[Chicago] Closest Index

Sun Jan 6 23:15:38 CET 2013

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.
Perhaps this could be a nice Sprint.

--- On Sun, 1/6/13, Oren Livne <livne at uchicago.edu> wrote:

From: Oren Livne <livne at uchicago.edu>
Subject: Re: [Chicago] Closest Index
To: "The Chicago Python Users Group" <chicago at python.org>
Date: Sunday, January 6, 2013, 7:32 AM

    Hi Brian,

      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.

      Shelia: the data sets are public. The A-array is in each of the
      files of
http://hapmap.ncbi.nlm.nih.gov/downloads/recombination/2011-01_phaseII_B37/genetic_map_HapMapII_GRCh37.tar.gz

      The B-arrays are the subset of positions on the product
http://www.affymetrix.com/browse/products.jsp?productId=131532&navMode=34000&navAction=jump&aId=productsNav#1_1

      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.

      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.

      Oren

      On 1/5/2013 10:05 AM, Brian Ray wrote:

      Oren:

        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?

        On Sat, Jan 5, 2013 at 9:26 AM, Oren
          Livne <livne at uchicago.edu>
          wrote:

            Dear Shelia

            These are great questions.

            A is a set of positions of genetic markers on a chromosome.
            It is read from an input data file and is sorted.

            As such, A has no duplicate elements.

            A's values have variable density along the chromosome. It is
            not easy to characterize. Can be locally dense.

            A is used once. However, I have 22 different (A,B) pairs for
            22 autosomal chromosomes.

                Oren

              On 1/5/2013 9:21 AM, sheila miguez wrote:

                I have naive questions.

                How did A get constructed? If an example of integers in
                A is

                1,1,2,3,3,3 is it a list of that, or a counter 2,1,3 or
                something

                else? What is the distribution of A? When you do the
                work do you have

                to construct A every time or will it live around for a
                while?

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        Brian Ray 
        @brianray
          (773) 669-7717

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