Monday 11/25/13

9:10a – 11:45p


  • Lab Meeting: private notes
  • Journal Club: notes
  • Mentoring Meeting
    • Bogdan will explore length dependence in Blue domains
    • BXC ~ 1900 nucleosomes — feasible scale for simulation

Polymer simulations

  • Bogdan attempting to get GPU accelerated openMM working on Cajal
  • Moved to Monet for safety. Unable to install easily.
  • NVIDIA CUDA 5.5 breaks compatability with 4.1, previous GPU acceleration for STORMrender
  • Attempting to reverse by uninstalling CUDA 5.5
  • OpenMM 5.1 is available on Odyssey.
  • CUDA not working on GPU still. TdrDelay had disappeared. Wrote new TdrDelay DWORD. System needs reboot for changes to be applied. Wait until after genome processing is done.

Cell Culture

  • Passaged cells
  • Froze 10 vials of Kc cells (combined 2 confluent 75 cm^2 chambers).
  • Tomorrow remember to move cells to LN2.


  • Building Fasta file from cufflinks GTF output
  • Need to ID most expressed isoform for each gene
  • Need to find the list of introns / utrs etc corresponding to that isoform, and the strand orientation
  • Go to the genome fasta files by chromosome and grab the corresponding sequences. Splice them all together and reverse complement if necessary.
  • info on GTF format.
  • Running conversion overnight


  • Finished O/N STORM imaging of D10
  • D08 (50kb Green) seems to stain alright. Not especially bright, background a bit high, but working.
  • running O/N STORM imaging of D08
  • Bogdan imaging on STORM2
  • notes on STORM2: slider tucked in dark box of cMOS camera is now the control to switch between camera ports on STORM2. Be careful not to turn the slider!
  • Moving the slider does require backport alignment to be repeated. (and beads to be re-imaged!)
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