Protected: Pairing Meeting, Day 1

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Thursday 10/23/14

10:00 am – 11:00 pm

Chromatin Project

  • prep slides for meeting with LM et al this evening


  • running more progressive condensation BLUE simulations
  • these work better than starting all sticky for the purposes of getting mixing.

PartlyStickyBlueGlobule2 BluePolymerInternalLinScale

BluePolymerInternalLogScale PartlyStickyBlueGlobule

Code development

  • update matlab-storm STORMfinder tutorial

Meetings & Seminars

  • postdoc seminar at 4:00 pm
  • discussion with ML and team: 5:30pm – 8:00pm
  • follow up discussion with BB: 8 – 9pm.

Notes from discussion with ML

  • should compute gyration tensors — radii of gyration along each principle component
  • try computing pairwise distance distributions for all points
  • would like theoretical framework for .2 scaling
  • need to demonstrate entire range (show transitions from .5 at small scales to .33 at large scales)

project 2:

  • see notes
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Protected: project 2 update: 10/22/14

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Wednesday 10/22/14

10:00 am – 9:00 pm,
remotely 10:00 pm – 1:00 am

Project 2

  • see post
  • quick update team meeting
  • XZ team meeting

Chromatin Project

  • working on manuscript text

Hi-C simulations

  • do we see TAD like structure in black chromatin simulations?
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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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Protected: project 2 update: 10/20/14

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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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Protected: lab meeting 10/20/14

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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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