Category Archives: Transcription Modeling

Protected: enhancer modeling

Posted on January 16, 2011 by admin

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extending enhancer modeling to snail data

Posted on January 12, 2011 by admin

Variation in activation state among cells is uniformly 10 fold larger in all data samples than expected by binomial statistics (independent cellular response with fixed probability) Maybe we need to correct for borders, because the vast majority of these missing … Continue reading →

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Coding

Posted on January 11, 2011 by admin

Downloading scipy to facilitate migrating simulation of code into python. Some trouble-shooting, but it works fine now:

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Protected: Modeling hb-shadow data

Posted on January 10, 2011 by admin

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writing

Posted on January 10, 2011 by admin

Continuing work on manuscript draft “Effect of binding site number…” (Bicoid_limits_paper.tex).  Moved to dropbox folder for easy multi-site editing.

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writing

Posted on January 8, 2011 by admin

Working on text and figures for “Effect of binding site number and spacing on transcription regulation” MS. General outline: Recap key conclusions from Gregor and Dostatni papers. Motivate developing a method for relating transcriptional activity to limits in concentration (integrated … Continue reading →

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Protected: hb enhancer modeling

Posted on January 7, 2011 by admin

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Comparison to Gregor data

Posted on January 6, 2011 by admin

To count all 770 molecules in the nucleus according to Thomas data (D =1, c=4.8, a=.003) would take 890 minutes (and give 3.6% diffusion error). naturally 100 molecules gives a std/mean 0f 10%, and is thus the natural threshold for … Continue reading →

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Protected: Comparison to hb data

Posted on January 6, 2011 by admin

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Protected: Transcription modeling hb activation

Posted on January 6, 2011 by admin

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