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I am developer at Ion Torrent. If you want to help hack the future of medicine, I am looking for Python and Django hackers to join my team in San Francisco. We

I am developer at Ion Torrent. If you want to help hack the future of medicine, I am looking for Python and Django hackers to join my team in San Francisco. We are a totally open source shop. We also need awesome electrical engineers, mechanical engineers, signal processing engineers, CUDA hackers, FPGA developers, statisticians (we use R too), bioinformatics folks, JavaScripters, UI people, distributed systems engineers, documentation and developer evangelists, DevOps and SREs, and testers. Not to mention all the wet lab bio stuff. email me at josh@gourneau.com if you are interested

steve19 14y ago
Hi Ion Torrent dev. This is a really exciting project. The article says "decipher a human genome in a few hours, and at the bargain-basement price of $1000". Does this mean the hardware will cost $1000, or does a complete sequence cost $1000 of consumables/depreciation?
- gourneau 14y ago
  That means the cost of consumables is $1000.
tocomment 14y ago
So how does Django relate to gene sequencing?
- gourneau 14y ago
  It helps to think of our machines as fancy scanners. We have to build software to help our users manage their petabytes 'scanned' of data. We also build developer tools to help the researchers and scientist extend our system with plugins. One cool thing is that all of our software is open source. Check out the Django project I work on here. https://github.com/iontorrent/TS/tree/master/dbReports https://github.com/iontorrent/TS/tree/master/dbReports
  - lifeisstillgood 14y ago
    Are you now open to receiving pull requests - there seemed to be a legal problem accepting a patch on the above, and if so what issues do you need fixed :-)
waiquoo 14y ago
Hi gourneau, I'm a grad student working on the hardware side of nanopore sequencing. Do you know anything about opportunities in nanofabrication/system design? Or does Dr. Rothberg come up with these things all on his own?
bioinformatics 14y ago
If I can telcommute I have some free time.
Natsu 14y ago
Incidentally, anyone who wants to play with some genome processing is encouraged to download pygr[1]. You can connect to worldbase[2] and explore all the different genomes they have on their server using Python. [1] http://code.google.com/p/pygr/ http://code.google.com/p/pygr/ [2] http://code.google.com/p/pygr/wiki/ServingDataUsingWorldbase http://code.google.com/p/pygr/wiki/ServingDataUsingWorldbase
JulianMorrison 14y ago
How big is a fully sequenced genome, as a file?
- xaa 14y ago
  http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ ~800MB for human genome
  - hyperbovine 14y ago
    That is roughly the size needed to represent 3.3 billion ACTGs , however sequencer output is much larger since each base is sequenced many times, and accompanying metadata (quality information) is also included. File sizes for current sequencer output is on the order of 100-300gb compressed. It's big enough to create real roadblocks when you are trying to do analysis.
    - Retric 14y ago
      It can also end up well below 800MB per person if you encode it as known sequences of DNA + tiny new random variations.
      - hyperbovine 14y ago
        True, but in order to do that you have to know what the new random variations are. Output from existing sequencers, as well as the current crop of algorithms, are not good enough to do that with high confidence. Thus, people tend to keep everything. You can get some gain by doing reference-based compression, but you're still looking at on the order of 100s of gb per sample.
  - tomkinstinch 14y ago
    When compressed relative to a reference genome, you can get a ~2.9Gbp human genome down to ~3.3MiB of data[1]. Sequences are actually pretty compressible in general, owing to conservation of functional domains and repeats. Data from next-gen sequencers have many small overlapping segments though, so the raw output takes up MUCH more space. By the way, for anyone looking for more information about some of the methods currently being used for sequencing (Illumina, 454), check out these videos from the WUSTL Genome Center: http://gep.wustl.edu/curriculum/course_materials_WU/introduction_to_genomics/nextgen_video_tour http://gep.wustl.edu/curriculum/course_materials_WU/introduc... They don't cover Ion Torrent, which is unfortunate because it is way cool. gourneau can probably point to a better video, but here are a couple for Ion Torrent: http://www.youtube.com/watch?v=W3jPTBU9vF8 http://www.youtube.com/watch?v=W3jPTBU9vF8 http://www.youtube.com/watch?v=yVf2295JqUg http://www.youtube.com/watch?v=yVf2295JqUg ...and the Nature paper: http://www.nature.com/nature/journal/v475/n7356/full/nature10242.html http://www.nature.com/nature/journal/v475/n7356/full/nature1... 1. http://dhruvbird.com/genome_compression.pdf http://dhruvbird.com/genome_compression.pdf
Kliment 14y ago
How do you deal with patents? In my view, an open source shop is not compatible with holding patents, but the space is very heavily patent-encumbered. How do you resolve the conflict?
noreply11 14y ago
I emailed you about meeting up at Pycon but I never heard back.

steve19 14y ago

Hi Ion Torrent dev. This is a really exciting project. The article says "decipher a human genome in a few hours, and at the bargain-basement price of $1000". Does this mean the hardware will cost $1000, or does a complete sequence cost $1000 of consumables/depreciation?

gourneau 14y ago
That means the cost of consumables is $1000.

tocomment 14y ago

So how does Django relate to gene sequencing?

gourneau 14y ago
It helps to think of our machines as fancy scanners. We have to build software to help our users manage their petabytes 'scanned' of data. We also build developer tools to help the researchers and scientist extend our system with plugins. One cool thing is that all of our software is open source. Check out the Django project I work on here. https://github.com/iontorrent/TS/tree/master/dbReports https://github.com/iontorrent/TS/tree/master/dbReports
- lifeisstillgood 14y ago
  Are you now open to receiving pull requests - there seemed to be a legal problem accepting a patch on the above, and if so what issues do you need fixed :-)

waiquoo 14y ago

Hi gourneau, I'm a grad student working on the hardware side of nanopore sequencing. Do you know anything about opportunities in nanofabrication/system design? Or does Dr. Rothberg come up with these things all on his own?

bioinformatics 14y ago

If I can telcommute I have some free time.

Natsu 14y ago

Incidentally, anyone who wants to play with some genome processing is encouraged to download pygr[1]. You can connect to worldbase[2] and explore all the different genomes they have on their server using Python. [1] http://code.google.com/p/pygr/ http://code.google.com/p/pygr/ [2] http://code.google.com/p/pygr/wiki/ServingDataUsingWorldbase http://code.google.com/p/pygr/wiki/ServingDataUsingWorldbase

JulianMorrison 14y ago

How big is a fully sequenced genome, as a file?

xaa 14y ago
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ ~800MB for human genome
- hyperbovine 14y ago
  That is roughly the size needed to represent 3.3 billion ACTGs , however sequencer output is much larger since each base is sequenced many times, and accompanying metadata (quality information) is also included. File sizes for current sequencer output is on the order of 100-300gb compressed. It's big enough to create real roadblocks when you are trying to do analysis.
  - Retric 14y ago
    It can also end up well below 800MB per person if you encode it as known sequences of DNA + tiny new random variations.
    - hyperbovine 14y ago
      True, but in order to do that you have to know what the new random variations are. Output from existing sequencers, as well as the current crop of algorithms, are not good enough to do that with high confidence. Thus, people tend to keep everything. You can get some gain by doing reference-based compression, but you're still looking at on the order of 100s of gb per sample.
- tomkinstinch 14y ago
  When compressed relative to a reference genome, you can get a ~2.9Gbp human genome down to ~3.3MiB of data[1]. Sequences are actually pretty compressible in general, owing to conservation of functional domains and repeats. Data from next-gen sequencers have many small overlapping segments though, so the raw output takes up MUCH more space. By the way, for anyone looking for more information about some of the methods currently being used for sequencing (Illumina, 454), check out these videos from the WUSTL Genome Center: http://gep.wustl.edu/curriculum/course_materials_WU/introduction_to_genomics/nextgen_video_tour http://gep.wustl.edu/curriculum/course_materials_WU/introduc... They don't cover Ion Torrent, which is unfortunate because it is way cool. gourneau can probably point to a better video, but here are a couple for Ion Torrent: http://www.youtube.com/watch?v=W3jPTBU9vF8 http://www.youtube.com/watch?v=W3jPTBU9vF8 http://www.youtube.com/watch?v=yVf2295JqUg http://www.youtube.com/watch?v=yVf2295JqUg ...and the Nature paper: http://www.nature.com/nature/journal/v475/n7356/full/nature10242.html http://www.nature.com/nature/journal/v475/n7356/full/nature1... 1. http://dhruvbird.com/genome_compression.pdf http://dhruvbird.com/genome_compression.pdf

Kliment 14y ago

How do you deal with patents? In my view, an open source shop is not compatible with holding patents, but the space is very heavily patent-encumbered. How do you resolve the conflict?

noreply11 14y ago

I emailed you about meeting up at Pycon but I never heard back.