Tuesday 10/20/14

9:30 am -5:50 pm, 7:30 pm – 12:00 am

chromatin simulations

  • check simulation project

Odyssey results

  • Now black behaves properly but yellow and blue are giving issues
  • yellow not equilibrating?
  • not sure what’s going on with blue, will require further investigation. Possible that large domains are swallowing smaller ones and growing too fast.
  • also possible that large domains are just splitting into multi-rosettes and small domains stay as singles.


New simulations

  • ‘WholeNucVOp5′ – 10% sticky blue, blue attraction 3.0 repulsion 3.0
  • ‘WholeNucVOp6′ – yellow back to no stiffness, run for 200 steps.
    • this does (as before) a good yellow black split.
  • New approach — successively add more sticky sites to BLUE. see if we get a better saturated state if it folds in steps.

Discussion with Xiaowei

  • XZ doesn’t like the yellow model as a faster equilibration to Eq. Globule from Fractal globule (due to energy or chain-crossing). Too much of a polymer explanation, not enough useful biology.
  • probably right, I think the modeling is actually rewarding and complex enough just with the blue.
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journal club

Multiplex single-molecule interaction profiling of DNA-barcoded proteins
Nature 2014, Church lab, Gu et al

presented by Pallav


  • current approaches = protein vs. library
  • rather do an everyobdy to everybody screen. One pot analysis not well-based screen


  • single-molecular interaction sequencing (SMI-seq)
  • barcode proteins with DNA.
  • on the mRNA add a barcode and a stalling tag downstream of a polypeptide linker. The ribosome now combines the mRNA and the protein together. (during an in vitro translation reaction following an in vitro transcription reaction).
  • can now mix proteins
  • barcoded RNA annealed to RNA with little tags.
  • create dilute array of polonies in acrylomide gel. Can now sequence.
  • have two different pools with two different primers. Only the ones with one of each primer can be decoded.
  • challenges: very different yields of different complexes. Can count total spots to get estimate of concentrations and thus get estimates of binding efficiency ?

ligand binding screening

  • small molecule binding to GPCR (g-protein coupled receptor) measure affinity based on GPCR’s change in affinity for binding protein arrestin. different ligand in each well.

library to library screening

  • library 1 antibody domains (a bunch of mutated variable forms)
  • library 2 human proteins
  • test 200 x 60. With Illumina reading propose could test 10,000 x 10,000
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Monday 10/20/14

10:00 am – 2:30 pm, 4:00 pm – 11:00 pm


  • lab meeting (see notes)
  • journal club (see notes)
  • discussion with XZ

Project 2

  • working on pipeline3
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Sunday 10/19/14

10:30 am – 6:20 pm, 10:30 pm – 12:00 am

Chromatin simulations

  • Anaconda called from sbatch actually worked to get save data.

issues with current simulations

  • black chromatin starts at .4 (and stays there).
  • writing new template to do the the fractal globule 2 step formation first before starting simulation
  • this is actually relatively slow, we may not want to do it fresh each time.

Summary of recent simulations

  • WholeNucV6p15 – 30+ runs of basic blue/black/yellow
    • yellow and black split off a bit too late, but with appropriate difference in slope
    • both yellow and black a bit too relaxed — yellow .5 black .4
    • blue is holding at correct Rg slope of .2 and a reasonable density, looks




New simulations

  • running on Odyssey rpt of V6p15 with stiffer yellow and slightly fewer sticky blue
  • testing on Monet new pipeline to generate and relax fractal globule all in same script (V7)
  • V7p2 looking a bit better:

Running V8p1 — trying to get black to initialize closer to .3 than .4. I think this is because the Random Walk Polymer initiation starts entangled. Trying a simulation with a condensed regular coil.

Meeting Ajaz

  • discuss PH project follow up
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Saturday 10/18/14

10:00 am – 1:00 pm, 7:00pm – 9:00pm,

Fly work

  • flip stocks


  • troubleshooting running polymer simulations on Odyssey GPU
  • issues using polymer load and save commands — requires joblib
  • testing out with Anaconda via sbatch command
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Friday 10/17/14

10:00 am – 11:00 pm

Project 2

  • see post

Chromatin project

  • working on manuscript
  • playing with chromatin simulations
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Thursday 10/16/14

10:00 am – 12:45 am

Chromatin Modeling


  • compressed random walk polymer maybe not best initial fractal globule state
  • try using a sticky polymer, these have pretty good fractal structure all the way down.
  • too sticky polymer settles down too slowly (even with local energy minimization).
  • starting from this condensed state and letting the system relax rapidly back to the new target density is also bad
    • in particular, the black chromatin rebounds faster than the yellow, and the yellow stays compressed.

Initial condition variation

  • starting on the same section of the same initial fractal globule has strong effects on behavior
  • fractal globules having all scales of loops have dramatic variation in the size of any given domain. It seems to me insufficient attention has been given to this variability in the literature.

effects of Energy minimization

  • energy minimization greatly helps compacting blue domains
  • energy minimization possibly expands the black domains at the expense of the softer yellow domains.
  • maybe if the yellows are sufficiently transparent they won’t get compressed?
  • not sure if this true — maybe just an artifact of the fact my circ permute domains got all my domains mixed up.


  • okay, debugged new permute domains. hopefully this works in disrupting the dependence on initial condition.
  • things looking a bit more promising. Need more averaging!



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