Wednesday 05/13/15

9:00 am – 10:15 pm

Geoff’s Defense (9:30 am – 11:00 am)

  • see post
  • short follow-up discussion with BB and GN

To Do

  • Travel reimbursements
  • write to XZ about LM travel schedule (done)

Chromatin Paper

  • Built new composite data structure (allData.matb) to avoid mixed data sets and crazy indexing.
    • some manual field alignment: print elements to Excel, ID missing fields, annotate back in by hand.
    • built new domainData2 structure which has the library number and positions (just positions was getting very confusing)
  • Completed assembly of Supplemental Figure on Intact Domain Histograms

Extended data Figure revisions (3pm – 5pm)

  • renumbering extended data figures in Main text, figures, and figure captions.
  • Writing new extended data figure captions.

New Extended Data Figure 8:

  • wrote generic bootstrapping function to compute confidence intervals.
  • set confidence intervals to 78% for errorbars, So probability two data points with confidence intervals that just overlap are not different ~.22^2 = 0.05.
  • alternatively could do the traditional SEM and the error bars would be smaller still.

Still to do

  • Write cover letter
  • Write description of domain selection
  • color connecting bars in Fig E6
  • print multiple versions of green/magenta/white contrast for Fig 2 and 3
  • combine probe fasta tables and update probe names with new conventions


  • Jeff will send script on new probe design for human genome
  • Try building a matlab class to handle library design?
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