Tag Archives: coding

Thursday 08/21/14

10:00 am – 10:00 pm Multicolor analysis Chromewarps This code is still not too robust. A few mismatched outliers constrain and skew the quality of the warp map. It also is harder when beads from a single field are very … Continue reading

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Sunday 08/03/14

10:15 am – 8:00 pm Probe making out of RNasin, out of Maxima, not able to proceed with probe making. really need to have back ups of these. Coding started to write SteveMosaicViewer GUI drag and drop of a mosaic … Continue reading

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Thusday 07/03/14

9:50 am – 7:30 pm coding found and fixed bug in ClusterStats.m Sequential hybes blead-back in of probe signal: probably a sign of not sufficiently sealed chamber. Try air drying sample and then sealing really tight. hybe2 stain initially very … Continue reading

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Wednesday 07/02/14

10:00 am – 11:35 pm Goals Remove panel (c), add multiple examples of 405-cy5 BX-C spots for oligo-secondaries for previous panel (e) Fix feducialDriftCorrection — github still preserves the lowercase name. maybe best fix is to correct spelling (FiducialDriftCorrection) write … Continue reading

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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

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Thursday 06/26/14

9:45 am – 1:30 am Chromatin Modeling continued Checking my simulation results from the polymer models I was running last night. Simulation Results BBv1 no attractive potential does give expected scaling: Adding an attractive potential does increase clustering. Has more … Continue reading

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Friday 06/20/14

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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Protected: project 2 update: 06/06/14

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Monday 05/05/14

9:00a – 5:00p Lab Meeting Guest speaker, see post. Multicolor STORM more trouble-shooting observed that 647 images look particularly weak, especially given the brightness of these spots. 15 min of max 405 completely bleaches the 647 spot. (~50K frames). 561 … Continue reading

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Wednesday 03/12/14

8:00a — 12:00a Research Organizing launched matlab-functions repository: a private repo with all my common functions. Better for hosting on github, managing between computers, and sharing with lab members.

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