Category Archives: Software Development


Polishing MERFISH code for public release. Plan take 140 gene library, create short fasta of just complete genes, run it through Launch OligoArray add parse OligoArray (as a function) into this script add assemble secondaries and target regions into as … 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 … Continue reading

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git remove binary files

See current file size. First need to git gc Alistair@MONET ~/Documents/Research/Projects/Chromatin/Code (master) $ git gc Counting objects: 713, done. Delta compression using up to 8 threads. Compressing objects: 100% (570/570), done. Writing objects: 100% (713/713), done. Total 713 (delta 257), … Continue reading

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Thursday 01/23/14

9:45a – 12:15a STORM analysis analyze bead data for BXC double stains analyze bead data for PhM Psc Finish O/N run of G05 quick look at ANTC data (just image based drift correction available at present) fewer localizations despite bright … Continue reading

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matlab-storm restructure

To do Push current individual branches to distinct user specific remotes (on user specific remote accounts). Reconfigure remotes on local repository so both the release and the development are present. This is a single repository on the local computer and … Continue reading

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