming Events ==<br />
<br><br />
'''Every Wednesday, 19:00-23:00''' #OpenHackuarium: our lab and space are open to the public. [mailto:hello@hackuarium.ch Get in touch!]<br />
<br><br />
:<li>'''2016.06.14''' Tuesday SAVE THE DATE [http://opendata.ch/2015/11/opendata-ch2016-am-14-juni-in-lausanne/ Opendata.ch/2016 Conference], Casino de Montbenon, Lausanne.<br />
:<li>'''2016.04.27''' Wednesday 19:30-21:00: [[Openhackuarium_vol._95 | Openhackuarium vol. 95]] T-shirt printing session!<br />
:<li>'''2016.04.13''' Wednesday 19:30-21:00: [[Openhackuarium_vol._93 | Openhackuarium vol. 93]] 'Genomic integrity' and DIY 'comet assay' on cheek cells.<br />
:<li>'''2016.04.06''' Wednesday 19:30-21:00: [http://wiki.hackuarium.ch/w/Openhackuarium_vol._92 Openhackuarium vol. 92] Darty Monkeys: 'Biofilia Night'.<br />
<br />
<br />
== Past Events ==<br />
<br><br />
Please find the list of our [[past events]].<br><br />
<br />
=Projects=<br />
Here, you will find the projects going on in the Hackuarium.<br />
<br />
== Active Projects ==<br />
<br />
* [[Open-Food-DNA |Open-Food-DNA]]<br />
* [[BeerDeCoded]]<br />
* [[Living Instruments]]<br />
* [[Bience | Bience (Beer and Science!)]]<br />
* [[Protein purification systems]]<br />
* [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Micro to Macro Water Pollution]] - with [http://www.hammerdirt.ch/ Hammerdirt] and [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Spectro-pointer]]<br />
* [[Darty_Monkeys]]<br />
* [http://octanis.org/ Octanis]<br />
* [[Edible wall]]<br />
* [[ZéBU CH]]<br />
* [[Grow%26Mix_Bioink]]<br />
* [[unmapping]]<br />
* [[Compost Bacteria]]<br />
* [[AGiR! for genomic integrity]]<br />
<br />
== Archived Projects ==<br />
<br />
* [[Mycelium Structures]]<br />
* [[Live Type]]<br />
* [[Projects:LivingLab Design|LivingLab Design]]<br />
* [[Projects:bioluminescence|Bioluminescence]]<br />
* [[Projects:Quantitative Anthropology|Quantitative Anthropology]]<br />
* [[Projects:Impression 3D|Impression 3D]]<br />
* [[Projects:Dépollution des stands de tirs Suisses]]<br />
* [[Incubateur bon marché]]<br />
* [[Space Seed]]<br />
* [[Reception d'images satellites]]<br />
<br />
= Practical Informations =<br />
<br />
Following this [[ Media:Univercite map2-01.png | link]] you will find a general plan of Hackuarium.<br><br />
Following this [[ Media:map1.png | link]], you will find the plan of Hackuarium with the position of equipment.<br />
<br />
== [[Life_Main | Rules at Hackuarium]] ==<br />
[[Life_Main | This page ]] describe the code of conduct for Hackuarium members.<br />
<br />
== [[Protocols | Protocols]] ==<br />
All the protocols that we use at Hackuarium can be found [[ BioP_Main | here ]]<br />
They are detailed and structured so that the main focus is on applications. The idea is to give crucial information on how to apply the most common techniques of the Biology toolbox. The protocols are structured as follow:<br />
::<li> A scheme describing each <br />
::<li> A brief description of the protocol and its use<br />
::<li> A description of the different ways of carrying out the protocol. Ideally there should be a description of a commercial kit and a DIY kit.<br />
::<li> A description of the safety issues and best practice<br />
::<li> Information specific to Hackuarium and where to find the components, tools and reagents.<br />
<br />
== [[Instru_Main | Instruments available]] ==<br />
[[Instru_Main | This page ]] describes all the instruments available at Hackuarium (work in progress..), their location and how to use them.<br />
<br />
== [https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing Liste à jour de nos besoins en matériel] ==<br />
This document contains all the instruments and tools we need. If you happen to have a piece of equipment we are (or may be) looking for, [mailto:hello@hackuarium.ch contact us]!<br />
<br />
== [[Where we shop | Where we shop]] ==<br />
===Wetware===<br />
Consumables can be purchased from [http://www.huberlab.ch Huber Lab].<br />
<br />
Swiss-based [http://www.smiples.ch Smiples] has a very extensive listing of second hand laboratory and technical items. These can be bought from their online shop or from [https://www.ricardo.ch/online-shop/smiples/?SellerNickName=Smiples Ricardo].<br />
<br />
===Hardware===<br />
Options for electronic parts<br />
* [http://www.ebay.com Ebay] (international)<br />
* [http://www.aliexpress.com AliExpress] (China)<br />
* [https://www.adafruit.com Adafruit] (UK)<br />
<br><br />
* [http://www.seeedstudio.com/depot/ seeedstudio] (China)<br />
* [http://www.tmart.com/ Tmart] (Hong Kong)<br />
* [https://www.pi-shop.ch/ Rasberry pi shop] (Switzerland)<br />
* [http://www.distrelec.ch/ distrilec] (Switzerland)<br />
<br />
== Tools and Equipment found at Hackuarium ==<br />
<br />
::<li>[[Tools#Working_Equipment Working Equipment|Working Equipment]]<br />
::<li>[[Tools#Equipment_that_need_a_bit_of_fixing Needs Help|Equipment needing fixing]]<br />
::<li>[[Where we shop]]<br />
<br><br />
<br />
== [[Editing the wiki | How to built a new project page on our Wiki]] ==<br />
<br />
== Library and Reading List ==<br />
<br />
== Media and Press ==<br />
<br />
* Newsletter<br />
<br />
== Wanted ==<br />
Do you want to contribute to making Hackuarium a diverse and lively community? Check out our wanted lists:<br />
::<li>Skills<br />
::<li>Ideas<br />
::<li>[https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing Equipment]<br />
::<li>Materials<br />
<br><br></div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Hackuarium&diff=6821Hackuarium2016-04-19T05:58:48Z<p>Sachiko: /* Projets */</p>
<hr />
<div>Bienvenue sur le '''wiki''' de l'association [http://www.hackuarium.ch/ Hackuarium]<br />
<br />
<div><br />
''[[Main_Page | Click here to view the english version of this wiki.]]'' <br />
</div><br />
<br />
Notre communauté regroupe les curieux et les bricoleurs de la région Lausannoise dans un laboratoire ouvert et citoyen situé avec d'autres activités au sein de [[UniverCité]], à Renens, une ville de Suisse Romande.<br />
<br />
La matière vivante est de plus en plus facilement cultivable, modulable, modifiable. Entre science et design, innovation et création artistique, Hackuarium est une rencontre entre citoyens de la région lausannoise qui veulent promouvoir ou pratiquer la biologie DIY. Le laboratoire communautaire d'Hackuarium offre à chacun la possibilité de découvrir, d’expérimenter et de contribuer ses compétences dans le cadre de projets.<br />
<br />
Comme vous pouvez le voir, cette page est en chantier et a été construite pendant le [[1st_Ever_Hackuarium_Wiki_Sprint | 1er Hackuarium Wiki Sprint]] qui a eu lieu le 7 décembre 2014 à UniverCité.<br />
<br />
Le membre du [[Working Group | groupe de travail]] qui peut vous aider à commencer à contribuer en cas de besoin et la personne de contact du [[Board | comité]] pour nos outils en ligne est [[User:Sam | Sam]]. Tout le groupe de travail est joignable rapidement via [[Slack]] sur [#wg-doc].<br><br />
<br />
__TOC__<br />
<br />
== Qu'est que la biologie DIY? ==<br />
<br />
La biologie do-it-yourself (DIY) vise à démocratiser la recherche en biologie, et en particulier ses outils.<br />
<br />
La biologie DIY est parfois appelée "Biohacking" mais elle n'est en fait qu'une partie de ce mouvement qui applique les règle du hacking à la biotechnologie et la santé.<br />
<br />
Plus d'information sur [https://en.wikipedia.org/wiki/Do-it-yourself_biology Wikipedia] (en anglais).<br />
<br />
== L'Association Hackuarium ==<br />
Hackuarium est une communauté de bricoleurs passionnés constituée en association. L'assemblée constitutive a eu lieu le 13 août 2014.<br />
<br />
Nos membres pratiquent une science ouverte et participative, en dehors des institutions traditionnelles, dans le respect de la [http://diybio.org/codes/draft-diybio-code-of-ethics-from-european-congress/ charte éthique] du mouvement DIYbio EU. Nous favorisons par tous les moyens l'interdisciplinarité, et nos projets sont portés aussi bien par des scientifiques que par des citoyens architectes, designers, informaticiens, journalistes ou retraités.<br />
<br />
Nos projets préférés incluent la plupart du temps une approche à bas coût (low-cost) et la technologie la plus simple possible (low-tech). Nous nous inscrivons également dans une démarche d'upcycling de matériel mis au rebut par les laboratoires de la région.<br />
<br />
Notre laboratoire est ouvert à tous ceux qui partagent nos valeurs et se situe à Renens, au sein d'UniverCité, un lieu d'innovation inauguré le 26 mai 2014.<br><br />
<br />
== Qui sommes-nous? ==<br />
<br />
Notre communauté est le pilier de l'association Hackuarium. Nos membres, au passé varié et aux motivations multiples vivent à Lausanne et dans ses environs.<br><br />
<br />
=== Membres ===<br />
<br />
Nous encourageons les personnes intéressées à participer régulièrement aux activités de l'association à devenir membres.<br />
<br />
Etre membre permet d'avoir accès au laboratoire 24h/24, 7j/7, de bénéficier d'autres offres (rabais sur l'utilisation de l'atelier), de voter à l'assemblée générale et donc de participer activement à la vie de la communauté et aux prises de décisions.<br />
<br />
Etre membre de l'association Hackuarium implique payer une cotisation mensuelle de 20 francs suisses.<br><br />
<br />
=== Comité ===<br />
<br />
Le [[Board|comité de l'association]] Hackuarium est aujourd'hui composé de:<br><br />
* Président & Trésorier: [[User:luchenry | Luc Henry]]<br />
* Secrétaire: [[User:mmastern | Michal Masternak]]<br />
* Responsable laboratoire: [[User:hekkcess | Yann Pierson]]<br />
* Administrateur des outils web: [[User:Sam | Sam Sulaimanov]]<br />
* Art et Design: [[User:Vlorenzo | Vanessa Lorenzo]]<br />
* Talent scout and evangelist: [[User:Randogp | Gianpaolo Rando]]<br />
* Evènements: [[User:Alpittet | Anne-Laure Pittet]]<br />
* Membre: Ana Roldan<br />
<br />
L'agenda de la dernière assemblée générale est disponible [[20160120_General_Assembly | ici]] (20 janvier 2016).<br />
L'agenda de la dernière rencontre du comité est disponible [[20160329_Board_meeting | ici]] (29 mars 2016).<br />
<br />
=== Les amis d'Hackuarium ===<br />
<br />
::<li>[http://www.univercite.ch UniverCité]<br />
::<li>[[Exodes_Urbains | Exodes Urbains]]<br />
<br />
== Où travaillons-nous? ==<br />
Notre laboratoire communautaire se situe au Chemin du Closel 5 à Renens, en Suisse, dans une commune de la région lausannoise en plein développement.<br />
Hackuarium est situé dans le bâtiment IRL et fait partie d'[http://www.univercite.ch Univercité], un espace d'innovation abritant un espace de coworking, l'atelier [http://made.univercite.ch Made@UniverCité], plusieurs associations, des startups, etc.<br />
<br />
== Evénements ==<br />
=== Evénements à venir ===<br />
<br><br />
::<li>'''Tous les mercredi, 19:00-23:00''' #OpenHackuarium: le laboratoire est ouvert au public.<br />
<br><br />
<br />
::<li>'''2016.06.14''' A vos agendas! Et venez participer à la [http://opendata.ch/2015/11/opendata-ch2016-am-14-juni-in-lausanne/ conference Opendata.ch/2016], Casino de Montbenon, Lausanne.<br />
::<li>'''2016.04.27''' Mercredi 19:30-21:00: [[Openhackuarium_vol._95 | Openhackuarium vol. 95]] Atelier impression T-shirt!<br />
::<li>'''2016.04.13''' Mercredi 19:30-21:00: [[Openhackuarium_vol._93 | Openhackuarium vol. 93]] 'Genomic integrity' and DIY 'comet assay' on cheek cells.<br />
<br />
=== Evénements passés ===<br />
::<li>'''2016.03.29''' Mardi 19h30-21:00: [[20160329_Board_meeting | Séance du comité]].<br />
::<li>'''2016.03.23''' Mercredi 19:30-21:30: [https://www.facebook.com/events/1220561621292105/ Openhackuarium vol. 90] présentation des projets de compostage et de fermentation du lactose<br />
::<li>'''2016.03.09''' Mercredi 19:30-21:30: Openhackuarium vol. 88 Visite et présentation informelle de [http://www.hammerdirt.ch/current-project.html Hammerdirt]<br />
::<li>'''2016.03.08''' Mardi 16:50 [[Events:Entre_Bière_Hackers_et_ADN_Café_Scientifique_au_Collège_Rousseau |Entre bière, hackers et ADN]] le projet [[BeerDeCoded| BeerDeCoded]] participe au café scientifique du Collège Rousseau (Genève).<br />
::<li>'''2016.03.04''' Vendredi 19:30-22:30: Visite des participants du [[GOSH_meeting | Gathering for Open Science Hardware]] (aka [http://openplant.org/oshwforscience/ GOSH!]).<br />
::<li>'''2016.02.12''' Vendredi 9:00-11:00: Le projet [[Living_Instruments| Living Instruments]] fait partie du programme officiel de la [http://liftconference.com/lift16/workshops/living-organisms-musical-instruments-unprecedented-performance conference Lift] à Genève.<br />
::<li>'''2016.02.10''', Mercredi 19:30-21:00: Sortie de classe au [http://www.le-bourg.ch Bourg] pour une [http://www.wespoke.ch/les-concerts/le-bourg-2-hackuarium/ soirée musique] avec le project [[Living_Instruments| Living Instruments]].<br />
::<li>'''2016.02.09''', Mardi 19:30-21:00: Exceptionnellement, l'[[Openhackuarium_vol._84|Openhackuarium vol. 84]] aura lieu un mardi soir pour accueillir des amis Parisiens qui nous parleront de Blockchain (en français).<br />
::<li>'''2016.02.06-07''' Samedi et dimanche 9:00-19:00 Encore un week-end dédié au projet d'innovation biomusicale avec le projet [[Living_Instruments| Living Instruments]].<br />
::<li>'''2016.02.04''' Jeudi 19:30-21:00: [[20160204_Board_meeting | Séance du comité]]<br />
::<li>'''2016.02.03''', Mercredi 19:30-21:00: Visite des participants de la [http://wiki.biodesign.cc/wiki/Winter_School Winterschool] de Biodesign.cc lors de l'[[Openhackuarium_vol._83 | Openhackuarium vol. 83]].<br />
::<li>'''2016.01.23-24''' Samedi et dimanche 9:00-19:00 Encore un week-end dédié au projet d'innovation biomusicale avec le projet [[Living_Instruments| Living Instruments]].<br />
::<li>'''2016.01.20''' Mercredi 19:30-20:30: [[20160120_General_Assembly | Assemblée Générale]] de l'association Hackuarium. Membres et non-membres bienvenus!<br />
::<li>'''2015.12.23''' Mercredi 19:30-21:00: [[Openhackuarium_vol._77 | Openhackuarium vol. 77]] fondue de fin d'année!<br />
::<li>'''2015.12.09''' Mercredi 19:30-21:00: [[Openhackuarium_vol._75 | Openhackuarium vol. 75]] avec une presentation du projet beMap.<br />
::<li>'''2015.12.02''' Mercredi 19:30-21:00: [[Openhackuarium_vol._74 | Openhackuarium vol. 74]] avec des presentations de projets open source!<br />
::<li>'''2015.11.28''' Saturday 9:30-15:30: [[DNA_Party_workchoppe_vol.2 | Le workchoppe]]. Inscrivez-vous! Les places sont limitées.<br />
::<li>'''2015.11.26''' Jeudi 19:30-21:00: [[20151128_Board_Meeting | Séance du comité]]<br />
::<li>'''2015.11.05''' Jeudi 19:00-22:00: Lausanne Open Data vol. 3 [[Data_sharing_-_Lausanne_Open_Data_Meetup | Special meetup on Biomedical Data & Ethics]] ([http://www.meetup.com/Lausanne-Open-Data-Meetup/events/223791979/ more here])<br />
::<li>'''2015.10.28''' Mercredi 19:30-23:00: [[Openhackuarium_vol._69 |OpenHackuarium vol. 60]] [http://hackteria.org Hackteria]: DIY bio in Indonesia and the Biology of cheese and wine. Dans le cadre d'une semaine avec les étudiants de la [http://www.hesge.ch/head/en HEAD]: [http://hackteria.org/wiki/The_Art_of_BioHacking_-_HEAD The Art of BioHacking]<br />
::<li>'''2015.09.24''' Jeudi 19:00-22:00: Lausanne Open Data vol. 2 ([http://www.meetup.com/Lausanne-Open-Data-Meetup/events/223791962/| more here])<br />
::<li>'''2015.09.19-21''' Samedi-Lundi 9:00-19:00: Un week-end prolongé dédié à l'innovation biomusicale dans le cadre du projet [[Living_Instruments| Living Instruments]]<br />
::<li>'''2015.08.27''' Jeudi 19:00-22:00: Lausanne Open Data vol. 1 ([http://www.meetup.com/Lausanne-Open-Data-Meetup/events/223762682/| more here])<br />
::<li>'''2015.08.26''' Mercredi 19:30-20:30: [[Openhackuarium_vol._60_%22Lac_Léman_Science_Hackathon%22_260815|#OpenHackuarium vol. 60: Do we need Lac Léman Science Hackathon?]]<br />
::<li>'''2015.08.20''' Jeudi 19:00-22:00: Drone Racing 101<br />
::<li>'''2015.08.05''' Wednesday 19:30-20:30: [[Openhackuarium_vol._57_%22Bi%C3%A8re%22 | #OpenHackuarium vol. 57 special Fermentation]]<br />
::<li>'''2015.07.22''' Wednesday 19:30-20:30: [[Openhackuarium_vol._55_-_22.07.15 | #OpenHackuarium vol. 55 special Urban/Vertical farming]]<br />
::<li>'''2015.07.18''' Saturday 9:30-15:30: [[DNA_Party_workchoppe_vol.1 | A first DNA workshop/workchoppe]]<br />
::<li>'''2015.04.22''' Wednesday 19:30-20:30: General Assembly of Hackuarium association.<br />
::<li>'''2015.04.16''' Thursday 19:00-21:00: Discussion with Le Pansement, a medical students association<br />
::<li>'''2015.04.15''' Wednesday 18:30-21:00: Practical Session "Garage Electrophoresis" with Le Pansement, a medical students association<br />
::<li>'''2015.03.29''' Sunday 13:30-18:30: [[2nd_Hackuarium_Wiki_Sprint | Hackuarium Wiki Sprint #2]]<br />
::<li>'''2015.03.28''' Saturday 10:00-18:30: [[Open_DNA_Seq_Workshop | Open DNA Sequencing Workshop]]<br />
::<li>'''2015.02.18''' [[Visite_du_FlyLab_Paris_chez_nous| Drone night with Flylab Paris (part of La Paillasse) (FR)]]<br />
::<li>'''2015.01.27''' Café Scientifique UNIL<br />
::<li>'''2014.12.07''' [[1st_Ever_Hackuarium_Wiki_Sprint | Hackuarium Wiki Sprint #1]]<br />
::<li>'''2014.11.27''' [[Events:BNSL_Roundtable | Roundtable at EPFL organised by BNSL]]<br />
::<li>'''2014.11.05''' [[Events:Bioart_NexTrends | NexTrends/ECAL Bioart conference at UniverCité]]<br />
::<li>'''2014.10.29''' Assemblée Générale Hackuarium [https://drive.google.com/folderview?id=0BwKVPtIVQtKqOEJ4bW5wTkd5X3M&usp=sharing#list]<br />
::<li>'''2014.10.22''' [[Events:Open_Access |Open Access conference at UniverCité]]<br />
::<li>'''2014.10.09''' Conférence de l'artiste française [http://liagiraud.com Lia Giraud]<br />
::<li>'''2014.09.25-27''' [[Events:Design_Days_2014 | Design Days 2014]]<br />
::<li>'''2014.09.24''' Conférence de [http://www.nicolasnova.net Nicolas Nova], co-fondateur du [http://nearfuturelaboratory.com Near Future Laboratory] et enseignant à la [http://www.hesge.ch/head/ HEAD], Genève.<br />
::<li>'''2014.08.27''' Présentation de [http://bricobio.org BricoBio] Montréal par Sarah Choukah<br />
::<li>'''2014.08.20''' Présentation de [http://lapaillasse.org La Paillasse] Paris par Clément Epié et Nicolas Loubet<br />
::<li>'''2014.08.13''' Assemblée Générale Hackuarium. Les documents fondateurs sont disponibles [https://drive.google.com/folderview?id=0BwKVPtIVQtKqOEJ4bW5wTkd5X3M&usp=sharing#list ici]<br />
::<li>'''2014.06.06-07''' [http://hackteria.org/wiki/Tech4Dev Water Hackathon organised by Hackteria]<br />
<br />
=== Partenariats ===<br />
::<li>'''2014.11 - 2014.12''' [http://www.gasthauszumbaeren.ch//wire-lab/re-thinking-food- Re-Thinking Food], [http://www.gasthauszumbaeren.ch/de/home Gasthaus zum Bären], [http://www.thewire.ch/en/ W.I.R.E.], Zurich, Switzerland<br />
::<li>'''2014.09.25 - 2015.02.22''' [http://www.museedelamain.ch LAB/LIFE Exhibition], Musée de la Main, Lausanne, Switzerland<br />
<br />
== [[Projects | Projets]] ==<br />
Hackuarium est une communauté rassemblée autour de différents projets. Si vous voulez en savoir plus, visitez les pages ci-dessous<br />
<br />
=== Projets Actifs ===<br />
<br />
* [[Open-Food-DNA |Open Food DNA]]<br />
* [[BeerDeCoded]]<br />
* [[Living Instruments]]<br />
* [[Bience | Bience (Bière et Science!)]]<br />
* [[APPS]]<br />
* [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Micro to Macro Water Pollution]] -avec [http://www.hammerdirt.ch/ Hammerdirt] et [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Spectro-pointer]]<br />
* [[Darty_Monkeys]]<br />
* [http://octanis.org/ Octanis]<br />
* [[Edible wall]]<br />
* [[ZéBU CH]]<br />
* [[Grow%26Mix_Bioink]]<br />
* [[unmapping]]<br />
<br />
=== Projets Archivés ===<br />
<br />
* [[Mycelium Structures]]<br />
* [[Projet Sylvan|Konkret Bacterien]] <br />
* [[Live Type]]<br />
* [[Projects:LivingLab Design|LivingLab Design]]<br />
* [[Projects:bioluminescence|Bioluminescence]]<br />
* [[Projects:Quantitative Anthropology|Quantitative Anthropology]]<br />
* [[Projects:Impression 3D|Impression 3D]]<br />
* [[Projects:Dépollution des stands de tirs Suisses]]<br />
* [[Incubateur bon marché]]<br />
* [[Space Seed]]<br />
* [[Reception d'images satellites]]<br />
<br />
== En pratique ==<br />
<br />
Sur [[ Media:Univercite map2-01.png | ce lien]] vous trouverez la carte montrant la vue d'ensemble d'Univercité.<br><br />
Sur [[ Media:map1.png | ce lien]] la carte montrant la vue d'ensemble d'Hackuarium détaillant ou se trouve la majorité du matériel.<br />
<br />
=== [[I m new | Je suis nouveau, je fais quoi ?]] ===<br />
Tu viens d'arriver? tu cherches tes repères? Alors commence alors par lire [[I m new | cette page ]].<br />
<br />
=== [[Life_Main | Règles de vie à Hackuarium]] ===<br />
[[Life_Main | Cette page ]] recense les codes de bonne conduite à adopter à Hackuarium ainsi que les quelques règles s'appliquant dans certains cas spécifiques.<br />
<br />
=== [[Protocols | Protocoles]] ===<br />
Tous les protocoles liés à Hackuarium se trouvent [[ BioP_Main | ici ]] (page en Anglais)<br />
Ils sont structurés et expliqués de façon à être axés sur les procédé de manipulation. L'idée est de donner les informations cruciales de manière à appliquer les techniques les plus communes appartenant à la boite à outils du biologiste. Les documents sont structurés comme suit:<br />
::<li> Un schéma décrivant le procédé<br />
::<li> Une explication brève du procédé et son utilité<br />
::<li> Un protocole décrivant les différentes procédures pour appliquer le procédé. Idéalement il y aurait une description pour le faire avec un kit commercial et un moyen DIY.<br />
::<li> Une partie détaillant les précautions à prendre pour travailler en toute sécurité.<br />
::<li> Des informations spécifiques à Hackuarium décrivant ou se trouve les instruments et comment les utiliser.<br />
<br />
=== [[Instru_Main | Instruments et leurs utilisation]] ===<br />
[[Instru_Main | Cette page ]](Anglais) recense tous les instruments disponibles sur le lieu, leur position ainsi que la manière dont ils doivent être utilisés.<br />
<br />
=== [https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing Liste à jour de nos besoins en matériel] ===<br />
Ce document présente le matériel dont nous avons besoin. Si il vous arrivait d'avoir une des pièce que nous recherchons faites nous le savoir, nous comptons sur vous! :-)<br />
<br />
=== [[Where we shop | Où faisons-nous nos achats]] ===<br />
<br />
=== [[Editing the wiki | Comment créer une nouvelle page de projet sur notre wiki]] ===<br />
<br />
== Bibliothèque et liste de lecture ==<br />
<br />
Notre espace contient une bibliothèque d'ouvrages de référence:<br />
<br />
- DELFANTI Alessandro, "Biohackers, The Politics of Open Science", 2013, London, Pluto Press<br />
<br />
- LALLEMENT Michel, "L'âge du faire. Hacking, travail, anarchie", 2015, Paris, Seuil<br />
<br />
Les liens suivants peuvent aussi vous intéresser:<br />
<br />
== Media and Press | Presse et média ==<br />
<br />
Si vous voulez des informations au sujet d'Hackuarium, n'hésitez pas à envoyer un email à hello[at]hackuarium[dot]ch.<br />
<br />
Vous trouverez dans le [[Press_kit | Press Kit]] tous les détails concernant notre passé médiatique. <br />
<br />
<br />
[[Category:Work In Progress]]</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Main_Page&diff=6820Main Page2016-04-19T05:58:28Z<p>Sachiko: /* Active Projects */</p>
<hr />
<div>Welcome to the wiki of [http://www.hackuarium.ch/ Hackuarium] community.<br />
<br />
At Hackuarium, we want to bring biology (and biologists) to the world, and the real world back to biology. Our laboratory is an excuse to meet and discuss, build and develop ideas in a neutral, open, noncompetitive and not-for-profit environment.<br />
<br />
<div><br />
''[[Hackuarium | Cliquez ici pour accéder à la version française de ce wiki.]]'' <br />
</div><br />
<br />
This page was launched during our [[1st Ever Hackuarium Wiki Sprint]] that took place on 7 December 2014. As you might notice quickly, it is a work-in-progress.<br />
<br />
Scroll down and find out what this is all about!<br />
<br />
__TOC__<br />
<br />
=DIY Bio=<br />
<br />
==What is DIYbio?==<br />
<br />
DIYbio (Do-It-Yourself biology) is a movement that wants to free the practice of biological research and innovation from the institutional and industrial laboratories. Pursued both by amateurs and professional biologists, DIYbio is developing low-cost and low-tech solutions to problems identified by the community.<br />
<br />
The movement is characterised by an extremely diverse set of practices and participants. Some call themselves 'biohackers', in reference to the hacker culture.<br />
<br />
[http://DIYbio.org DIYbio.org] and [http://DIYbio.eu DIYbio.eu] are the portals of the international and european communities, respectively.<br />
<br />
For more information, visit the [http://www.wikipedia.org Wikipedia] page dedicated to [https://en.wikipedia.org/wiki/DIYbio DIYbio].<br />
<br><br />
<br />
=Hackuarium=<br />
<br />
Hackuarium is a not-for-profit association aiming at democratizing science through public engagement.<br />
<br><br />
<br />
Our laboratory in Renens (Switzerland) is open to anyone sharing the values of the association and who is dedicated to follow the [http://diybio.org/codes/draft-diybio-code-of-ethics-from-european-congress/ DIYbio Europe ethical guidelines].<br />
<br />
Our projects are initiated and carried out by scientists as well as non-scientists from a variety of background. They are passionate about tinkering with biology in particular, and technology in general. Some are engineers, architects, designers, IT and computer scientists or retired professionals, but others have no scientific education. They are mostly citizens interested in open and participatory research and innovation, outside the contrains of traditional institutions.<br />
<br />
Hackuarium members want to investigate new ways of carrying out interdisciplinary research and innovation, by making their results accessible (low-cost), simple and easily reproducible (low-tech) and by promoting an open source philosophy.<br />
<br />
Hackuarium is proudly using infrastructures provided by [http://www.univercite.ch UniverCité], an unconventional innovation hub opened in May 2014. Our equipment is mostly upcycled material from institutions and industries from western Switzerland.<br />
<br />
=Who we are=<br />
<br />
Renens is a hopping hub - and our members reflect the diversity that is in and around Lausanne/Renens.<br />
<br><br />
[[People | Check us out]], and find out what makes Hackuarium a good mix.<br />
<br><br />
<br />
==Committee==<br />
<br />
The current [[Board|committee]] is composed of the following people:<br />
<br />
* President & Treasurer: [[User:luchenry | Luc Henry]]<br />
* Secretary: [[User:mmastern | Michal Masternak]]<br />
* Lab Manager: [[User:hekkcess | Yann Pierson]]<br />
* Online tools administrator: [[User:Sam | Sam Sulaimanov]]<br />
* Art and Design coordinator: [[User:Vlorenzo | Vanessa Lorenzo]]<br />
* Talent scout and evangelist: [[User:Randogp | Gianpaolo Rando]]<br />
* Events and coordinator: [[User:Alpittet | Anne-Laure Pittet]]<br />
* Member: Ana Roldan<br />
<br />
The Agenda of the last board meeting can be found [[20151128_Board_Meeting | here]].<br />
<br />
==Members and Membership==<br />
<br />
Hackuarium operates on a membership basis at this current time.<br />
<br />
The monthly membership fee is 20 CHF. It gives 24/7 access to the lab.<br />
<br />
Please ask a member of the board if you want to join as a member.<br />
<br />
All events are open to anyone, including non-members.<br />
<br />
==Friends of Hackuarium==<br />
<br />
Spaces:<br />
::<li>[http://www.univercite.ch UniverCité]<br />
::<li>[http://lapaillasse.org La Paillasse, Paris]<br />
::<li>[https://lapaillassaone.wordpress.com Paillasse Saône, Lyon]<br />
<br><br />
<br />
Projects:<br />
::<li>[[Exodes_Urbains | Exodes Urbains]]<br />
::<li>[http://echopen.org/index.php?title=Main_Page EchOpen]<br />
<br><br />
<br />
==Where we are==<br />
Hackuarium is one of the association active at UniverCité, an innovation space under construction since May 2014 in the IRL building in Renens. We have documented our working environment as it has evolved.<br><br />
As of December 2015, UniverCité regroups a laboratory, a workshop and co-working space.<br />
<br><br />
<br />
=Events=<br />
<br />
== Upcoming Events ==<br />
<br><br />
'''Every Wednesday, 19:00-23:00''' #OpenHackuarium: our lab and space are open to the public. [mailto:hello@hackuarium.ch Get in touch!]<br />
<br><br />
:<li>'''2016.06.14''' Tuesday SAVE THE DATE [http://opendata.ch/2015/11/opendata-ch2016-am-14-juni-in-lausanne/ Opendata.ch/2016 Conference], Casino de Montbenon, Lausanne.<br />
:<li>'''2016.04.27''' Wednesday 19:30-21:00: [[Openhackuarium_vol._95 | Openhackuarium vol. 95]] T-shirt printing session!<br />
:<li>'''2016.04.13''' Wednesday 19:30-21:00: [[Openhackuarium_vol._93 | Openhackuarium vol. 93]] 'Genomic integrity' and DIY 'comet assay' on cheek cells.<br />
:<li>'''2016.04.06''' Wednesday 19:30-21:00: [http://wiki.hackuarium.ch/w/Openhackuarium_vol._92 Openhackuarium vol. 92] Darty Monkeys: 'Biofilia Night'.<br />
<br />
== Past Events ==<br />
::<li>'''2016.03.29''' Tuesday 19:30-21:00: [[20160329_Board_meeting | Board meeting]]<br />
::<li>'''2016.03.09''' Wednesday 19:30-21:30 Openhackuarium vol. 88 Presentation by and brainstorming with [http://www.hammerdirt.ch/current-project.html Hammerdirt]<br />
::<li>'''2016.03.08''' Tuesday 16:50 [[Events:Entre_Bière_Hackers_et_ADN_Café_Scientifique_au_Collège_Rousseau |Entre bière, hackers et ADN]] The [[BeerDeCoded| BeerDeCoded project]] on stage at the Café Scientifique of Collège Rousseau (Geneva).<br />
::<li>'''2016.03.04''' Friday 19:30-22:30 Visite of Hackuarium by participants of the [[GOSH_meeting | Gathering for Open Science Hardware]] (aka [http://openplant.org/oshwforscience/ GOSH!]).<br />
::<li>'''2016.02.12''' Friday 9:00-11:00: The [[Living_Instruments| Living Instruments]] project will be featured as part of the official [http://liftconference.com/lift16/workshops/living-organisms-musical-instruments-unprecedented-performance Lift Conference] program.<br />
::<li>'''2016.02.10''' Wednesday 19:30-21:00: School trip to the music venue [http://www.le-bourg.ch le Bourg] for an [http://www.wespoke.ch/les-concerts/le-bourg-2-hackuarium/ Openhackuarium vol. 84 special music] featuring the [[Living_Instruments| Living Instruments]] project.<br />
::<li>'''2016.02.04''' Thursday 19:30-20:30 [[20160204_Board_meeting | Board meeting]]<br />
::<li>'''2016.02.03''' Wednesday 19:30-21:00 Participants to the Biodesign.cc [http://wiki.biodesign.cc/wiki/Winter_School Winterschool] visit [[Openhackuarium_vol._83 | Openhackuarium vol. 83]].<br />
::<li>'''2016.01.23-24''' Saturday and Sunday 09:00-19:00 Another week-end dedicated to biomusical innovation with the [[Living_Instruments| Living Instruments]] project<br />
::<li>'''2016.01.20''' Wednesday 19:30-20:30: [[20160120_General_Assembly | General Assembly]] of the Hackuarium association. Please come, as a member, or as a friend!<br />
::<li>'''2015.12.09''' Wednesday 19:30-21:00: [[Openhackuarium_vol._75 | Openhackuarium vol. 75]] with a presentation of the project beMap.<br />
::<li>'''2015.12.02''' Wednesday 19:30-21:00: [[Openhackuarium_vol._74 | Openhackuarium vol. 74]] with presentations about open source projects in protein science and more!<br />
::<li>'''2015.11.28''' Saturday 9:30-15:30: [[DNA_Party_workchoppe_vol.2 | The real Beer DNA workshop]] Sign-up! Limited space available.<br />
::<li>'''2015.11.26''' Jeudi 19:30-21:00: [[20151128_Board_Meeting | Board Meeting]]<br />
::<li>'''2015.11.05''' Thursday 19:00-22:00: Lausanne Open Data vol. 3 [[Data_sharing_-_Lausanne_Open_Data_Meetup|Special meetup on Biomedical Data & Ethics]] ([http://www.meetup.com/Lausanne-Open-Data-Meetup/events/223791979/| more here])<br />
::<li>'''2015.10.28''' Wednesday 19:30-23:00: [[Openhackuarium_vol._69 |#OpenHackuarium vol. 60]] [http://hackteria.org Hackteria]: DIY bio in Indonesia and the Biology of cheese and wine. Part of a week-long experiment with [http://www.hesge.ch/head/en HEAD]: [http://hackteria.org/wiki/The_Art_of_BioHacking_-_HEAD The Art of BioHacking]<br />
::<li>'''2015.09.19-21''' A long week-end dedicated to biomusical innovation with the [[Living_Instruments| Living Instruments]] project<br />
::<li>'''2015.08.27''' Thursday 19:00-22:00: Lausanne Open Data vol. 1 ([http://www.meetup.com/Lausanne-Open-Data-Meetup/events/223762682/| more here])<br />
::<li>'''2015.08.26''' Wednesday 19:30-20:30: [[Openhackuarium_vol._60_%22Lac_Léman_Science_Hackathon%22_260815|#OpenHackuarium vol. 60: Do we need Lac Léman Science Hackathon?]]<br />
::<li>'''2015.08.20''' Thursday 19:00-22:00: Drone Racing 101<br />
::<li>'''2015.08.05''' Wednesday 19:30-20:30: [[Openhackuarium_vol._57_%22Bi%C3%A8re%22 | #OpenHackuarium vol. 57]] special Fermentation.<br />
::<li>'''2015.07.22''' Wednesday 19:30-20:30: [[Openhackuarium_vol._55_-_22.07.15 | #OpenHackuarium vol. 55]] special Urban/Vertical farming.<br />
::<li>'''2015.07.18''' Saturday 9:30-15:30: [[DNA_Party_workchoppe_vol.1 | A first DNA workshop/workchoppe]].<br />
::<li>'''2015.04.22''' Wednesday 19:30-20:30: General Assembly of Hackuarium association.<br />
::<li>'''2015.04.16''' Thursday 19:00-21:00: Discussion with Le Pansement, a medical students association.<br />
::<li>'''2015.04.15''' Wednesday 18:30-21:00: Practical Session "Garage Electrophoresis" with Le Pansement, a medical students association.<br />
::<li>'''2015.03.29''' Sunday 13:30-18:30: [[2nd_Hackuarium_Wiki_Sprint | Hackuarium Wiki Sprint #2]].<br />
::<li>'''2015.03.28''' Saturday 10:00-18:30: [[Open_DNA_Seq_Workshop | Open DNA Sequencing Workshop]].<br />
::<li>'''2015.02.18''' [[Visite_du_FlyLab_Paris_chez_nous| Drone night]] with Flylab Paris (part of La Paillasse) (FR).<br />
::<li>'''2014.12.07''' [[1st_Ever_Hackuarium_Wiki_Sprint | Hackuarium Wiki Sprint #1]].<br />
::<li>'''2014.11.27''' [[Events:BSNL_Roundtable | Roundtable at EPFL organised by BNSL]].<br />
::<li>'''2014.11.05''' [[Events:Bioart_NexTrends | NexTrends/ECAL Bioart conference]] at UniverCité.<br />
::<li>'''2014.10.22''' [[Events:Open_Access | Open Access conference]] at UniverCité.<br />
::<li>'''2014.10.09''' Conference by French artist [http://liagiraud.com Lia Giraud].<br />
::<li>'''2014.09.25-27''' [[Events:Design_Days_2014 | Design Days 2014]].<br />
::<li>'''2014.09.24''' Conference by [http://www.nicolasnova.net Nicolas Nova], co-fondateur du [http://nearfuturelaboratory.com Near Future Laboratory] et enseignant à la [http://www.hesge.ch/head/ HEAD], Genève.<br />
::<li>'''2014.08.27''' Introduction to [http://bricobio.org BricoBio] Montreal by Sarah Choukah.<br />
::<li>'''2014.08.20''' Introduction to [http://lapaillasse.org La Paillasse] Paris by Clément Epié and Nicolas Loubet.<br />
::<li>'''2014.06.06-07''' [http://hackteria.org/wiki/Tech4Dev Water Hackathon] organised by Hackteria.<br />
<br />
== Participation to External Events ==<br />
::<li>'''2014.11 - 2014.12''' [http://www.gasthauszumbaeren.ch//wire-lab/re-thinking-food- Re-Thinking Food], [http://www.gasthauszumbaeren.ch/de/home Gasthaus zum Bären], [http://www.thewire.ch/en/ W.I.R.E.], Zurich, Switzerland<br />
::<li>'''2014.09.25 - 2015.02.22''' [http://www.museedelamain.ch LAB/LIFE Exhibition], Musée de la Main, Lausanne, Switzerland<br />
<br />
=Projects=<br />
Here, you will find the projects going on in the Hackuarium.<br />
<br />
== Active Projects ==<br />
<br />
* [[Open-Food-DNA |Open-Food-DNA]]<br />
* [[BeerDeCoded]]<br />
* [[Living Instruments]]<br />
* [[Bience | Bience (Beer and Science!)]]<br />
* [[Protein purification systems]]<br />
* [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Micro to Macro Water Pollution]] - with [http://www.hammerdirt.ch/ Hammerdirt] and [http://biodesign.cc/ BIO-DESIGN for the REAL WORLD]<br />
* [[Spectro-pointer]]<br />
* [[Darty_Monkeys]]<br />
* [http://octanis.org/ Octanis]<br />
* [[Edible wall]]<br />
* [[ZéBU CH]]<br />
* [[Grow%26Mix_Bioink]]<br />
* [[unmapping]]<br />
* [[Compost Bacteria]]<br />
* [[AGiR! for genomic integrity]]<br />
<br />
== Archived Projects ==<br />
<br />
* [[Mycelium Structures]]<br />
* [[Live Type]]<br />
* [[Projects:LivingLab Design|LivingLab Design]]<br />
* [[Projects:bioluminescence|Bioluminescence]]<br />
* [[Projects:Quantitative Anthropology|Quantitative Anthropology]]<br />
* [[Projects:Impression 3D|Impression 3D]]<br />
* [[Projects:Dépollution des stands de tirs Suisses]]<br />
* [[Incubateur bon marché]]<br />
* [[Space Seed]]<br />
* [[Reception d'images satellites]]<br />
<br />
= Practical Informations =<br />
<br />
Following this [[ Media:Univercite map2-01.png | link]] you will find a general plan of Hackuarium.<br><br />
Following this [[ Media:map1.png | link]], you will find the plan of Hackuarium with the position of equipment.<br />
<br />
== [[Life_Main | Rules at Hackuarium]] ==<br />
[[Life_Main | This page ]] describe the code of conduct for Hackuarium members.<br />
<br />
== [[Protocols | Protocols]] ==<br />
All the protocols that we use at Hackuarium can be found [[ BioP_Main | here ]]<br />
They are detailed and structured so that the main focus is on applications. The idea is to give crucial information on how to apply the most common techniques of the Biology toolbox. The protocols are structured as follow:<br />
::<li> A scheme describing each <br />
::<li> A brief description of the protocol and its use<br />
::<li> A description of the different ways of carrying out the protocol. Ideally there should be a description of a commercial kit and a DIY kit.<br />
::<li> A description of the safety issues and best practice<br />
::<li> Information specific to Hackuarium and where to find the components, tools and reagents.<br />
<br />
== [[Instru_Main | Instruments available]] ==<br />
[[Instru_Main | This page ]] describes all the instruments available at Hackuarium (work in progress..), their location and how to use them.<br />
<br />
== [https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing Liste à jour de nos besoins en matériel] ==<br />
This document contains all the instruments and tools we need. If you happen to have a piece of equipment we are (or may be) looking for, [mailto:hello@hackuarium.ch contact us]!<br />
<br />
== [[Where we shop | Where we shop]] ==<br />
===Wetware===<br />
Consumables can be purchased from [http://www.huberlab.ch Huber Lab].<br />
<br />
Swiss-based [http://www.smiples.ch Smiples] has a very extensive listing of second hand laboratory and technical items. These can be bought from their online shop or from [https://www.ricardo.ch/online-shop/smiples/?SellerNickName=Smiples Ricardo].<br />
<br />
===Hardware===<br />
Options for electronic parts<br />
* [http://www.ebay.com Ebay] (international)<br />
* [http://www.aliexpress.com AliExpress] (China)<br />
* [https://www.adafruit.com Adafruit] (UK)<br />
<br><br />
* [http://www.seeedstudio.com/depot/ seeedstudio] (China)<br />
* [http://www.tmart.com/ Tmart] (Hong Kong)<br />
* [https://www.pi-shop.ch/ Rasberry pi shop] (Switzerland)<br />
* [http://www.distrelec.ch/ distrilec] (Switzerland)<br />
<br />
== Tools and Equipment found at Hackuarium ==<br />
<br />
::<li>[[Tools#Working_Equipment Working Equipment|Working Equipment]]<br />
::<li>[[Tools#Equipment_that_need_a_bit_of_fixing Needs Help|Equipment needing fixing]]<br />
::<li>[[Where we shop]]<br />
<br><br />
<br />
== [[Editing the wiki | How to built a new project page on our Wiki]] ==<br />
<br />
== Library and Reading List ==<br />
<br />
== Media and Press ==<br />
<br />
* Newsletter<br />
<br />
== Wanted ==<br />
Do you want to contribute to making Hackuarium a diverse and lively community? Check out our wanted lists:<br />
::<li>Skills<br />
::<li>Ideas<br />
::<li>[https://docs.google.com/spreadsheets/d/1agHVlyMzcg_cdjTlg8bABzjHnOc7Gu0B8v2FGhcEabU/edit?usp=sharing Equipment]<br />
::<li>Materials<br />
<br><br></div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=6775Micro to Macro Water Pollution2016-04-13T08:31:55Z<p>Sachiko: /* Relevant Links */</p>
<hr />
<div>== Background Information ==<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation can be found here:[http://www.slideshare.net/RogerErismann/hammerdirt-project-iii How we can work together]<br />
<br><br><br />
<br />
== Aims ==<br />
To answer: Does the presence of macropollutants on the shores of Lac Leman correlate with micropollutants (biological, chemical, particulate, etc.) in the lake water?<br />
<br><br><br />
<br />
== Brainstorm Results ==<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
<br />
== Collaboration Defined ==<br />
The collaboration between Hammerdirt and BIO-DESIGN for the REAL WORLD as of 2016<br><br />
1st stage:<br><br />
* water collection protocols appropriate for each read-out<br />
* coliform bacteria counting<br />
::* easygel<br />
::* DIY version<br />
* community bioreporter kit field version for Switzerland<br />
::* robust hardware<br />
::* easy to manipulate wetware (remove possibility of error in the protocol - including standard curve generation, etc.)<br />
* a water multimeter<br />
::* pH, conductivity, dissolved O2, temperature<br />
<br><br><br />
<br />
== Action Plans ==<br />
* Hammerdirt collects baseline and routine water samples for testing<br />
* Research what other relevant datasets are out there and document it<br />
<br><br><br />
=== Documentation and Collaboration Tools ===<br />
----<br />
Agree on documentation and collaboration tools<br />
* Internal communication - hackuarium slack<br />
* Calendar? - we have a biodesign google calendar<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
=== Water Collection Protocols ===<br />
----<br />
<br><br><br />
<br />
=== Coliform Bacteria Counting ===<br />
----<br />
Coliform bacteria is an indirect indication of fecal contamination of the waters. There are several methods to distinguish coliform bacteria vs other microorganisms that may grow on an agar plate.<br />
==== Easy Gel ====<br />
Micrology Labs [http://www.micrologylabs.com/page/93/Coliscan-Easygel Coliscan Easygel]<br />
* Rachel orders a coliform bacteria testing medium (done)<br />
[http://www.micrologylabs.com/page/95/Instructions Protocol] from the Micrology Labs<br><br />
==== DIY protocol ====<br />
<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br />
==== Other Methods ====<br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
----<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br />
<br />
=== Water Multi-meter ===<br />
----<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br><br />
<br />
== References ==<br />
=== Literature ===<br />
=== Relevant Links ===<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=6774Micro to Macro Water Pollution2016-04-13T08:30:27Z<p>Sachiko: /* Collaboration Defined */</p>
<hr />
<div>== Background Information ==<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation can be found here:[http://www.slideshare.net/RogerErismann/hammerdirt-project-iii How we can work together]<br />
<br><br><br />
<br />
== Aims ==<br />
To answer: Does the presence of macropollutants on the shores of Lac Leman correlate with micropollutants (biological, chemical, particulate, etc.) in the lake water?<br />
<br><br><br />
<br />
== Brainstorm Results ==<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
<br />
== Collaboration Defined ==<br />
The collaboration between Hammerdirt and BIO-DESIGN for the REAL WORLD as of 2016<br><br />
1st stage:<br><br />
* water collection protocols appropriate for each read-out<br />
* coliform bacteria counting<br />
::* easygel<br />
::* DIY version<br />
* community bioreporter kit field version for Switzerland<br />
::* robust hardware<br />
::* easy to manipulate wetware (remove possibility of error in the protocol - including standard curve generation, etc.)<br />
* a water multimeter<br />
::* pH, conductivity, dissolved O2, temperature<br />
<br><br><br />
<br />
== Action Plans ==<br />
* Hammerdirt collects baseline and routine water samples for testing<br />
* Research what other relevant datasets are out there and document it<br />
<br><br><br />
=== Documentation and Collaboration Tools ===<br />
----<br />
Agree on documentation and collaboration tools<br />
* Internal communication - hackuarium slack<br />
* Calendar? - we have a biodesign google calendar<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
=== Water Collection Protocols ===<br />
----<br />
<br><br><br />
<br />
=== Coliform Bacteria Counting ===<br />
----<br />
Coliform bacteria is an indirect indication of fecal contamination of the waters. There are several methods to distinguish coliform bacteria vs other microorganisms that may grow on an agar plate.<br />
==== Easy Gel ====<br />
Micrology Labs [http://www.micrologylabs.com/page/93/Coliscan-Easygel Coliscan Easygel]<br />
* Rachel orders a coliform bacteria testing medium (done)<br />
[http://www.micrologylabs.com/page/95/Instructions Protocol] from the Micrology Labs<br><br />
==== DIY protocol ====<br />
<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br />
==== Other Methods ====<br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
----<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br />
<br />
=== Water Multi-meter ===<br />
----<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br><br />
<br />
== Relevant Links ==<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=6773Micro to Macro Water Pollution2016-04-13T08:29:31Z<p>Sachiko: /* Water Collection Protocols */</p>
<hr />
<div>== Background Information ==<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation can be found here:[http://www.slideshare.net/RogerErismann/hammerdirt-project-iii How we can work together]<br />
<br><br><br />
<br />
== Aims ==<br />
To answer: Does the presence of macropollutants on the shores of Lac Leman correlate with micropollutants (biological, chemical, particulate, etc.) in the lake water?<br />
<br><br><br />
<br />
== Brainstorm Results ==<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
<br />
== Collaboration Defined ==<br />
The collaboration between Hammerdirt and BIO-DESIGN for the REAL WORLD as of 2016<br><br />
1st stage:<br><br />
* coliform bacteria counting<br />
::* easygel<br />
::* DIY version<br />
* community bioreporter kit field version for Switzerland<br />
::* robust hardware<br />
::* easy to manipulate wetware (remove possibility of error in the protocol - including standard curve generation, etc.)<br />
* a water multimeter<br />
::* pH, conductivity, dissolved O2, temperature<br />
<br><br><br />
<br />
== Action Plans ==<br />
* Hammerdirt collects baseline and routine water samples for testing<br />
* Research what other relevant datasets are out there and document it<br />
<br><br><br />
=== Documentation and Collaboration Tools ===<br />
----<br />
Agree on documentation and collaboration tools<br />
* Internal communication - hackuarium slack<br />
* Calendar? - we have a biodesign google calendar<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
=== Water Collection Protocols ===<br />
----<br />
<br><br><br />
<br />
=== Coliform Bacteria Counting ===<br />
----<br />
Coliform bacteria is an indirect indication of fecal contamination of the waters. There are several methods to distinguish coliform bacteria vs other microorganisms that may grow on an agar plate.<br />
==== Easy Gel ====<br />
Micrology Labs [http://www.micrologylabs.com/page/93/Coliscan-Easygel Coliscan Easygel]<br />
* Rachel orders a coliform bacteria testing medium (done)<br />
[http://www.micrologylabs.com/page/95/Instructions Protocol] from the Micrology Labs<br><br />
==== DIY protocol ====<br />
<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br />
==== Other Methods ====<br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
----<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br />
<br />
=== Water Multi-meter ===<br />
----<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br><br />
<br />
== Relevant Links ==<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=6772Micro to Macro Water Pollution2016-04-13T08:29:15Z<p>Sachiko: /* Documentation and Collaboration Tools */</p>
<hr />
<div>== Background Information ==<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation can be found here:[http://www.slideshare.net/RogerErismann/hammerdirt-project-iii How we can work together]<br />
<br><br><br />
<br />
== Aims ==<br />
To answer: Does the presence of macropollutants on the shores of Lac Leman correlate with micropollutants (biological, chemical, particulate, etc.) in the lake water?<br />
<br><br><br />
<br />
== Brainstorm Results ==<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
<br />
== Collaboration Defined ==<br />
The collaboration between Hammerdirt and BIO-DESIGN for the REAL WORLD as of 2016<br><br />
1st stage:<br><br />
* coliform bacteria counting<br />
::* easygel<br />
::* DIY version<br />
* community bioreporter kit field version for Switzerland<br />
::* robust hardware<br />
::* easy to manipulate wetware (remove possibility of error in the protocol - including standard curve generation, etc.)<br />
* a water multimeter<br />
::* pH, conductivity, dissolved O2, temperature<br />
<br><br><br />
<br />
== Action Plans ==<br />
* Hammerdirt collects baseline and routine water samples for testing<br />
* Research what other relevant datasets are out there and document it<br />
<br><br><br />
=== Documentation and Collaboration Tools ===<br />
----<br />
Agree on documentation and collaboration tools<br />
* Internal communication - hackuarium slack<br />
* Calendar? - we have a biodesign google calendar<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
=== Water Collection Protocols ===<br />
<br />
=== Coliform Bacteria Counting ===<br />
----<br />
Coliform bacteria is an indirect indication of fecal contamination of the waters. There are several methods to distinguish coliform bacteria vs other microorganisms that may grow on an agar plate.<br />
==== Easy Gel ====<br />
Micrology Labs [http://www.micrologylabs.com/page/93/Coliscan-Easygel Coliscan Easygel]<br />
* Rachel orders a coliform bacteria testing medium (done)<br />
[http://www.micrologylabs.com/page/95/Instructions Protocol] from the Micrology Labs<br><br />
==== DIY protocol ====<br />
<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br />
==== Other Methods ====<br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
----<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br />
<br />
=== Water Multi-meter ===<br />
----<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br><br />
<br />
== Relevant Links ==<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=6768Micro to Macro Water Pollution2016-04-07T17:45:01Z<p>Sachiko: /* Community Bioreporter Kit for Switzerland */</p>
<hr />
<div>== Background Information ==<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation can be found here:<br />
<br><br><br />
<br />
== Aims ==<br />
To answer: Does the presence of macropollutants on the shores of Lac Leman correlate with micropollutants (biological, chemical, particulate, etc.) in the lake water?<br />
<br><br><br />
<br />
== Brainstorm Results ==<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
<br />
== Collaboration Defined ==<br />
The collaboration between Hammerdirt and BIO-DESIGN for the REAL WORLD as of 2016<br><br />
1st stage:<br><br />
* coliform bacteria counting<br />
::* easygel<br />
::* DIY version<br />
* community bioreporter kit field version for Switzerland<br />
::* robust hardware<br />
::* easy to manipulate wetware (remove possibility of error in the protocol - including standard curve generation, etc.)<br />
* a water multimeter<br />
::* pH, conductivity, dissolved O2, temperature<br />
<br><br><br />
<br />
== Action Plans ==<br />
* Hammerdirt collects baseline and routine water samples for testing<br />
* Research what other relevant datasets are out there and document it<br />
<br><br><br />
=== Documentation and Collaboration Tools ===<br />
----<br />
Agree on documentation and collaboration tools<br />
* Internal communication - hackuarium slack<br />
* Calendar? - we have a biodesign google calendar<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
=== Coliform Bacteria Counting ===<br />
----<br />
Coliform bacteria is an indirect indication of fecal contamination of the waters. There are several methods to distinguish coliform bacteria vs other microorganisms that may grow on an agar plate.<br />
==== Easy Gel ====<br />
Micrology Labs [http://www.micrologylabs.com/page/93/Coliscan-Easygel Coliscan Easygel]<br />
* Rachel orders a coliform bacteria testing medium (done)<br />
[http://www.micrologylabs.com/page/95/Instructions Protocol] from the Micrology Labs<br><br />
==== DIY protocol ====<br />
<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br />
==== Other Methods ====<br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
----<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br />
<br />
=== Water Multi-meter ===<br />
----<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br><br />
<br />
== Relevant Links ==<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=6767Micro to Macro Water Pollution2016-04-07T17:44:40Z<p>Sachiko: /* Other Methods */</p>
<hr />
<div>== Background Information ==<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation can be found here:<br />
<br><br><br />
<br />
== Aims ==<br />
To answer: Does the presence of macropollutants on the shores of Lac Leman correlate with micropollutants (biological, chemical, particulate, etc.) in the lake water?<br />
<br><br><br />
<br />
== Brainstorm Results ==<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
<br />
== Collaboration Defined ==<br />
The collaboration between Hammerdirt and BIO-DESIGN for the REAL WORLD as of 2016<br><br />
1st stage:<br><br />
* coliform bacteria counting<br />
::* easygel<br />
::* DIY version<br />
* community bioreporter kit field version for Switzerland<br />
::* robust hardware<br />
::* easy to manipulate wetware (remove possibility of error in the protocol - including standard curve generation, etc.)<br />
* a water multimeter<br />
::* pH, conductivity, dissolved O2, temperature<br />
<br><br><br />
<br />
== Action Plans ==<br />
* Hammerdirt collects baseline and routine water samples for testing<br />
* Research what other relevant datasets are out there and document it<br />
<br><br><br />
=== Documentation and Collaboration Tools ===<br />
----<br />
Agree on documentation and collaboration tools<br />
* Internal communication - hackuarium slack<br />
* Calendar? - we have a biodesign google calendar<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
=== Coliform Bacteria Counting ===<br />
----<br />
Coliform bacteria is an indirect indication of fecal contamination of the waters. There are several methods to distinguish coliform bacteria vs other microorganisms that may grow on an agar plate.<br />
==== Easy Gel ====<br />
Micrology Labs [http://www.micrologylabs.com/page/93/Coliscan-Easygel Coliscan Easygel]<br />
* Rachel orders a coliform bacteria testing medium (done)<br />
[http://www.micrologylabs.com/page/95/Instructions Protocol] from the Micrology Labs<br><br />
==== DIY protocol ====<br />
<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br />
==== Other Methods ====<br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
----<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br><br />
=== Water Multi-meter ===<br />
----<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br><br />
<br />
== Relevant Links ==<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=6766Micro to Macro Water Pollution2016-04-07T17:44:27Z<p>Sachiko: /* Coliform Bacteria Counting */</p>
<hr />
<div>== Background Information ==<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation can be found here:<br />
<br><br><br />
<br />
== Aims ==<br />
To answer: Does the presence of macropollutants on the shores of Lac Leman correlate with micropollutants (biological, chemical, particulate, etc.) in the lake water?<br />
<br><br><br />
<br />
== Brainstorm Results ==<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
<br />
== Collaboration Defined ==<br />
The collaboration between Hammerdirt and BIO-DESIGN for the REAL WORLD as of 2016<br><br />
1st stage:<br><br />
* coliform bacteria counting<br />
::* easygel<br />
::* DIY version<br />
* community bioreporter kit field version for Switzerland<br />
::* robust hardware<br />
::* easy to manipulate wetware (remove possibility of error in the protocol - including standard curve generation, etc.)<br />
* a water multimeter<br />
::* pH, conductivity, dissolved O2, temperature<br />
<br><br><br />
<br />
== Action Plans ==<br />
* Hammerdirt collects baseline and routine water samples for testing<br />
* Research what other relevant datasets are out there and document it<br />
<br><br><br />
=== Documentation and Collaboration Tools ===<br />
----<br />
Agree on documentation and collaboration tools<br />
* Internal communication - hackuarium slack<br />
* Calendar? - we have a biodesign google calendar<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
=== Coliform Bacteria Counting ===<br />
----<br />
Coliform bacteria is an indirect indication of fecal contamination of the waters. There are several methods to distinguish coliform bacteria vs other microorganisms that may grow on an agar plate.<br />
==== Easy Gel ====<br />
Micrology Labs [http://www.micrologylabs.com/page/93/Coliscan-Easygel Coliscan Easygel]<br />
* Rachel orders a coliform bacteria testing medium (done)<br />
[http://www.micrologylabs.com/page/95/Instructions Protocol] from the Micrology Labs<br><br />
==== DIY protocol ====<br />
<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br />
==== Other Methods ====<br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br><br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
----<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br><br />
=== Water Multi-meter ===<br />
----<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br><br />
<br />
== Relevant Links ==<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=6765Micro to Macro Water Pollution2016-04-07T17:43:52Z<p>Sachiko: /* Coliform Bacteria Counting */</p>
<hr />
<div>== Background Information ==<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation can be found here:<br />
<br><br><br />
<br />
== Aims ==<br />
To answer: Does the presence of macropollutants on the shores of Lac Leman correlate with micropollutants (biological, chemical, particulate, etc.) in the lake water?<br />
<br><br><br />
<br />
== Brainstorm Results ==<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
<br />
== Collaboration Defined ==<br />
The collaboration between Hammerdirt and BIO-DESIGN for the REAL WORLD as of 2016<br><br />
1st stage:<br><br />
* coliform bacteria counting<br />
::* easygel<br />
::* DIY version<br />
* community bioreporter kit field version for Switzerland<br />
::* robust hardware<br />
::* easy to manipulate wetware (remove possibility of error in the protocol - including standard curve generation, etc.)<br />
* a water multimeter<br />
::* pH, conductivity, dissolved O2, temperature<br />
<br><br><br />
<br />
== Action Plans ==<br />
* Hammerdirt collects baseline and routine water samples for testing<br />
* Research what other relevant datasets are out there and document it<br />
<br><br><br />
=== Documentation and Collaboration Tools ===<br />
----<br />
Agree on documentation and collaboration tools<br />
* Internal communication - hackuarium slack<br />
* Calendar? - we have a biodesign google calendar<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
=== Coliform Bacteria Counting ===<br />
----<br />
Coliform bacteria is an indirect indication of fecal contamination of the waters. There are several methods to distinguish coliform bacteria vs other microorganisms that may grow on an agar plate.<br />
==== Easy Gel ====<br />
Micrology Labs [http://www.micrologylabs.com/page/93/Coliscan-Easygel Coliscan Easygel]<br />
* Rachel orders a coliform bacteria testing medium (done)<br />
[http://www.micrologylabs.com/page/95/Instructions Protocol] from the Micrology Labs<br><br />
==== DIY protocol ====<br />
<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br><br />
==== Other Methods ====<br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br><br><br />
<br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br><br />
<br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
----<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br><br />
=== Water Multi-meter ===<br />
----<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br><br />
<br />
== Relevant Links ==<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=6764Micro to Macro Water Pollution2016-04-07T17:39:15Z<p>Sachiko: /* Collaboration Defined */</p>
<hr />
<div>== Background Information ==<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation can be found here:<br />
<br><br><br />
<br />
== Aims ==<br />
To answer: Does the presence of macropollutants on the shores of Lac Leman correlate with micropollutants (biological, chemical, particulate, etc.) in the lake water?<br />
<br><br><br />
<br />
== Brainstorm Results ==<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
<br />
== Collaboration Defined ==<br />
The collaboration between Hammerdirt and BIO-DESIGN for the REAL WORLD as of 2016<br><br />
1st stage:<br><br />
* coliform bacteria counting<br />
::* easygel<br />
::* DIY version<br />
* community bioreporter kit field version for Switzerland<br />
::* robust hardware<br />
::* easy to manipulate wetware (remove possibility of error in the protocol - including standard curve generation, etc.)<br />
* a water multimeter<br />
::* pH, conductivity, dissolved O2, temperature<br />
<br><br><br />
<br />
== Action Plans ==<br />
* Hammerdirt collects baseline and routine water samples for testing<br />
* Research what other relevant datasets are out there and document it<br />
<br><br><br />
=== Documentation and Collaboration Tools ===<br />
----<br />
Agree on documentation and collaboration tools<br />
* Internal communication - hackuarium slack<br />
* Calendar? - we have a biodesign google calendar<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
=== Coliform Bacteria Counting ===<br />
----<br />
Coliform bacteria is an indirect indication of fecal contamination of the waters. There are several methods to distinguish coliform bacteria vs other microorganisms that may grow on an agar plate.<br />
<br />
<br />
==== Easy Gel ====<br />
<br />
* Rachel orders a coliform bacteria testing medium (done)<br />
<br><br><br />
==== DIY protocol ====<br />
<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br><br />
==== Other Methods ====<br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br><br><br />
<br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br><br />
<br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
----<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br><br />
=== Water Multi-meter ===<br />
----<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br><br />
<br />
== Relevant Links ==<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=6763Micro to Macro Water Pollution2016-04-07T17:37:45Z<p>Sachiko: /* Action Plans */</p>
<hr />
<div>== Background Information ==<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation can be found here:<br />
<br><br><br />
<br />
== Aims ==<br />
To answer: Does the presence of macropollutants on the shores of Lac Leman correlate with micropollutants (biological, chemical, particulate, etc.) in the lake water?<br />
<br><br><br />
<br />
== Brainstorm Results ==<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
<br />
== Collaboration Defined ==<br />
1st stage:<br><br />
* coliform bacteria counting<br />
::* easygel<br />
::* DIY version<br />
* community bioreporter kit field version for Switzerland<br />
::* robust hardware<br />
::* easy to manipulate wetware (remove possibility of error in the protocol - including standard curve generation, etc.)<br />
* a water multimeter<br />
::* pH, conductivity, dissolved O2, temperature<br />
<br><br><br />
<br />
<br />
== Action Plans ==<br />
* Hammerdirt collects baseline and routine water samples for testing<br />
* Research what other relevant datasets are out there and document it<br />
<br><br><br />
=== Documentation and Collaboration Tools ===<br />
----<br />
Agree on documentation and collaboration tools<br />
* Internal communication - hackuarium slack<br />
* Calendar? - we have a biodesign google calendar<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
=== Coliform Bacteria Counting ===<br />
----<br />
Coliform bacteria is an indirect indication of fecal contamination of the waters. There are several methods to distinguish coliform bacteria vs other microorganisms that may grow on an agar plate.<br />
<br />
<br />
==== Easy Gel ====<br />
<br />
* Rachel orders a coliform bacteria testing medium (done)<br />
<br><br><br />
==== DIY protocol ====<br />
<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br><br />
==== Other Methods ====<br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br><br><br />
<br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br><br />
<br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
----<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br><br />
=== Water Multi-meter ===<br />
----<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br><br />
<br />
== Relevant Links ==<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=6762Micro to Macro Water Pollution2016-04-07T17:20:43Z<p>Sachiko: </p>
<hr />
<div>== Background Information ==<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation can be found here:<br />
<br><br><br />
<br />
== Aims ==<br />
To answer: Does the presence of macropollutants on the shores of Lac Leman correlate with micropollutants (biological, chemical, particulate, etc.) in the lake water?<br />
<br><br><br />
<br />
== Brainstorm Results ==<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, conductivity, temperature<br />
::* DIY free NH2<br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
<br />
* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
<br />
<br />
== Collaboration Defined ==<br />
1st stage:<br><br />
* coliform bacteria counting<br />
::* easygel<br />
::* DIY version<br />
* community bioreporter kit field version for Switzerland<br />
::* robust hardware<br />
::* easy to manipulate wetware (remove possibility of error in the protocol - including standard curve generation, etc.)<br />
* a water multimeter<br />
::* pH, conductivity, dissolved O2, temperature<br />
<br><br><br />
<br />
<br />
== Action Plans ==<br />
<br />
* Hammerdirt collects some water samples for testing<br />
* Rachel orders a coliform bacteria testing medium (done)<br />
* Research what other relevant datasets are out there and document it<br />
=== Documentation and Collaboration Tools ===<br />
* Protocols - [http://openwetware.org/]?<br />
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events? <br />
* Data entry and sharing - Hammerdirt github, compliance with the international standards<br />
* Hardware design - [https://github.com/BioDesignRealWorld biodesign github]<br />
<br><br><br />
<br />
=== Coliform Bacteria Counting ===<br />
Coliform bacteria is an indirect indication of fecal contamination of the waters. There are several methods to distinguish coliform bacteria vs other microorganisms that may grow on an agar plate.<br />
<br />
<br />
==== Easy Gel ====<br />
<br><br><br />
==== DIY protocol ====<br />
==== Automatic Colony Counter and Plate Counting ====<br />
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]<br />
<br><br><br />
From Lifepatch, we have set this up [http://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ DIY automatic colony counter].<br />
<br><br><br />
==== Other Methods ====<br />
Biodesign has tried:<br><br />
* [http://biodesign.cc/2013/03/28/coliform-bacteria-detection-by-pcr/ Hack-a-Taq]<br />
* This [http://biodesign.cc/2013/03/15/mobile-lab-ase-coli-detection/ early post] has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.<br />
<br><br><br />
<br />
==== Scaling ====<br />
Basic calculation for cost for one time analysis:<br />
<br><br><br />
<br />
:: number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control<br />
<br />
<br><br><br />
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.<br />
<br><br><br />
<br />
=== Community Bioreporter Kit for Switzerland ===<br />
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.<br />
* The protocol for the bioreporter assay needs to be simplified.<br />
Otherwise, the [http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field system for working with the bioreporters] has been [http://biodesign.cc/2014/08/29/field-testing-approved/ approved with the Swiss authorities].<br />
<br />
<br><br><br />
=== Water Multi-meter ===<br />
* (Art)ScienceBLR<br />
* Student Project 2016<br />
<br><br><br />
== Relevant Links ==<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]<br />
<br />
Electronic Lab Notebooks<br />
* [http://bioinformatics.oxfordjournals.org/content/29/13/1710.long A universal open-source Electronic Laboratory Notebook] Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Unmapping&diff=6575Unmapping2016-03-18T18:02:07Z<p>Sachiko: /* Conjuring beyond 2D */</p>
<hr />
<div><span style="font-family:Georgia;"><br />
<big>"It is not down in any map; true places never are."</big><br><br />
:::::::::<small>- Herman Melville, ''Moby Dick'', 1888</small><br><br />
</span><br />
<br><br />
=WHAT=<br />
Inspired by the conversations of the first D+arty Monkeys [[Darty_Monkeys#Virtual_roundtable_09.2F10.01.16 Global Virtual Hangouts]] on 9 January 2016, we found a common thread. UN-MAPPING.<br><br />
While mapping immediately conjures associations (matrix operations, physical maps, cartography, GPS tracking, ...) we would like to turn mapping around to ask what it can be.<br><br />
<br />
<br><br />
These are the beginnings of brainstorms. More soon...<br />
<br><br><br />
<br />
=WHO=<br />
* Vanessa - explore digital media to unfold information otherwise from nature and environment.<br />
* Sachiko - my interest is to deconstruct the ideas of [http://biodesign.cc/2014/05/05/mapping-in-yogyakarta/ mapping] around the BIODESIGN for the REAL WORLD project<br />
<br><br />
<br />
=HOW=<br />
This is a process to define what unmapping as a process could be<br><br />
Some directional questions in our minds: <br><br />
* how could mapping be if we removed the anthropocentric perspective?<br />
* what if north is not north?<br />
* what is a map if it comes from rememberance?<br />
<br><br />
<br />
=Inspirations=<br />
===Unconference===<br />
* 24 hrs. The Unconference PARENTHESIS - An Unconference organized by SARN :: Swiss Artistic Research Network [https://vimeo.com/122789999]<br />
<br />
===Remembrance===<br />
* Tega Brain Kilowatt-Hours [http://tegabrain.com/KiloWatt-Hours]: "Over time, the work forgets"<br />
<br />
* [http://www.tessmartinart.com/breda-on-my-mind/ Breda on my Mind]: a project by artist Tess Martin where people are invited to draw a map of their city from memory. ([https://vimeo.com/85241916 short clip on the making of])<br />
<br />
* [http://sensorymaps.com Sensory Maps]: the site of Kate McLean, an artist and designer, creator of smellmaps. "alternative sensory modes for individual and shared interpretation of place" ([http://sensorymaps.blogspot.ch her blog]).<br />
<br />
* [http://singaporerivermap.blogspot.ch/2010/09/documentation-shape-of-singapore-river.html Shape of Singapore River]: artist/archivist/cartographer Debbie Ding's 20 illustrations based on collected sketches made by people and what they think the shape of the Singapore River looks like, without making reference to anything else.<br />
<br />
* "Converging, layered ecologies" - an art&science field laboratory about converging ecologies Fieldnotes Hybridmatters [http://fieldnotes.hybridmatters.net/]<br />
<br />
* World Day of Water: In 2016, the theme is "Water and Jobs," [http://www.unwater.org/campaigns/world-water-day/en/]<br />
<br />
===Interactivity===<br />
* Waterwheel is an interactive, collaborative platform for sharing media, knowledge, ideas, performances and presentations about or inspired by water. [http://water-wheel.net/]<br />
* Interactive topography sand box [https://www.facebook.com/video.php?v=1420726251558170]<br />
<br />
===Conjuring beyond 2D===<br />
<br />
* Adrien Siegal's Mollata Meander [http://www.adriensegal.com/#!molalla-meander/c1wj6]: alluvial flows over 15 years of a section of the Molalla River in the Cascade Range of Clackamas County in NW Oregon<br />
<br />
* Luke Jerram's Tōhoku Japanese Earthquake [http://www.lukejerram.com/tohoku-japanese-earthquake/]: sculpture seismogram of the 2011 earthquake<br />
<br />
* Crime Reports by information designer Sha [http://postarchitectural.com/Crime-Reports]<br />
<br />
* Trash collages - Your junk is beautiful [https://youtu.be/eEfKXCbi154]<br />
<br />
* Hard Data by R. Luke DuBois string quartet and website, 2009 [http://archive.turbulence.org/Works/harddata/]: "open-source “information score” of the U.S.- led war in Iraq, taking economic, social (including casualty), political, and cultural statistics from both Iraq and the United States over the course of the war and placing them on a timeline."<br />
<br />
* The Center for Genomic Gastronomy 2011 [http://genomicgastronomy.com/work/2011-2/smog-tasting/ Smog Tasting] - uses egg foams to harvest air pollution. Smog from different locations can be tasted and compared. and a subsequent sonification 2015: [http://genomicgastronomy.com/work/2015-2/smog-synthesizer/ Smog Synthesizer]<br />
<br />
* "White clothing becomes grey after a few hours" Environmental science: Pollution patrol by Kat Austen, Nature 2015[http://www.nature.com/news/environmental-science-pollution-patrol-1.16654]<br />
<br />
* 3D map as a music player [https://youtu.be/XdE_L-cOwM0 Citymusic project] by Akko Goldenbeld<br />
<br />
<br />
<br><br></div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Unmapping&diff=6574Unmapping2016-03-18T18:01:36Z<p>Sachiko: /* Inspirations */</p>
<hr />
<div><span style="font-family:Georgia;"><br />
<big>"It is not down in any map; true places never are."</big><br><br />
:::::::::<small>- Herman Melville, ''Moby Dick'', 1888</small><br><br />
</span><br />
<br><br />
=WHAT=<br />
Inspired by the conversations of the first D+arty Monkeys [[Darty_Monkeys#Virtual_roundtable_09.2F10.01.16 Global Virtual Hangouts]] on 9 January 2016, we found a common thread. UN-MAPPING.<br><br />
While mapping immediately conjures associations (matrix operations, physical maps, cartography, GPS tracking, ...) we would like to turn mapping around to ask what it can be.<br><br />
<br />
<br><br />
These are the beginnings of brainstorms. More soon...<br />
<br><br><br />
<br />
=WHO=<br />
* Vanessa - explore digital media to unfold information otherwise from nature and environment.<br />
* Sachiko - my interest is to deconstruct the ideas of [http://biodesign.cc/2014/05/05/mapping-in-yogyakarta/ mapping] around the BIODESIGN for the REAL WORLD project<br />
<br><br />
<br />
=HOW=<br />
This is a process to define what unmapping as a process could be<br><br />
Some directional questions in our minds: <br><br />
* how could mapping be if we removed the anthropocentric perspective?<br />
* what if north is not north?<br />
* what is a map if it comes from rememberance?<br />
<br><br />
<br />
=Inspirations=<br />
===Unconference===<br />
* 24 hrs. The Unconference PARENTHESIS - An Unconference organized by SARN :: Swiss Artistic Research Network [https://vimeo.com/122789999]<br />
<br />
===Remembrance===<br />
* Tega Brain Kilowatt-Hours [http://tegabrain.com/KiloWatt-Hours]: "Over time, the work forgets"<br />
<br />
* [http://www.tessmartinart.com/breda-on-my-mind/ Breda on my Mind]: a project by artist Tess Martin where people are invited to draw a map of their city from memory. ([https://vimeo.com/85241916 short clip on the making of])<br />
<br />
* [http://sensorymaps.com Sensory Maps]: the site of Kate McLean, an artist and designer, creator of smellmaps. "alternative sensory modes for individual and shared interpretation of place" ([http://sensorymaps.blogspot.ch her blog]).<br />
<br />
* [http://singaporerivermap.blogspot.ch/2010/09/documentation-shape-of-singapore-river.html Shape of Singapore River]: artist/archivist/cartographer Debbie Ding's 20 illustrations based on collected sketches made by people and what they think the shape of the Singapore River looks like, without making reference to anything else.<br />
<br />
* "Converging, layered ecologies" - an art&science field laboratory about converging ecologies Fieldnotes Hybridmatters [http://fieldnotes.hybridmatters.net/]<br />
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* World Day of Water: In 2016, the theme is "Water and Jobs," [http://www.unwater.org/campaigns/world-water-day/en/]<br />
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===Interactivity===<br />
* Waterwheel is an interactive, collaborative platform for sharing media, knowledge, ideas, performances and presentations about or inspired by water. [http://water-wheel.net/]<br />
* Interactive topography sand box [https://www.facebook.com/video.php?v=1420726251558170]<br />
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===Conjuring beyond 2D===<br />
<br />
* Adrien Siegal's Mollata Meander [http://www.adriensegal.com/#!molalla-meander/c1wj6]: alluvial flows over 15 years of a section of the Molalla River in the Cascade Range of Clackamas County in NW Oregon<br />
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* Luke Jerram's Tōhoku Japanese Earthquake [http://www.lukejerram.com/tohoku-japanese-earthquake/]: sculpture seismogram of the 2011 earthquake<br />
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* Crime Reports by information designer Sha [http://postarchitectural.com/Crime-Reports]<br />
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* Trash collages - Your junk is beautiful [https://youtu.be/eEfKXCbi154]<br />
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* Hard Data by R. Luke DuBois string quartet and website, 2009 [http://archive.turbulence.org/Works/harddata/]: "open-source “information score” of the U.S.- led war in Iraq, taking economic, social (including casualty), political, and cultural statistics from both Iraq and the United States over the course of the war and placing them on a timeline."<br />
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* The Center for Genomic Gastronomy 2011 [http://genomicgastronomy.com/work/2011-2/smog-tasting/ Smog Tasting] - uses egg foams to harvest air pollution. Smog from different locations can be tasted and compared. and a subsequent sonification 2015: [http://genomicgastronomy.com/work/2015-2/smog-synthesizer/ Smog Synthesizer]<br />
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* "White clothing becomes grey after a few hours" Environmental science: Pollution patrol by Kat Austen, Nature 2015[http://www.nature.com/news/environmental-science-pollution-patrol-1.16654]<br />
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* Map as a music player [https://youtu.be/XdE_L-cOwM0 Citymusic project] by Akko Goldenbeld</div>Sachikohttps://wiki.hackuarium.ch/index.php?title=Micro_to_Macro_Water_Pollution&diff=6569Micro to Macro Water Pollution2016-03-14T10:28:07Z<p>Sachiko: /* Relevant Links */</p>
<hr />
<div>== Background Information ==<br />
[http://www.hammerdirt.ch/ Hammerdirt] came to the [http://biodesign.cc BIO-DESIGN for the REAL WORLD]'s [http://wiki.biodesign.cc/wiki/Winter_School Winter School] with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.<br />
<br><br />
The presentation can be found here:<br />
<br><br><br />
<br />
== Aims ==<br />
To answer: Does the presence of macropollutants on the shores of Lac Leman correlate with micropollutants (biological, chemical, particulate, etc.) in the lake water?<br />
<br><br><br />
<br />
== Brainstorm Results ==<br />
[[File:hammerdirt_todolist.jpg|200px|thumb|right|brainstorm board]]<br />
At Open Hackuarium #88, we came up with some initial ideas.<br />
<br />
* Data Analysis<br />
::* Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach<br />
::* synching the above data with a phone application in the internationally accepted format<br />
::* Add lake existing data (lake current, meterology, etc.)<br />
<br />
* Water collection and Analysis<br />
::* Standardizing Collection Methods <br />
::* Water chemistry testing - turbidity, pO2, pH, <br />
::* Microparticle counting - DIY<br />
::* Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or<br />
::* Make a fluorescent plate reader for higher throughput '''(CAUTION: still need P1 to use bioreporters here)'''<br />
::* antibiotic resistant bacteria '''(CAUTION: we cannot amplify/concentrate possible pathogens)'''<br />
::* Fish diseases - ask Maison de la Rivière?<br />
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* Awareness Raising - Recycling<br />
::* Recycle plastics using the extruder and use it to 3D print objects<br />
::* Biodegradation with mycelium<br />
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== Action Plans ==<br />
* Hammerdirt collects some water samples for testing<br />
* Rachel orders a coliform bacteria testing medium (done)<br />
* Research what other relevant datasets are out there and document it<br />
<br />
== Relevant Links ==<br />
Discard Studies publishes interesting articles on Water Pollution<br />
* [http://discardstudies.com/2016/01/29/cfp-pharmaceuticals-out-of-bounds/ Pharmaceuticals Out of Bounds] - conference coming up in 2016<br />
* [http://discardstudies.com/2015/12/21/building-diy-citizen-science-technology-to-see-invisible-marine-plastics/ DIY Plastics Collector "Babylegs"]<br />
* [http://discardstudies.com/2016/01/19/article-alert-redefining-pollution-and-action-the-matter-of-plastics/ Redefining pollution and action - article]</div>Sachiko