Tuesday 04/02/13

9:45A – 5:00P, 8:00P – 10:00P


  • Exploring parameter space of site-interaction-number models.
  • Bursty regime:
    1. fraction of time in the transcribing state is low (kon/(kon+koff))
    2. Transcription rate in the on phase
  • cooperativity noise
    1. Most obvious at low induction
    2. In general appears to require low noise
    3. Need to have some weak basal transcription so noise doesn’t kick up towards infinity at low induction
    4. mRNA decay needs to be slow. — this also keeps the low mRNA number / stochastic decay noise down.
  • Can get good evidence of cooperativity noise in the bursty regime. Just not in the short-lived mRNA regime.
  • enhancer increased transition rates — should be kb+km, not just km.
  • Working on figures to illustrate states.

Banff workshop prep

  • Reminder emails to invited participants Banff
  • Pretty good reply rate. Should send out next round tomorrow.

STORM Analysis

  • Running Ph-FLAG and PhM-FLAG round 1 STORM analysis
  • Set up O/N DaoSTORM analysis of 512×512 Fab7 STORM data


  • implemented multi-version support for STORMfinder and its daughter GUIs
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