Thursday 01/24/13

9:30 A – 7:30P STORM
* Finish O/N run by 10A.
* Run Z-calibration
* Copy and delete data!  Remove external hard-drive
* Image BX-C + H3K27me3-488 slide (at 4C in PBT).  maybe we should store these in 2x SSCT? STORM analysis

  • Running InsightM using new STORMfinder interface on 3 original BX-C clusters run.  
  • BX-C_3D_3 BX-C_3D_2 BX-C_3D_1 HP1_3D_2 HP1_3D
  • 3D HP-1 clusters (dense images) and BX-C labeled complex, (zoomed in small images).
  • The z-calibration appears to be off — dots span the whole range up and down.  This same z-curve on my bead data does very poor.
  • default_zpars_nogood
  • Even worse at z = 0
  • zcal_fails_at0 Coding

  • Troubleshooting ‘AnalyzeAllDax’ command for method  ‘GPUmultifit’

  • WriteMoleculeList needs all fields populated.  With this fix, the thing now works.
  • Troubleshooting suddenly slow processing speed of insightM on large data sets:
    • fclose in WriteInfoFile takes 10 seconds
    • fclose(ftemp) in write dax file takes 10 seconds
    • InsightM takes 77 seconds to find molecules in a single frame
    •  –> problem of working across network.  Especially when folder is already being accessed to copy files from STORM2 computer.  Runs fast locally.
  • Updating STORMrender

    • Change over to new mlist format (maybe just write a converter as a stopgap?)
      • changed plot_STORM and plot_STORM_zcolor to new mlist format.
      • All single color functions now use new mlist format
    • load drag and drop bin files (into channel of choice?)
      • drag and drop bin files now quick load into STORMrender in channel 1 if users selects to use STORMrender.  Otherwise a molecule list is read into memory.
      • Quick load button now tries to read the global ‘binfile’ (generally defined by drag-and-drop). Fly work
  •  get flies from mailroom

  • collect virgins: sim[D] Espl[D],  Communication

  • Accept review request (due Feb 7th)

  • Stas proposes I write a short BJ letter on a probablistic model of shadow enhancers.  I promised to work this out and send him a draft.
  • Reply to Banff team about contacting participants  
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