[Baypiggies] Proposal for Baypiggies meeting, July 25, 2013

John Wegis jwegis at gmail.com
Fri Jul 12 19:53:33 CEST 2013


On Fri, Jul 12, 2013 at 10:44 AM, Tony Cappellini <cappy2112 at gmail.com>wrote:

> Hello Everyone,
> Jared Maquire from Counsyl has offered to do a presentation on *Python
> for Clinical Genomics, *at the July Baypiggies meeting.
> Since the details of the Python Hack nights are still being worked on, I
> wanted to ensure we have a presentation  for July,
> and to allow extra time to put together a fun session for the Python Hack
> night. We can easily schedule the Python Hack nights
> in addition to our regular meetings in the future.
> Vote +1 if you are interested in attending the *Python for Clinical
> Genomics* presentation in July
> *Python for Clinical Genomics
> *
> Generally computational biology workflows harken back to ancient days when
> Perl programmers roamed the Earth. Lately though, genomics analysis has
> been moving to Python -- in particular the excellent Pysam library has
> brought the state of the art DNA sequence manipulation tools to the world
> of Python.
> In this talk I'll demonstrate the basic tools that I use as part of my
> daily work in a Clinical Next-Generation Sequencing company. We use Pysam
> and Pygr to work with the DNA directly, Django to manage our wet lab and
> organize our genetics knowledge, and Numpy and Scipy for developing novel
> assays and for general numerical analysis.
> We'll work through a live demonstration that takes clinical genetics data
> all the way from the DNA sequencer's output to the final result that we
> share with the patient.
> Along the way I'll introduce the basic concepts of genomics for a computer
> science audience. If you're a computer scientist or engineer and you've
> ever been curious about making the jump to genomics, the time has never
> been better. Genomics right now is like computers were in 1973 -- a huge
> wave about to break.
> *About Jared Maguire
> *
> Jared spent the last five years at the Broad Institute of Harvard and MIT laying
> much of the analytical groundwork for the new wave of DNA sequencing
> technologies. During that time he was a senior analyst on key projects such
> as the 1000 Genomes project, which gave him the chance to be one of the
> first people on earth to map out the patterns of genetic variation in
> thousands of whole human genomes.
> Now he's moved to Counsyl where he's working to help bring the new wave of
> genomics technologies from the research lab into the clinic.
> *About Counsyl*
> Counsyl is a medical genomics startup whose goal is to make the human
> genome practically useful for life-altering decisions.  Over the last few
> years, we’ve grown from a Stanford dorm room to become one of the largest
> clinical genome centers in the world.  Our pre-pregnancy genetic test is
> now prescribed by physicians for more than 2.5% of all births in the United
> States.
> Thank You
> Tony
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