BIO-DESIGN for the REAL WORLD
BIOENG-390 SV Bachelor Project
5ECTs
Expectations
- 1 Friday morning a week – in person contact with the mentors, with the exception of the first 2 weeks
- At least 1 full day working outside of the in-person contact hours
- Regular exchange with the collaborators (skype/google hangout/email/chat/meetings)
- Documentation of the project process on biodesign.cc (at minimum one entry every other week, including project proposal, and final prototype details – see here for guidelines)
Mid-term:
Project presentation
End-of-term:
Final presentation and prototype demonstration
Participation in the Water Hackathon at the tech4dev conference 6, 7 June 2014
Your Grade is based on:
Participation, initiative
Authorship on online documentation
Q&A on mid-term and final presentation
Syllabus
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Week
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Objectives
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1
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24.02-01.03
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28 February
10:15-14:00
Room SV 3.715
-Meet and Greet & course expectations
-10:40 google hangout Meet and Greet with India and Indonesia
-Prototypes so far
-Hello-World of (Introduction to) Arduinos
-How to prepare for the next week's consultation session
-To prepare:
Please read the final report (https://wiki.epfl.ch/biodesign-realworld/2013/report), and familiarize yourself with the biodesign.cc website
-To do for next week:
Arduino LED+light detector (get familiar with platform)
Think about directions:
- Mobile lab
- Taking GMOs in the field (how ?)
- Mapping
- Device (fluorescence, other)
- Other ?
Prepare questions to ask to Prof. van der Meer and Dr. Leuenberger.
Write ~1 paragraph about *your* project. Make a short video of working arduino setup. Prepare for blog entry.
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2
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03.03-08.03
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7 March
10:15-12:00
Room SV 3.615 (different room!)
-Exchange feedback from the first week Q&A and mind-map from the week before
-10:30-11:30am Heads-on Consultation and Brain-storming Session with Prof. van der Meer (bioreporter expert, arsenic reporter is from his lab) and Dr. Leuenberger (Biosafety Office)
-Schedule a wetlab session
Action Items (for next week)
- Contact Jan van der Meer and organize lab session to learn handling and use of bioreporter bacteria.
- Read blog entry about Swiss law concerning GMO
- Contact Sabrina Leuenberger to setup a meeting
- Research sample vials suitable for detection and containment
- Make a biodesign.cc entry
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3
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10.03-15.03
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14 March
10:15-12:00
Room SV 3.715
-Check over the action items from last week
-Go over the sample vial ideas from Bastien and Falco
-Prepare for wetlab, and Bern visit
Action Items (for next week)
- Tuesday 8am Learn how to do the arsenic reporter assay @ van der Meer lab with Siham
- Write a draft template email explaining the project
- Look at Arsenic Kits from last year's research, pick some and contact for samples (or buy)
- Presentation on Sample holder summary (biodesign.cc entry)
- Send email to Sabrina
- Choose a 3D modeling program (look into options)
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4
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18.03-22.03
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21 March
10:15-12:00
Room SV 3.615 (different room!)
-Check over the action items from last week
-Try the evolved prototype from prototype 2 with FITC dextran and green fluorescent beads
Action Items (for next week)
- Find out the state of bacteria in Arselux
- Contact Siham for the map, understand whether we can/ how to modify the antibiotic resistance, conjugation
- General waste handling after use
- Contact Bern
- Read the law
- Play with the detector box
- Contact India for a meeting next week (arsenic kit)
- Entry on biodesign.cc the direction we will take in the semester
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5
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24.03-29.03
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28 March
Preparation for the Presentation in Bern
Skype updates with Yashas
Action Plan for Next Session
- Make the 10 slides for the Presentation
- Arsolux - know all details to make the slide (from bacteria preparation to waste disposal and their results from field testing - Bangladesh?)
- Read primary papers/Siham to have information on slide for the plasmid construction
- Write up what your ideal field detector box will have?
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6
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31.03-05.04
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9 April
Action Plan for Next Session
- Finalize 10 slides for the Presentation
- Follow up on Bern to schedule a meeting
- Get feedback on presentation with Sabrina
- Have an electronics session with Robin
- Sachiko > order vials and LED display
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9
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21.04-26.04
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Easter break |
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10
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28.04-03.05
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1 May
8:00-10:00 @ BAFU, Bern
Presentation of Project and Biosafety Containment to authorities
Action Plan for Next Session
- biodesign.cc entry of the preparations for and the visit itself, with conclusions
- obtain and complete the notification form so that field studies are formally included in our activities
- follow up on informing other contacts within EPFL (Sachiko)
- Make a list of all of the design issues for making the final box prototype
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11
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05.05-10.05
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May 9
Action Plan for Next Session
- Complete the notification form so that field studies are formally included in our activities - by Tuesday 13 May
- follow up on informing other contacts within EPFL (Sachiko)
- Finish the hardware toggle between absorbance (turbidity) and fluorescence
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12
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12.05-17.05
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16 May
Troubleshooting of circuit
- Meet Monday 10am for components
- Start writing final report
- Follow up on the final presentation date
- Finish the circuit
- Prepare for bacterial samples
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13
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19.05-24.05
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23 May
Test the protototype
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