2015 Final Report

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2015 Team at EPFL

2015 EPFL team.jpg

Mathilde Vidal studies in the third year of life sciences at EPFL. She is 22 years old and she comes from France.
This project attracted her because it crosses biology with many engineering domains she learns during her studies. She sees in this project a good way to apply the theory in the concrete and human case of making an arsenic detector. She also likes the do-it-yourself aspect of the device development, because she likes doing handmade creation. Out of her studies, she is keen of sport, especially rowing and fitness.

Colombine Verzat is also a 3rd-year student in life sciences at EPFL.
Coming from the north of France, she moved to Paris for highschool. She started her studies in Lausanne as a way to experience freedom and live a true student life.
She chose this bachelor project because of its open-hardware concept: communicate with the rest of the world about a common project and exchange ideas. With this project, she wants to acquire new engineering skills. She likes to dance Rock and is fond of cinema.

Marie Duc is a 22 years old coming from Switzerland.
She is a third year student in Life Sciences at EPFL. She particularly likes computer science, it is why she is a teaching-assistant in programming.
What attracts her in this project is the humanitarian aspect that could have a direct impact in the real world. Trying to solve a real global problem, not only theoretically but more concretely. She enjoys walking and traveling everywhere to discover the world and she really likes watching movies.

Dounia Droubi is a french student in her third year at EPFL in life Sciences.
She chose this project as her Bachelor Project because the multidisciplinary part allows to work on different domains, like biology, electronics, etc, which can be an advantage in her future studies. She also likes the international and humanitarian side of this project, working with Indian and Indonesian teams is very interesting. Out of studies she likes to do hiking and sport.

Marie Willemin was born in the Jura. That is a very little country-side region in Switzerland. She likes very much her origin close to nature. In 2010, she left the Jura to go in the city and start studies at the EPFL in life sciences. Next to her studies, she has a student job which means a lot to her : She works as monitor for people with mental disabilities.
She commits now to the biodesign project because she is interested in the interdisciplinarity and do-it-yourself aspect as well as the humanitarian angle.

Introduction

Welcome to our final report page. This report will explain the bachelor project of the EPFL team 2015 during this semester.

Our work was to improve the prototype and we decided to work on different orientations. But the first few weeks, we got in touch with the project as a whole. We first learnt to build the prototype (by doing some soldering and electronics). Then we learnt how to behave in a Lab working with bacteria and we performed an experiment to test the LSS mOrange bioreporter. Finally, we got in touch with Arduino, making some LED blink for example. After this introduction of the project, we separated into three subprojects. Marie W. and Dounia worked on the prototype debugging, Marie D. and Colombine on Arsenic sonification and finally Mathilde worked on facilitating and securing the sample in the field and made few lab sessions on characterize the new bioreporter LSS mOrange .

The aim of our work this semester was based on:

  • LSS mOrange characterization : getting familiar with the protocol, comparing it with eGFP, the bioreporter used at this moment, and finally proposing some possible experiments to characterize LSS mOrange.
  • The prototype debugging: light scattering analysis. We would like to know if the light scattering distorts the results.
  • The Sonification of Arsenic: the aim was to make the prototype more intuitive by producing a sound output depending on the arsenic water concentration.
  • Facilitating and securing water sample collection in the field : the idea was to make a double cap which connects the bioreporter vial containing GMO and the collected water vial together. They must be linked from field collection sample when we bring together the two  vials until the moment we return in the lab, where we destroy the GMO. This cap must be hermetic to prevent the GMO outflow.

The plan of our report is below. We wish you a pleasant reading!



LSS mOrange bioreporter


We wanted to separate the excitation and emission wavelengths of the bioreporter to be able to distinguish better the emitted light from the LED light with our Arsenic-Prototype-3-0.
Read more about our LSS mOrange bioreporter.

Prototype debugging


2015 custom box.png

This part of the project was to quantify, observe and test how much of the detected light comes from light scattering of our bacteria reporters in the prototype.
To determine if the sensor also detects blue light from the LED, we wanted to compare eGFP bacteria and lysed eGFP bacteria. To test this assumption we realized a cell lysis protocol.
Read more about Prototype debugging, or browse through the sections.

  1. Introduction
  2. The Light Scattering
  3. Cell lysis
  4. Test
  5. Conclusion



Sonification of Arsenic


Sonification is

  « the use of non-speech audio to convey information or perceptualize data. Auditory perception has advantages in temportal, spatial, amplitude and frequency resolution that open possibilities as an alternative or complement to visualization techniques. ». from the wikipedia

It can also be simply seen as an interface between the human and the machine.
The Aim of the Sonification of Arsenic was to improve the actual prototype to make it more intuitive.

  1. The Idea behind Sonification
  2. First Circuits
  3. Music Box
    • Prototype Music Box
    • Printed Circuit
  4. Working with a Shield
    • With a Counter
    • With an Interrupt
    • With two Arduinos
  5. Sonification Future Directions and Conclusion



Assuring secure sample collection in the field


Made.jpeg

So far, what is approved for us to take out the bioreporter into the fields (in CH), is a vial with a cap with a silicon septum covering the bioreporter vial we can fill with a syringe. Thanks to properties of the septum material, the hole created by the syringe clogs by itself. It assures secure collection sample in the field but the syringe presents extra wastes and is a potential source of damage and contamination.
This is an alternative design to eliminate the need for syringes using a Double Cap Design.

  1. Motivation for Double Cap Design
  2. Workflow of the double cap
  3. Design of the double cap:
    • Defining the optimal dimensions
      Modeling of the double cap
      By hand making of the double cap
      3D printing of the connector
      3D printing of the whole double cap
      Potential improvements
  4. Sealing the vials
  5. Legal aspect
  6. Conclusion



Conclusion

What we first liked about this project is the fact that it seemed quite different from other projects and that it had a multidisciplinary and humanitarian aspect. At the end of this semester, we realised that we had been the whole time working as a team, even if we did not work on the same things; We had a global vision on the entire project.

In May, we presented our work at the STIL (Salon des Technologies et de l'Inovation de Lausanne). This motivated us, because we were well welcomed and people were really interested in what we were doing. They were trying to find solutions that we did not necessarily thought of. In the end, we had a concrete external feedback on our project, which made us proud of it. (Read our Biodesign entry to know more about it).

What we will remember about this project:

The concept of Open Source, which was new for us. We discorvered that it helped to share. That it is what makes Science evolve faster.

The notion of Community, which was reinforced by the fact that we worked the whole semester at Hackuarium, a place where we felt like home and where we could share with other people.

And finally the Do-It-Yourself aspect of the project, which makes us believe that the democratisation of science is possible, that building with their own hands will make people concerned about the problem and provoke more easily reflexion.

Eventually we want to thank Sachiko Hirosue and Robin Scheibler for the experience they made us live. The Hackuarium team for the place and welcome they did. And all the other people that were there when we needed some help.

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