Monthly Archives: June 2014

Monday 06/23/14

Posted on June 23, 2014 by admin

10:00 am – 5:00 pm, 10:00 pm – 12:30 am Lab stuff Finally found and installed drivers for Cajal’s AMD Radeon 6900 graphics card (this card is still driving the monitors). installed new NVIDIA Quadro K4000 for GPU computing (still … Continue reading →

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Protected: ANT-C PH clusters

Posted on June 23, 2014 by admin

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Sunday 06/22/14

Posted on June 22, 2014 by admin

10:20 am – 11:15 pm New simulations sticky polymer simulations. same as blue simulations but reduce binding energy 10 fold. index*epsilon * .0001 * (step(r-rm)*(r-rm)^4 * (1- step(r-2*rm))+ (rm)^4*step(r-2*rm)); now running with 10 polymers, log scaled from 10 to 500 … Continue reading →

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Saturday 06/21/14

Posted on June 21, 2014 by admin

9:30 am – 5:45 pm Simulations To Analyze OpenMM free Polymer sims Odyssey Matlab periodic bonds OpenMM free Polymers Only a single run, but not quite the right scaling — expect 0.60. And a y-intercept at 0. See previous simulations … Continue reading →

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Protected: project 2: update 06/21/14

Posted on June 21, 2014 by admin

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Friday 06/20/14

Posted on June 20, 2014 by admin

10:00 am – 11:55 pm Simulations simulations with more nodes (1 every 300 bp) of blue regions don’t ‘work’, simulation time not long enough for distributions to converge. too many nodes such that larger regions never experience bonding interactions. Maybe … Continue reading →

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Thursday 06/19/14

Posted on June 19, 2014 by admin

10:00 am – 8:15 pm Working on Python OpenMM simulations goal, attempt to execute some of Mirny’s example code. Attempting to run demos e.g. scaffoldExample.py complains about notfinding joblib. installed this, required instlaling this complains about not finding mirnylib, which … Continue reading →

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Protected: project 2 update 6/18/14

Posted on June 18, 2014 by admin

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Wednesday 06/18/14

Posted on June 18, 2014 by admin

9:30 am – 7:30 pm, 10:00 pm – 12:30 am Tasks Revise figure for XZ New Library Design Final checks for lib5 send Fasta file to Marcelo and request for quote to Alec and Matt Sequential staining Lib2 F05 + … Continue reading →

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Tuesday 06/17/14

Posted on June 17, 2014 by admin

10:00 am – 5:00 pm, 7:00 pm – 11:40 pm Literature interesting article on FACs smFISH sequencing from vanO group. interesting article on noise models for single cell sequencing from vanO group as well STORM D01 finished smoothly setting up … Continue reading →

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