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

Tony Cappellini cappy2112 at gmail.com
Fri Jul 12 19:44:50 CEST 2013

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

Thank You

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