Thursday 04/18/13

9:30 A – 9:00 P, 9:30 P – 1:00 A

Computantional OligoPaint probe design

Research Computing (RC) doesn’t intend access nodes to be used to submit batch jobs
bsub batch submission not working. Wrote to RC for help.
Working on parsing sequences in probe files.
Jeff’s Parse probes does not properly extract names. Maybe it’s easier just to textscan this thing into a cell array?
Batch analysis submitted on bsub after fixing Bsub script
Batch files may not run on multiple cores in parallel queue if multiple cores are not requested
Launching too many files at once from OligoArray causes OligoArray to complain in log file that too many are open (>200 at least seems to cause problems).
Requested 30 cores on parallel server. Now running as a single job (saving in 2013-04-18_oligos).
Split up genome into a separate fasta file for each gene. Launching a separate OligoArray for each gene to normal_serial queue. Now despatching thousands of jobs to queue: (saving in 2013-04-18_oligos).

Finish O/N STORM run on PhM2
Ran out of memory, forgot to delete previous files. Set up new run to get a few more cells before Graham starts imaging this afternoon.
Setting up new storm run on PhM1_B coverslip.

Finished EtOH precipitation and resuspension of probes 1-3. Ready for gel extraction.
pour 2 5% agarose gels
Attempt to cast more 10% urea PAGE gels
Ran 10% urea gel — most samples hardly entered gel after first 45 minutes. (see gel image)
DNA mostly gone after running in re-heated buffer for a second 45 minutes. Where’d it go?!
Gels ugly enough to kill small rotons:

helping Jiang determine relative protein concentrations in viral filaments
developed matlab script for basic analysis using nuclear masks and filament masks.
saved in Jiang’s folder on Cajal.