Author Archives: admin

Sunday 11/17/13

Posted on November 17, 2013 by admin

10:00a – 7:30p, 10:15p – 12:00a Ph Project Coding Cleaning up Ph simulation codes moving more stuff to functions sped up pivotMove removed loop in plotting function Most computation time now taken up by Mex Function call in pdist. see … Continue reading →

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Saturday 11/16/13

Posted on November 16, 2013 by admin

6:30p -8:00p Polymer simulation PRC1 simulations finished without error Need to optimize axes and binning for distribution plots. Free Polymer radius of gyration calibration still running, (last update, round 6 1024 link polymer). polynomial fits (don’t extrapolate well without taking … Continue reading →

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Friday 11/15/13

Posted on November 15, 2013 by admin

7:30a – 11:15a General stuff installed windows updates on Monet installed new RAM (now 32GB) sent (final?) version of Banff report to co-organizers. Send to BIRS on Mon. Chromatin simulations functionalizing chromatin simulation code attempting to increase simulation speed distance … Continue reading →

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Protected: project2

Posted on November 15, 2013 by admin

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Thursday 11/14/13

Posted on November 14, 2013 by admin

9:30a – 11:45p Coding / Genomics Fixing fastaread to avoid memory errors Matlab calls char on the list of sequences. If there are short sequences and very long sequences mixed together in the fasta file, this can introduce many gigabytes … Continue reading →

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Protected: project 2

Posted on November 14, 2013 by admin

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Wednesday 11/13/2013

Posted on November 13, 2013 by admin

10:00a – 7:15p Other Reply to BJ with final corrections / proofs Deep sequencing analysis scatterplot correlations on log10 scale Coding Interesting matlab fact: Nested functions have access to the parent workspace. Got CIGAR and MD parser from Jeff to … Continue reading →

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Tuesday 11/12/13

Posted on November 12, 2013 by admin

9:30a – 11:30p Analysis to do: Finish analyzing E10 data! analyze E08 data E01 data, first image looks okay, rest have no obvious dots. STORM movies not too much blinking Presentation to do: Spot analysis Pool all regions analyzed, plot … Continue reading →

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Monday 11/11/13

Posted on November 11, 2013 by admin

8:40a – 1:15a Ph project Get S2 cells for Ajaz Running more simulations to explore appropriate range and parameters for the effect of PhM concentration on clustering. For the moment let’s ignore the unbound populations of molecules. Surprisingly I observe … Continue reading →

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Protected: Lab meeting 11/11/13

Posted on November 11, 2013 by admin

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