Wednesday 03/13/13

10:00 A – 9:30P, 11:00P – 12:55 A


  • Finish O/N run on STORM2

STORM Analysis

  • Launch Analysis of all fab7 data collected on STORM2 — now running on Cajal in small batches.
  • Finish configuring local repo on TUCK to run analysis. Had to fix matlab core path files, no idea how these got screwed up on Tuck
  • Launched all STORM3 collected fab7 data on TUCK.
  • Switching and brightness clearly better on STORM3. Should compare no-quad-view: STORM3_switching_wins
  • Monet crashed when trying to remote connect. Crashed data analysis on Tuck. (Cajal resumed correctly).
  • Relaunched data analysis on Tuck.


  • Fixed bug in primer selection
  • Need to Re-do probe design: pasting homology-free 20mers together to make 64mers is not a good approach for building homology free 64mers.
  • Figuring out how to call R code from HHMt

Figuring out details of HHMt algorithm

  • First PCA the 54 dimensional data-set down to 3 dimensions
  • Apply the BauerWelch HHM model to the first 3 principle components (saves memory, should get same classes).
  • Wrote R script \Chromatin\Code\Functions\applyHHMt.R
  • Wrote Matlab wrapper script \Chromatin\Code\Functions\SimulateColorData.m
  • Works! hhmt_success
  • (class numbers are arbitrary, but the correspondence should be the same (i.e. class1 in true data may be class4 in simulation).


  • package for dealing with big data matrices in R

Coding to Do:

  • Role out updated version of STORMfinder
    1. Need DemoData
    2. Need short tutorial
    3. Need screenshots
    4. Need link to STORMfinderBeta
  • Role out STORMrenderBeta
    1. Need DemoData
    2. Need short tutorial
    3. Need screenshots
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