<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">The group also likes to do Sprints. I originally left biology for computer science back when I had hopes that one could model the lymphatic system using computers.<div><br></div><div>Perhaps this could be a nice Sprint.<br><br>--- On <b>Sun, 1/6/13, Oren Livne <i><livne@uchicago.edu></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Oren Livne <livne@uchicago.edu><br>Subject: Re: [Chicago] Closest Index<br>To: "The Chicago Python Users Group" <chicago@python.org><br>Date: Sunday, January 6, 2013, 7:32 AM<br><br><div id="yiv581513959">
<div>
<div class="yiv581513959moz-cite-prefix">Hi Brian,<br>
<br>
I would love to! Unfortunately I can never attend on Thursday
nights due to another obligation. If I ever get the chance I'll
let you know. In fact I think the discussion should be expanded
more generally to python problems arising in genetic applications.<br>
<br>
Shelia: the data sets are public. The A-array is in each of the
files of
<a rel="nofollow" class="yiv581513959moz-txt-link-freetext" target="_blank" href="http://hapmap.ncbi.nlm.nih.gov/downloads/recombination/2011-01_phaseII_B37/genetic_map_HapMapII_GRCh37.tar.gz">http://hapmap.ncbi.nlm.nih.gov/downloads/recombination/2011-01_phaseII_B37/genetic_map_HapMapII_GRCh37.tar.gz</a><br>
<br>
The B-arrays are the subset of positions on the product
<a rel="nofollow" class="yiv581513959moz-txt-link-freetext" target="_blank" href="http://www.affymetrix.com/browse/products.jsp?productId=131532&navMode=34000&navAction=jump&aId=productsNav#1_1">http://www.affymetrix.com/browse/products.jsp?productId=131532&navMode=34000&navAction=jump&aId=productsNav#1_1</a><br>
I don't know if they have a public download for their marker list.
Or maybe the AWS data set has them - look for Affymetrix chip 5.0
or 6.0.<br>
<br>
Yes, there would be natural applications for map-reduce
parallelization. Not this particular task, but other far-more
extensive tasks. Would be great to discuss in the ChiPy meeting.
This is truly a great mailing list.<br>
<br>
Oren<br>
<br>
<br>
On 1/5/2013 10:05 AM, Brian Ray wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Oren:
<div><br>
</div>
<div style="">Why don't we carve out some time in our next
meeting (Thurs) and talk about possible approaches? Are you
open to leading that discussion?</div>
</div>
<div class="yiv581513959gmail_extra">
<br>
<br>
<div class="yiv581513959gmail_quote">On Sat, Jan 5, 2013 at 9:26 AM, Oren
Livne <span dir="ltr"><<a rel="nofollow" ymailto="mailto:livne@uchicago.edu" target="_blank" href="/mc/compose?to=livne@uchicago.edu">livne@uchicago.edu</a>></span>
wrote:<br>
<blockquote class="yiv581513959gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Dear Shelia<br>
<br>
These are great questions.<br>
A is a set of positions of genetic markers on a chromosome.
It is read from an input data file and is sorted.<br>
As such, A has no duplicate elements.<br>
A's values have variable density along the chromosome. It is
not easy to characterize. Can be locally dense.<br>
A is used once. However, I have 22 different (A,B) pairs for
22 autosomal chromosomes.<span class="yiv581513959HOEnZb"><font color="#888888"><br>
<br>
Oren</font></span>
<div class="yiv581513959im yiv581513959HOEnZb"><br>
<br>
On 1/5/2013 9:21 AM, sheila miguez wrote:<br>
<blockquote class="yiv581513959gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
I have naive questions.<br>
<br>
How did A get constructed? If an example of integers in
A is<br>
1,1,2,3,3,3 is it a list of that, or a counter 2,1,3 or
something<br>
else? What is the distribution of A? When you do the
work do you have<br>
to construct A every time or will it live around for a
while?<br>
</blockquote>
<br>
</div>
<div class="yiv581513959HOEnZb">
<div class="yiv581513959h5">
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-- <br>
Brian Ray
<div>@brianray
<div>(773) 669-7717</div>
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