<div dir="ltr">+1</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Jul 12, 2013 at 10:44 AM, Tony Cappellini <span dir="ltr"><<a href="mailto:cappy2112@gmail.com" target="_blank">cappy2112@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>Hello Everyone,<br><br><br><br>Jared Maquire from Counsyl has offered to do a presentation on <b style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">Python for Clinical Genomics, </b><span style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">at the July Baypiggies meeting.</span><br>
<br>Since the details of the Python Hack nights are still being worked on, I wanted to ensure we have a presentation for July, <br>and to allow extra time to put together a fun session for the Python Hack night. We can easily schedule the Python Hack nights <br>
in addition to our regular meetings in the future.<br><br>Vote +1 if you are interested in attending the <b style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">Python for Clinical Genomics</b> presentation in July<br>
<br><br><b style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">Python for Clinical Genomics<br></b><br style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">
<span style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">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.</span><br style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">
<br style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif"><span style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">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.</span><br style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">
<br style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif"><span style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">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. </span><br style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">
<br style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif"><span style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">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.</span><br style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">
<br style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif"><br style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">
<b style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">About <span style="background-color:rgb(255,255,204)">Jared</span> Maguire<br>
</b><br style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif"><span style="background-color:rgb(255,255,204);color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px">Jared</span><span style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif"> spent the last five years at the Broad Institute of Harvard and </span><span style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">MIT</span><span style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif"> 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. </span><br style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">
<br style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif"><span style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">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. </span><br style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">
<br style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif"><div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">
<br></div><div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif"><b>About Counsyl</b></div><div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">
<br></div><div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">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.</div><br><br>Thank You<span class="HOEnZb"><font color="#888888"><br><br><br>Tony<br>
</font></span></blockquote></div><br></div>