Sunday 05/07/15

Posted on June 7, 2015 by admin

10:00 am – 7:00 pm, 9:30 pm – 12:30 am (remotely)

Chromatin manuscript

Discussing Equilibrium Globule

  • Definitions in literature
    • Erez 2009 Hi-C paper: ““equilibrium globule”: a compact, densely knotted configuration originally used to describe a poly- mer in a poor solvent at equilibrium (26, 27).”
    • Mirny 2011: “the density of monomers is independent of the polymer length and is uniform inside the globule. This uniform-density contrasts with that of an ideal chain”
    • Mirny 2011 adds R(s) ~ s^(1/2) for s< N^(2/3) and const for s > N^(2/3) in the definition, to distinguish from fractal (crumpled globule), R(s) ~ s^(1/3).
    • presumably “being at equilibrium” is part of the definition implied by the name.

data organizing

  • moved Hi-C data to dropbox. Fixed up PlotHiC function to change filepaths better (should add filepath to varargin optional inputs).
  • moved van Steensel color data to dropbox. Fixed PlotSmoothDamID to accept a filepath argument to work from multiple computers/ directories.
  • moved raw fasta files for probe data to dropbox

manuscript revisions

  • discuss and address equilibrium globule comparison
  • tune a few things in the methods — add expanded discussion of pairing.
  • devising alternative final sentence versions
  • sent to JM
  • BB fixing up figures and updated in dropbox.
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