DNA sequencing on your smartphone

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Problem. When traveling, a drink containing microbes not adapted to your gut can be a bad experience.

  • Serious example. Contaminated with 100+ bad microbes, dirty water sends 1B people to the toilet and kills other 2M every year.
  • Silly example. Brewed with 100+ good microbes, craft beer has a overwhelming taste palette. Each new bottle is a blind test: either you love that kind of fermentation or vomit.

Take a drop from your next drink. Which microbes are swimming inside? Is there a way to learn about them before consumption? Is there an App for that?

Solution. DNA sequencing on your smartphone. Today you can spot the presence of any microbe in a drop of water by reading their DNA traces. The machine to do that - the DNA sequencer - can be as small as an USB-key.

I founded BeerDeCoded to make a completely open DNA sequencing process. Open chemical reagents ▸▸ open sequencing hardware ▸▸ open data analysis software ▸▸ open data.

Can we design a scalable and sustainable process to improve the next drink of every people in the world? I believe so and I need your help to make it happen.

Category: 
Health
Contacts: 

Gianpaolo Rando
I'm a life scientist. I do academic research at Unige, working at the interface between food and DNA. Find me on twitter @randogp or write me at 96well at gmail

I run BeerDeCoded at Hackuarium.ch (Renens, VD)
Hackuarium is a bio-hacking community working in a non-institutional, open and fully equipped laboratory part of UniverCity, a vibrant ecosystem including also a Coworking space, a Makerspace, and a Hackerspace. Founded in August 2014 and growing steadily since, Hackuarium is now the home of 40+ people working part-time on a variety of projects ranging from Antarctica exploration to bioelectronic sensors for water pollutants and, of course beer DNA. We have open nights every Wednesday. You should join one of our #openHackuarium

Skills Being Sought: 

You did not learn to code by reading a book. Practice is key. I believe in learning by doing. I'm looking for people comfortable to translate their skills into bio-hacking.

At the core DNA sequencing and other biochemical reactions is the mix of small drop of liquids (reagents). After incubation at different temperatures, the reagents change some physical property. Measuring the change is the key. 

I'm looking for people that can attack the following problems.

Hardware:

  • how to automate and simplify the movement of tiny (sub-microliter) amounts of liquid (microfluidics, electrowetting).
  • how to read changes in physical properties on tiny amounts of liquids (pH, conductivity, light absorbance, fluorescence, other).
  • how to operate these devices using a smartphone.

Software:

  • how to parse big (Gigabytes) of text (A, T, C, G letters) and compare it to a reference database in seconds.
  • how to visualize and geolocate big data.
  • how to make an interactive App, in which people can browse the data available so far or contribute new data.
Weekend Goals: 
  1. Meet people that may be a good fit for a collaborative long-term project.
  2. Software: build a prototype App to browse data of fictional beers/water. We may use open data previously generated by a city-scale DNA sequencing project in NYC.
  3. Hardware: brainstorm ideas on liquid handling and perhaps build a small prototype able to mix some liquids.
  4. Document our work in so that people can build on our work at a next hackathon or next #openHackuarium.
References and Background Material: 

BeerDeCoded kickstarter campaign (succesfully funded June 29, 2015).

BeerDeCoded is the funny branch of the Open Food DNA project. In short we build an open workflow, from food to data visualisation, that enables citizens to understand what they are eating/drinking. In the past, the focus has been on science communication / fun. At this hackathon I want to test the potential for Health applications.

More references and background material on this Hackpad page. http://bit.ly/DNA_WebFest_CERN

Prerequisites: 
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Express your Interest to work on this Idea !!

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