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analysis cell culture cell labeling chromatin cloning coding communication confocal data analysis embryo collection embryo labeling figures fly work genomics hb image analysis image processing images in situs Library2 literature making antibodies matlab-storm meetings modeling MP12 mRNA counting Ph planning presentation probe making project 2 project2 result results sectioning section staining shadow enhancers sna snail staining STORM STORM analysis troubleshooting writing-
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Category Archives: Chromatin
openMM simulation notes
Recommendations from Anton for avoiding exploding polymers Initial recommendations integrator choice: variableLangevin integrator recommended takes an error tolerance instead of a timestep variable (e.g. 10^-4) thermostat = high values high friction mass_scale = argument of init of simulation (see openmmlib.py) … Continue reading
Protected: chromatin data analysis
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Tuesday 04/01/14
10:30a – 1:20a STORM imaging Microscope computer blue-screen crash during the night on prism2 Jiang reports having seen similar issues on prism2 Presentation Prep Making slides for Friday’s team meeting with Wu group see googledocs presentation. This took the half … Continue reading
Protected: work with Pallav
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Posted in Chromatin
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Protected: thoughts on chromatin structure
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Thursday 04/27/14
10:15a – 12:30a Goals Data processing copy C05 and C06 data to hard-drives Launch analysis of C03-C06 data plate, fix, prep and hybe new cells Probe making RT reactions test gel probe purfication cell staining wash out probes image multi-color … Continue reading
Posted in Chromatin
Tagged cell staining, chromatin, images, probe making, STORM
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Protected: Oligo-Secondaries figure
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Protected: PH project update
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dataset curation
Compressing Bead movies from the following data files ‘M:\2013-11-01_F07\splitdax’ ‘M:\2013-11-02_D11\splitdax’ ‘M:\2013-10-29_E10\splitdax’ ‘M:\2013-10-28_E08\splitdax’ ‘M:\2013-10-27_E01\splitdax’ ‘K:\2013-10-26_D12\splitdax’ ‘K:\2013-10-25_D11\splitdax’ ‘K:\2013-10-11_F10\splitdax’ ‘K:\2013-10-10_F11\splitdax’ ‘J:\2013-10-06_no405Primary\splitdax’ ‘J:\2013-10-05_E06\splitdax’ ‘J:\2013-10-04_G05\splitdax’ ‘J:\2013-10-03_E02\splitdax’ ‘J:\2013-10-02_D09\splitdax’ ‘J:\2013-10-01_G10\splitdax’ ‘H:\2013-10-09_F01V2\splitdax’ ‘H:\2013-10-07_F09\splitdax’ ‘H:\2013-09-24_F6-405\splitdax’ ‘H:\2013-09-23_F6\splitdax’ ‘H:\2013-09-09_G4\splitdax’ ‘H:\2013-09-05_G6\splitdax’ ‘H:\2013-09-04_G3\splitdax’ ‘H:\2013-09-02_G2\splitdax’ ‘H:\2013-08-22_Ubx\splitdax’ ‘H:\2013-08-21_AbdA\splitdax’ All 561quad_movies downsampled to 1 Hz, introduce … Continue reading
Protected: Draft outline for chromatin paper
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Posted in Chromatin
Tagged chromatin colors
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