Winter School

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BRAAVOO Workshop and Creative Design Course / Winter School, Biodesign for the Real World


Welcome to the wiki page about the BRAAVOO Workshop and Creative Design Course & Biodesign for the Real World Winter School!
Participants will build a bioreporter (molecular biology) and a DIY fluorescence detector. There will be hands-on activities, evening lectures and a special visit to Hackuarium, the local biohackerspace.

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Short Description

The oil-responsive bacterial biosensor cell culture 'lights up' with green fluorescence signal in oil-contaminated liquids

The BRAAVOO Workshop and Creative Design Course, organized in collaboration with the Envirobot Project and BioDesign for the Real World, will provide an opportunity for 5 days of intensive learning and hands-on experience in biosensor theory and practice, culminating with the construction and use of both a bacterial biosensor and a field-portable DIY fluorescence detector. The course will offer possibilities to design, produce, and test a variety of heavy metal or organic compound biosensors.

Course lectures will be given in English, and are planned to offer a dynamic and interactive opportunity to explore aspects of biosensor development and use in environmental monitoring.

The program will furthermore include evening lectures, a visit to Hackuarium, a local biohacker space, and a public discussion about the course and use of biosensors to detect pollutants.

An announcement of this 'DIY biosensor' course
and
the announcement about the public discussion, which will also be seen in the local metro during the week of the course,
BRAAVOO Announcement TSOL 8.jpg

are available here to pass on to anyone interested.

Independent researchers, artists, Master and PhD students and postdoctoral fellows at the interface between microbiology and engineering are particularly invited to attend.
The idea is to encourage multidisciplinary integration of biology and engineering to help solve real-world problems.

When

  • 31 January 2016 (SUN): Arrival
  • 01-05 February 2016 (MON-FRI): Hands-on-Sessions and evening lectures
  • 06 February 2016 (SAT): Departure

Enrollment

You must enroll to be selected for the 20 places available for the course.
In order to be considered for participation, please fill in the form.

Certificates of participation will be provided after successful completion of the course, and each participant can come home with a DIY fluorescence sensor rig!

Important Dates and Deadlines

  • 01 November 2015: Enrollment form open
  • 11 December 2015: deadline for registration
  • 16 December 2015: Candidates will be informed about acceptance to the course
  • 23 December 2015: Fees due, to guarantee participation in the course for accepted candidates


Special news (18 December)
20 candidates have been informed of their acceptance and invited to pay the appropriate fee, but others are still welcome to register their interest (just in case...)!

Fees

  • Independent researchers, Masters students: 150chf
  • PhD students, and postdoctoral researchers: 300chf
  • Senior researchers: 350chf
  • Corporate/Industrial participants: 500chf


These fees will include all training materials, use of facilities, lunches, five dinners and coffee breaks.
The registration fee does not include costs of accommodation, travel or transport to the UNIL.

Participants are encouraged to take advantage of research travel scholarships and other funding opportunities.
Interested people without sufficient financial resources may directly contact Jan Roelof van der Meer (janroelof.vandermeer@unil.ch).

Payment should be made by bank transfer to the UNIL, with relevant account details provided in your acceptance note, which will be sent to the email address provided in the the online registration form after 16 December 2015.
Please make sure to include the comment ‘BRAAVOO Creative Design Course’ and your full name, when making your payment.

Each participant’s place in the course will only be guaranteed once payment has been received.

Venues

UNIL Amphipole and Teaching Labs
Unil map.jpg
Here is a a clickable map of the UNIL.
Evening lectures will be held in the seminar room of the Biophore (2917.2)

Other points of interest.

Accomodations and Travel

The participant is responsible for their own accommodation and travel costs.
(Please take advantage of travel scholarships, and funding, as mentioned above.)
Participants are requested to organize their own hotel reservations to stay locally 6 nights (31Jan-5Feb).
Accommodation exchanges will be possible, matching out-of-town guests with in-town participants.

  • Lausanne has several nice airbnb options - recommended to stay in a place accessible by the m1 or m2 metro lines
  • The Lausanne tourism office can also facilitate finding accommodation and any further site-seeing plans participants might make to further explore the region.

Accommodation Exchange HOST/GUESTs

At this point, we have 9 people who would like to be guests of local hosts, and all is set.


Tentative Program

microbiology course at UNIL

Sunday, 31 January 2016

Arrival (UNIL, Biophore)
16h Registration and Welcome

‘speed-dating’ among participants
Social Dinner in Lausanne

Monday, 1 February 2016

8h30 - 12h Biosensor design: introduction, preparation of DNA parts
12-13h30 lunch
13h30 - 17h Electronic design: introduction, and assembly
18h dinner
19h30 Lecture: Shimshon Belkin, Bacterial biosensors and applications

Tuesday, 2 February 2016

8h30 - 12h Biosensor construction: parts ligation and transformations
12-13h30 lunch
13h30 - 17h Sensor building: soldering and programming
18h dinner
19h30 Lecture: Vivian Lu & Kristin Schirmer, Using live cells for ecotoxicology assessment

Wednesday, 3 February 2016

8h30 - 12h Biosensor building: verifying constructions, storage, test preparations
12-13h30 lunch
13h30 - 17h Sensor building: testing electronic functions
17h30 Lecture: Laura Lechuga, Principles and applications of nanoimmunobiosensors
19h Visit Hackuarium, DIYBio biohackerspace - Renens
Round-table and brainstorming (and invitation to Friday’s Public Event)

Thursday, 4 February 2016

8h30 - 12h Calibration of biosensor responses in standard laboratory settings
12-13h30 lunch
13h30 - 17 h Biosensor testing on field samples
18h Dinner
19h30 Lecture: Auke Ijspeert, Robotics and automated sensor platforms

Friday, 5 February 2016

08h30 – 12h As necessary: repetition of biosensor experiments, wrapping up results, quantitative data analyses
12-13h30 lunch
13h30 - 14h30 Preparation for Public Event - Debriefing from the week + move to l'éprouvette for space preparation
15h30-17h30 OPEN PUBLIC EVENT of the BRAAVOO Workshop and Creative Design Course: transdisciplinary workshops and environmental biosensors, Public Discussion at the Eprouvette a public lab at the UNIL.

19h30 Farewell dinner for Participants

Planned OPEN Events

Hackuarium CC_BY_SA 3.0 funambuline

Hackuarium Visit



WHAT: Meet the local biohacking scene, at Hackuarium's OpenHackuarium night at UniverCité.
WHEN: 3 February 2016, starting 19:00pm
WHERE:Hackuarium how to get there


transdisciplinary workshops and environmental biosensors: Public Discussion


BRAAVOO Announcement TSOL 8.jpg

Français

Discussion publique: BRAAVOO Workshop & Creative Design Course
Participer à la conversation après un atelier d’une semaine sur la réalisation d’un système de détection ‘fait soi-même’ avec biosenseurs bactériens pour la surveillance environnementale de polluants dans l'eau.
* Comment utiliser les bactéries pour la surveillance environnementale?
* Comment intégrer les biosenseurs bactériens dans un appareil électronique?
QUAND: vendredi 5 février, de 15h30 à 17h30 (entrée libre)
OÙ: l'Eprouvette, UNIL (see 'Venues' section above, also for a clickable map)

English

Public Discussion: BRAAVOO Workshop and Creative Design Course
Join the conversation after a week-long transdisciplinary workshop on making a DIY detection device with bacterial bioreporters for environmental pollutants - for detecting heavy metals and oil spills in the water.
* How can bacteria be used for environmental monitoring?
* How can a biological sensor be integrated in an electronic device?
WHEN: February 5, 2016, Friday, 15:30 - 17:30pm (drop by any time)
WHERE: l'Eprouvette, UNIL (see 'Venues' section above, also for a clickable map)



looking for a volunteer English/French translator

We are looking for a volunteer who would be willing to translate between English and French during this event, as not all participants will speak French. If you are interested, please contact sachiko dot hirosue at epfl.ch


This public event will be publicised on the local metro line during the week of the course, so it will be interesting to see who shows up!

Optional Weekend Events

Apéro at the Sauvetage de Montreux

WHERE: Quai de Vernex 1 1820 Montreux
In front of the Stravinsky Hall on the lake

How to get there: Take the train from Lausanne station to Montreux. Walk down to the lake, make a right on the promenade on the lake (go west).
If you need parking, contact Roger.

Bring your own BBQ material
Drinks available on site:

1.50CHF beer and soft drinks
12.00CHF bottle of wine
7.00CHF half a bottle of wine


Suggested Things to Do

  • Rocher de Naye - high above Montreux, on a clear day, you can see the jet of water in Geneva
  • Gruyere - very nice medieval town, good for fondue and the swiss Mac'n Cheese
  • Lavaux vineyards - it is a UNESCO world heritage site - you can take a walk through some of the small towns in the vineyard (train stations Epesse, St-Saphorin) - or the vinorama is a nice place to taste several wines of the region. Otherwise, enjoy some wines in villages closer to Lausanne (Lutry, number 9 bus from Saint Francois)

Protocols and Documentation on Prototype

Biosensor Construction

We will be constructing arsenic, mercury, and 'oilspill' E. coli bioreporters.
Protocols for Biosensor Construction.

Arsenic-Prototype-4-0

The prototype for DIY eGFP detection and turbidity normalization is documented here (work in progress)

Testing the Bioreporters

The newly minted bioreporters are tested with a standard curve and field samples for respective compounds both in the 96 well format (read in a conventional fluorescent plate reader), and in the Arsenic Prototype 4.0.

Communications

Tags

#braavoo
#UNIL
#biosensor
#creativedesign
#winterschool
#biodesign
#biodesignrealworld
#environmentalmonitoring

Core Team

BRAAVOO Project Manager
Rachel Aronoff, SCIPROM

Instructors
Sachiko Hirosue, EPFL
Robin Scheibler, EPFL
Yoann LeDigabel, UNIL
Siham Beggah, UNIL
Jan Roelof van der Meer, UNIL
Shreyasi Kar, Srishti School of Art Design and Technology

In collaboration with:

Hackteria Open Source Biological Art, DIY Biology, Generic Lab Equipment

Invited Speakers
Laura Lechuga, CSIC-CIN3, Barcelona - Spain
Shimshon Belkin, Hebrew University Jerusalem – Israel
Auke Ijspeert, EPFL - Switzerland
Vivian Lu, Eawag, Dübendorf – Switzerland
Kristin Schirmer, Eawag, Dübendorf – Switzerland

With Financial Support from:

BRAAVOO logo 72dpi 100x30mm.png

BRAAVOO aims to develop innovative solutions for real-time in-situ measurement of high impact and difficult to measure marine pollutants.

The concept of BRAAVOO is based on a unique combination of three types of biosensors, which will enable the detection of both a number of specific marine priority pollutants and also general biological effects that can be used for early warning.
The BRAAVOO consortium comprises 9 partners from 7 different countries, and includes four research groups specialised in biosensor strategies and 5 different small or medium-sized enterprises (SMEs). Two SMEs focus on microengineering, nano-tech solutions for signal acquisition and microfluidics; and the others specialise in 1) marine buoys and autonomous vessels, 2) project management, and 3) the algal biosensor systems.

BRAAVOO is an FP7 collaborative project funded by the 'Ocean of Tomorrow' call of the European Union.
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More information about the project and a contact form are available on the BRAAVOO website


Participants

Meet the participants!
(data from just before the workshop)

Country of residence
Country of residence

Background in molecular biology
Background in molecular biology

Have you heard of an arduino?
Have you heard of an arduino?

Materials and Preparations

What to bring as a participant

  • a laptop: if possible, please already download: https://www.arduino.cc/en/Main/Software
  • something for note-taking
  • a camera/phone for documentation
  • if you have an easy to transport soldering station let us know
  • shoes appropriate to go collect some water (either in a lake, or a nearby stream)
  • a box if you would like to make your own housing
  • anything you would like to show to share with an open-hardware community


Provided by UNIL and BIODESIGN for the REAL WORLD

  • Basic molecular biology laboratory equipment (UNIL)
  • Necessary molecular biology reagents necessary to make the biosensor (UNIL)
  • Pieces for the DIY sensor Winter School Prototype v4 (BD4RW)
  • 20 soldering stations - (BD4RW)



Links and References

Reading

Technical Basics

There are many background sites on molecular cloning, and basic electronics. These are only some suggestions. Google is your friend.


Bioart, DIYbio and biohackerspaces

If you enjoyed the visit to hackuarium, find your own local space.

Bioart - introductory exploatory links:


Other

The official course announcement is available as a pdf from a clickable box on the right side of the BRAAVOO website.

More information about the open community lab space in Lausanne, the Hackuarium, is available here.

Press and other Documentation

There are already a couple of news items on the BRAAVOO site about this course. These 'scroll' on the BRAAVOO project's main site, and can be directly accessed from Blogger