Friday 12/06/13

9:50a – 10:45p


  • Presentation prep for meeting with XZ (meeting rescheduled)
  • Coding:
    • work on new z-calibration algorithm
    • add run silent options to STORMrender
    • update template ini and xml parameters to contain new ROI defaults
  • Probe Making
    • HPLC cy7 secondary
    • set up RT reactions for probe synthesis using primers P1a405 and P3a405

Coding matlab-storm

  • issues with ReadDax
  • To do:
    • integrate memory-map based ROI from ReadDaxBeta into ReadDax.
    • Add CheckSystemMemory script to system.
  • issues with git: BogdanBeta locked when attempting merge to master. Lock prevents switching branch back to Alistair
    • apparently a Windows issue. Rebooting the system fixed this.
    • Remember to git checkout master and git merge alistair into master in order to update master. Git push master just updates remote master with local master (which otherwise has not been updated).

Probe making

Secondary Labeling

  • Dye labeling and HPLC purification of secondary L2S3Cy7
  • see HPLC notes
  • very poor dye incorporation. Maybe new dye pack will work better? 95% + of DNA unlabeled.
  • proceeding with evap

Probe making RT reactions:

  • Maxima protocol
  • 9 uL RNA + 6 uL dNTPs + 8 uL 100 uM primer
  • denature at 65C 5 min, then chill on ice.
  • Enzyme mix for 30 uL totoal = 6 uL buffer, 1 uL RNase inhibitor.
  • Master = 108 uL buffer + 18 uL RNase inhibitor + 2 uL Maxima Enzyme. Add 7 uL per reaction.
  • Incubate at 48C for 1 hr.


  • wind maps!,-71.02,13,1
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