Wednesday 08/26/12

9:45 A – 7:30P, 9:30P – 12:15 A

Coding (To do)

  • Convert all function calls in STORMrenderer that are not button press objects to separate, free-living functions.  (Maybe make subfolder ‘routines’ and save in there?) This way these functions can all be easily called by batch-process scripts.
  • Incorporate data-cuts buttons into from STORMcuts into STORMrenderer

snail I (revisions)

  • exploring some other wt data sets.  First chosen set is pretty representative for range of intensity values, density etc.
  • changing figure colors:
  • change boxplots to plot solid boxes (uses findobj thickness = 4 and replaces with thicker choice (i.e. 15) to make ‘filled in’ boxes.
  • Adding mRNA counts from species comparisons.  Back to raw data.
  • Substantial literature analysis on RNA PolII traffic jams and consideration of to what degree ‘pushing of pol II’ by trailing polII can increase elongation efficiency.  See this post.  I suspect the anti-traffic jam literature is largely overselling — at low densities it probably helps keep nucleosomes off, keeps local pol II high, maybe an occassional push, but at high densities with stochastic translocation rates things are going to back up.
  • working through other reviewer comments.


  • started Application to Gordon conference.  Text here.
  • Scouting out places to apply for conference funding.   Reply to co-organizers.  Nee to check NSF / NIH grant cycles & deadlines.
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