Monthly Archives: December 2010

Protected: Discussions with G. Oster

Posted on December 15, 2010 by admin

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gap shadow paper

Posted on December 14, 2010 by admin

Revisions back from Levine.

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Markov Paper

Posted on December 14, 2010 by admin

Meeting with Peter and Steve 3:00P – 5:15P Revise model state description.  Revise discussion of two types of pausing: regulated pausing and other pausing. Need to fix reference citation in Appendix G. Fix labeling of supplemental figures: S1 sample chip, … Continue reading →

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Fly Work

Posted on December 14, 2010 by admin

Flip Collection cages 2:55 P Flip cages 6:30 P Fix embryos 8:00 P Water crosses

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Organizing

Posted on December 14, 2010 by admin

Organizing Markov Paper References Organizing Transcription / Pol pausing references Added google analytics tracking (directions here) to Notebook.

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Testing hb models

Posted on December 13, 2010 by admin

Implement Holloway model (see model_hb_bcd.m in Git repository). Modified model to use only a single promoter (not separate hb and bcd responsive promoters).  Changing binding site number still only effects sharpness of response to bicoid, does not reposition threshold.

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Revising Markov Modeling Paper

Posted on December 13, 2010 by admin

Revisions back from Steve.  Review and respond to comments.   Send back to Peter and Steve. Revisions to Supplement also received.  Still need to review and reply.

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Summarizing hb models

Posted on December 13, 2010 by admin

Desplan et al and Ma et al biochemical analysis Desplan et al and Dostatni et al transgenic / enhancer analysis Barkai, Gregor, Holloway models Notes:  Hb reading Ma Biochemistry Paper (1996) by DNAse protection assay, less than 4x increase in … Continue reading →

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Fly Work

Posted on December 13, 2010 by admin

Collect virgin fog mutants Flipped collection cages 12:30 (pre-lay) Flip collection cages 1:30P, 3:30P (age) Fix: 5:30P (MP11/CyO, MP3/CyO, sna18,MP10 Hz). Water crosses (all 12 DB3 HbZ crosses look infertile).  Pool flies. Collect virgin fog flies (11:00P)

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BioE Final Presentations

Posted on December 13, 2010 by admin

Evaluating BioE 190/290D final presentations from MIT and Berkeley, 8:30A – 12:00P

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