Question: Bioinformatics Applications With The Raspberry Pi?
6
gravatar for Egon Willighagen
6.1 years ago by
Maastricht
Egon Willighagen5.2k wrote:

I am thinking of using a Raspberry Pi in bioinformatics education, as an example of how bioinformatics is used to work with experimental data on conference floors. Does anyone know of a project that links the output you can measure with a Raspberry Pi with bioinformatics software?

• 5.9k views
ADD COMMENTlink modified 6.1 years ago by Pierre Lindenbaum124k • written 6.1 years ago by Egon Willighagen5.2k
1

I ordered a Parallella cluster www.parallella.org) with little to no clue on how or what to use it for. I do know why: fun!

ADD REPLYlink written 6.1 years ago by Martin A Hansen3.0k
5
gravatar for Pierre Lindenbaum
6.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum124k wrote:

I know @bilouweb worked with Raspberry Pi but I don't know it it fulfills your needs.

"Minia on Raspberry Pi Assembling a 100 Mbp genome on a Credit Card Sized Computer"

http://hal.inria.fr/docs/00/84/20/27/PDF/13_Jobim.pdf

enter image description here

ADD COMMENTlink written 6.1 years ago by Pierre Lindenbaum124k

Interesting, but indeed I am looking for something simpler... something to demo on open days... and, importantly, that takes live input, such as spit from a passing audience...

ADD REPLYlink modified 6.1 years ago • written 6.1 years ago by Egon Willighagen5.2k
1

Well, then you would need to have some sort of device that measures something in the spit and produces live results. Maybe when the MinION is available you could do real-time sequencing. But that is going to be awhile yet.

ADD REPLYlink written 6.1 years ago by Dan Gaston7.1k

IMHO, bioinformatics is not only sequence stuff...

ADD REPLYlink written 6.0 years ago by Egon Willighagen5.2k
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That's true of course, but I'm trying to think of things you can collect live, do analysis on, and that involves bioinformatics where the bioinformatics is the hard part. Any sort of biomarker you can measure that quickly is going to be the result of the device used to measure it, with usually some sort of trivial output that quantifies the amount or activity of the substance (ie an assay of some sort). Even microarrays would take too long to do for it to be a live demo.

ADD REPLYlink written 6.0 years ago by Dan Gaston7.1k
2
gravatar for pld
5.7 years ago by
pld4.8k
United States
pld4.8k wrote:

I've always wanted to see these used with Oxford Nanopore's MinION sequencer. It would be a killer tool for epidemiology in virus outbreaks.

ADD COMMENTlink written 5.7 years ago by pld4.8k
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