Monday 02/11/13

9:30 A – 7:15, 10:00P – 11:45P

Postdoc candidate

Fly Work

  • Flip collection cage 9:30A. O/N collection poor, not worth fixing.
  • good collection at 1P, should probably flip around 1:30 and fix later.
  • Collect AM virgins
  • esc/esc,CyO compared to Sp/esc,CyO ~ around 1:3. (previously ~1:5)
  • Scoring second round of complementation backcrosses for recombineering:
  • da[10]/inv-Gla x esc2/CyO getting ready to emerge
  • Move to bottles: dorsal deletion, Da deletion, twi deletion.
  • collect virgins, PM
  • All MATtub x shRNAi lines from 2/1 are parental cleared. Ready for emerging F1s by the end of the week.
  • MATtub x Psc-shRNAi2, MTD x Psc-shRNAi2, MATtub x Su(Z)12-shRNAi all F1 x F1 at 29C (just emerging)
  • Fix 5-9 hr scm shRNAi embryos
  • fix 5-9 hr scm shRNAi embryos (round 2)
  • Flip collection cage, 11:40 P


  • interesting paper by Schwabe et al on stochastic models of transcription. Also takes an analytical approach using laplace transforms similar to ours approach with paused promoters in PLoSCB.
  • may be useful in analytical formulation of shadow enhancer model.


  • Finish basic implementation of generalized chromatic warping

STORM Analysis

  • For 3D chromatic bead correction, having the same bead in all 10 images is pretty important for the quality of the fit. Might need to increase thresholds to reject weak beads more and increase search range.
  • It seems to me the stage drift correction is backwards — it compresses the actual z-range explored when the z-range explored is stretched by z-drift. Maybe fixable by a sign error switch in computing the offset to nm conversion ratio?
  • # See if we can fix z-offset error.
  • # Analyze all bead data.

Presentation stuff

  • Prep a few slides for discussing project with post-doc candidates
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