Monday 04/01/13

10:00 A – 7:00P, 9:00P-10:00P


  • hp psc1200 printer not printing color correctly.
  • lab meeting (notes)
  • journal club (notes)

Review writing

  • Insight 1: enhancer switching between obstructed and unobstructed case is the bursting model with different tx rates from ‘off’ and ‘on’ promoter states. (and non-exponential waiting times).
  • No decay -> law of large numbers is just going to send the variance to zero.
  • Fast switching also just going to get the law of large numbers average of the obstructed and unobstructed states
  • Insight 2: can’t just look at raw CoV as a function of A — the effect of low TF on noise washes out the effect of the promoter architecture. Should look at fold change for each value of A.
  • changed ModelMoments to return functions mu_vs_A and Cov_vs_A

STORM Analysis

  • Running DaoSTORM Analysis on Monet of Ph-FLAG (11 movies).
  • Analysis competing with copy (previously copied from Temp1 to Temp2, not to Alistair10).

Chromatin OligoPaint probes

  • planning experiments for oligo-paint probes
  • GREEN and YELLOW probe labels SWITCHED in my order form Brian’s library. Must check and correct
  • Ordered primers

**Thoughts on next primer-probe design*

  • try less overhang on tertiary (2 bp? no bp? get that 405 closer).
  • make secondary longer — 32 bp homology + space in-between, allows homology of PPT primary which may lose some bases.

Serious system failure

  • MATLAB crashed, 5PM.
  • won’t re-launch.
  • closed additional version of matlab running STORM analysis
  • Matlab still won’t re-launch
  • Attempting to remote desktop to Tuck or Cajal to use their Matlab
  • Remote Desktop won’t connect.
  • Saving processes, aborting all analysis, restarting computer.
  • Restarted copying data
  • Restarted analysis. Picked up at frame ~1000, I thought it was closer to 30,000, but maybe that was the molecule number. Vaguely worried it might be double counting / not resuming analysis correctly….
  • Matlab goes java lang error beserk (both versions, running analytical manipulation of matrices and running spotfinding). Closed both
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