2015 Project Expectations


BIOENG-390 SV Bachelor Project


  • 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)
Project presentation - DATE:
Final workshop of working prototype
Your Grade is based on:
Participation, initiative
Authorship on online documentation
Q&A on mid-term and final presentation







20 February
8:00 -13:00

-Meet and Greet & course expectations
-11:00am google hangout Meet and Greet with India and Indonesia

-Hello-World (Introduction to) the fluorimeter/turbidity meter
-How to prepare for the next week's session

-To prepare:

Please read the final report (https://wiki.epfl.ch/biodesign-realworld/2014/report), and familiarize yourself with the biodesign.cc website

Action Items (for next week)

  • make a biodesign.cc entry and a wiki entry on the 2015 team
  • download arduino software http://arduino.cc/en/main/software and if you want a sneak peek, check out the electronics and arduino primers here.
  • read the protocol and background papers for the arsenic bioreporter assay - especially the Trang et al. and the bioreporter review
  • it may be interesting to see the "other detection methods" folder




27 February
8:00 - 13:00
Swartz Lab meet at SV Hall  (different at EPFL!!)

-Exchange feedback from the first week
-Wet-lab familiarization with the Bioreporter Assay

-Meet and Greet with Art(Science)BLR

-Discuss possible project directions

Action Items (for next week)
  • Brainstorm possible project directions (see link above, sub projects are fine) and draft a specific proposal (what you will do, and when will you do it = timeline, what resources and mentoring do we need? >>> 3 slides, bullet list format is fine)
  • Do an analysis of the results from 27.02 - what can you conclude - did the experiment meet the aims? what are the next experiments?
  • Make a biodesign.cc entry and on the wiki for the 2015 team
  • Detail your lab notebook
  • google arduino projects

feel free to contact us, and others!!



6 March

8:00 -13:00

- Going over the results from LssmOrange vs eGFP reporter from last week

- Introduction to arduino - the blink, the RGB LED, the potentiometer

- The Frog Collective "Find True North" exercise from their "Collective Action Kit" suggested by our Indian Partners

-Finalize project group and directions

- Skype with Yashas (IN)

Action Items (for next week)
  • Download GitHub - software and desktop client. https://github.com/BioDesignRealWorld/
  • Discuss the project with your "grandma" or someone who would be the target group of the workshop - look at the booklet from Friday on the interview section and then note down the reflections.
  • Write the Final Goals for mid-term presentation (feasibility studies) for Tuesday 10 March - Robin by Skype
    • (Marie D., Colombine) Background Research (also go through suggestions by Marc and Yashas, itemize some parts necessary.
    • (Mathilde) Meet with Prof. van der Meer, background reading, CAD drawing of the proposed vial.
    • (Marie W., Dounia) Understand the background of prototype I, make the publiclabs spectro and look at the blue LED, red LED, and the blue and red LED through the plastic lens.



10 March

Prof. Gatica-Perez (http://www.idiap.ch/scientific-research/news/sensecityvity)

WHEN: 9:15-10:00am CH, 12:45pm IN, 15:15pm ID
WHERE: AI 2.142 CH


13 March

separate schedules until we meet at 12 noon at EPFL - AAB 239

HACKUARIUM - Sachiko will be at hackuarium at 8am til we go back to EPFL.

  • Marie Duc and Colombine - work together on prototype for sonification
  • Marie Willemin - the prototype I final characterization - please bring the publiclabs spectrum device

EPFL - Thomas will be at EPFL

  • Mathilde - comparison of eGFP and LSSmOrange

Together at EPFL, go over

  • discussions with "grandmas"
  • progress on the projects
  • week to week plans
  • what we want to learn from the workshop
Action Items (for next week)
  • Discuss to identify the workshop audience (age group, etc., and where/how you will find them) - (Marie, Marie, Colombine, Dounia, Mathilde)
  • Look at Personas (and other links from Prof. Gatica-Perez) and the Frog Design Collective Action Toolkit and other tools to delineate a workshop that taps into the audience needs/ interests (everyone)
  • biodesign.cc entry
    • the cap (Mathilde)
    • meeting with Prof. Gatica-Perez (Sachiko and anyone else please contribute)
    • innovation forum Lausanne talk (Sachiko)
    • the LED driver (Robin)
  • Make a Markdown template for experiments (Marie W.)
  • Projects
    • Light-to-sound connection (Marie D., Colombine)
    • Spectruino as a sensor stabilize configuration (Marie W., Dounia)
    • LSSmOrange results and contact Prof. van der Meer (Mathilde)



20 March

11-13 Hackuarium

  • work on the projects
  • any Q&A
  • clarification of the week by week plan
  • follow up on the previous week

(also a possibility: Les Rencontres de l’Eau 2015 http://www3.unil.ch/wpmu/h2o/)


Action Items (for next week)


  • PRESENTATION / DEMO for next week

AIM: to get direct feed-back for this year's projects


  • bring a schema, your prototype, something concrete to illustrate the project direction
  • no more than 10 minutes talking + demonstration (calculate 1 slide/min)
  • the content should include Project Aim, Motivation, Proposed Plan, Timeline, Possible Limitations, Plan B (if your Plan does not work, what will you do?)


    • Double Cap (Mathilde)
      • finish biodesign.cc entry
      • make a physical prototype / mock-up
    • Lss-mOrange Reporter (Mathilde)
      • Repeat a timecourse in comparison with eGFP
      • Make conclusions
      • Summarize literature findings and translate them to experiment plans using the MarkDown template made by Marie
    • Sonification of Arsenic (Marie D., Colombine)
      • use GitHub to branch off your code
      • modify the code of the 4th try to produce different sounds according the displayed frequency
      • look closer to the current arduino code of the prototype
      • try an arduino shield (order it) to produce good music (see simple audio player in arduino)
      • modify the code to calculate directly the absorbance
      • Change the order of the turbidity and fluorescence counting
  • Spectruino as a sensor stabilize configuration (Marie W., Dounia)
    • - Finish to draw a new prototype 1 to make various tests (we should can remove lens and filter anytime)
    • - learn to use adobe illustrator (tutorial in web) [Marie]
    • - start to make pieces (with help of Thomas)  [Marie]
    • - influence of bacteries (scattering) - 500nm beads and dextran - old prototype (Dounia)
    • - research bacteria lysis buffer to release the eGFP
    • - Talk to Robin to understand tje circuit that can be used to adjust the power of the LED in software to help with the experiment- put together a biodesign.cc entry



27 March

10AM - hackuarium

Mid-term Presentation - discussion to agree on direction, gain feedback

External Experts Present: Prof. J van der Meer, Dr. S. Leuenberger

Action Items (for next week)



  • agreed on doing a stand / having a table at the STIL
  • decide > the aim of doing the workshop (for those conducting the workshop, and for the audience)


  • co-write a biodesign.cc entry on the feedback you received


    • add the spectrometer to the prototype
    • figure out conditions for cell lysis and eGFP extraction
    • figure out the SD shield
    • get feedback from Yashas, Marc (both still in India), and Andreas (Lifepatch)





3 April - EASTER - no in-person meeting on Friday
Action Items (for next week)




10 April - SPRING VACATION - no in person meeting on Friday
Action Items (for next week)




17 April

11:30am meeting at EPFL

Action Items (for next week)


AIM: introduce the project, and the concept of open souce - also citizen science

  • Contact Marion Badi-Dubois (Sachiko)
  • Poster (shared drive)
  • 3 panels, 2 tables, 6 chairs
  • extension cords + plugs
  • White T shirt


  • scale up extraction
  • cut the prototype to fix the spectruino
  • look into the code to connect the spectra on publiclab


  • design a version that works for the STIL
    • what samples will you use to demonstrate waiting time and ready to measure?
    • how will you address the standard curve vs samples
    • how will the user interact with your device with sound output?
  • continue working on resolving the timer issue with the prototype and the shield

Double Cap

  • Work out a method to print the double cap as a single unit (3D printing, or contact others)
  • Price estimation
  • 2D industrial drawing




24 April

12:00 meeting

Action Items (for next week)


  • Sachiko to get the forms on Tuesday
  • Poster idea - in dropbox
  • Doodle for T-shirt printing day


  • Test the spectruino with
    • free GFP from cell lysis on previous Tuesday
    • GFP within bacteria
    • fluorescent dextran
    • fluorescent beads
  • biodesign.cc entry on eGFP extraction


  • STIL prototype - build the box + buttons for On/OFF, potentiometer for volume and speed
  • discuss with Robin the timer 1, 2 issue

Double Cap

  • Change the 3D printing material PLA not ABS
  • Libre CAD for the 2D technical drawings
  • Open source documentation
  • Vial information



1 May
Action Items (for next week)




8 May
Action Items (for next week)




13 May STIL stand


15 May
Action Items (for next week)




22 May
Action Items (for next week)




29 May
Action Items (for next week)