9:10a – 11:45p
Meetings
- 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.
Genomics
- 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
STORM
- 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!)