Friday 09/05/14

10:00 am – 12:00 am

Update on running Analysis

  • Cajal and Tuck still building library, 20-40% complete.
    • Won’t be done for another 24 hours at the earliest.
    • maybe longer as the day brings competition of these cores and my programs are “polite” and launch at low priority.
  • Interaction analysis still running, should finish before tonight
  • refitting BB black D12

Internal black analysis

  • D11 — conventional images useless, STORM images not promising. fortunately I already repeated this one myself
  • D12 — out of focus spots are overly large
    • spots also pretty dim for Alexa647
    • large spots only get off-center localizations when multiple spots are called in the same frame.
    • looks promising if we can refit the data.
    • first pass at refitting totally mismatched files / images. Copying data, will repeat this.
  • D08 — D08_08_05_2015 conventional images are more or less blank. Most STORM images very close to blank.
  • D09 — data looks reasonable. Reprocessed.
  • D09-10 conv looks okay, lots of storm movies missing or no reasonable data. 2-10 might be good.
    • fiducial drift correction failed or extremely poor.
    • Correlation based drift correction looks to be sufficient accuracy


New Stains

  1. D10 S1-647, D09 S3-750
  2. D11 S1-647, D12 S3-750
  3. D08 S1-647
  4. D10 S1-647
  5. E05 S1-647 + E04 S3-750
  6. E08 S1-647 + E07 S3-750

passaged cells, replaced media.
tossed old cells (after 2 months in culture).

For later

  • E05 S1-647 + E04 S3-750
  • F04 S1-647 + F03 S3-750
  • L4E2 S2-647, L4E1 S3-750

Chromatin region analysis

  • processing L4E17 data (15 kb of BXC)
  • processing L4E17-19: 45 kb of BXC
  • Need to fix G09 is a (75%) internal part of C05, not an end to end domain
  • processed black 2 color data: L4E1 + L4E2.
    • 750 missing in most images,
    • partly due to laser off-center
    • largely due to buffer death
  • re-processed internal black domains as indicated above.
  • some results

Attempting batch jobs on Odyssey

  • see Bogdan’s email
  • array launch still goes into queue
    • jobs actually launched.
    • individual output files and error reports also generated.
  • what if we request 500 cores and then do a bunch of system([task,' &']) commands in a loop? On a desktop these go out to separate cores. Lets see if this simple approach can work on the remote.
    • all java commands die with memory errors. (didn’t actually expect them all to launch, so maybe this is progress).
    • actually started running all these java files. I see even _oligos.txt files for a bunch of genes, some even with data and probes.
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