Monthly Archives: October 2014

10:00 am – 11:00 pm Project 2 see post Chromatin project working on manuscript playing with chromatin simulations

10:00 am – 12:45 am Chromatin Modeling initalization compressed random walk polymer maybe not best initial fractal globule state try using a sticky polymer, these have pretty good fractal structure all the way down. too sticky polymer settles down too … Continue reading →

Chromatin Model revisions Add sticky and non-sticky blue (so not all nodes are sticky) helps blue mixing updates to chromatin model working on Polymer simulations

10:00 am – 2:45 am Chromatin Literature reading Mirny 2011 review Simulations Data for Bogdan send volume table to Bodgan to explore densities send table of internal volumes send table of intact Rgs send table of internal Rgs To plot … Continue reading →

11:00 am – 11:00 pm Computation investigate local data running on Odyssey CPU does not look straight-forward. Writing to RChelp for more info Project 2 run threshold scans on Cajal — now going on original test dataset and new dataset … Continue reading →

10:00 am – 8:00 pm Modeling Calculations fractions of chromatin types in genome of the 120 Mb of classified sequence (some 60 Mb ‘other’ class) estimate: from Pc track, 1 – 3% ‘Blue’ estimate: from yellow/red Filion data: 34% ‘Yellow’ … Continue reading →

9:45 am – 12:15 am Project 2 see post Chromatin Openmm configuration updated openmm-polymer in Python26/Lib/site-packages/ to latest download archived old openmm-polymer in Research/Software/OpenMMchromatin/Archive (this had some of my scripts as well) reorganizing OpenMMchromatin into Archive Templates Simulations Functions Scratch … Continue reading →

10:00 am – 12:15 am Project 2 see post. Chromatin heard back from Geoff got example code of fractal globule, need to run and test Computer sent quote request to Dell discussed pricing with Matt discussed quote request with PCSFE