Protected: project 2: fig3 & 4

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Monday 10/27/14

9:30 am – 12:30 am

Setting up Server part 1

  • unpacked server yesterday
  • collecting cables for new server: MORGAN.
  • installed Windows 2012 Server edition.
  • submitted purchase requests for Server 2012 R2 Standard license and 5 per user CAL remote desktop
  • contacted IT about getting ethernet and Adobe and Office installed
  • Alec will install wheels tomorrow

Project 2

  • analysis and meeting prep (see google presentation)
  • see protected post for details.
  • meeting with XZ
  • follow up meeting with team
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Protected: project 2 update

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Protected: Pairing Meeting Day 2

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Protected: Pairing Meeting, Day 1

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Protected: project 2 update: 10/24/14

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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

Simulations

  • 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.

OdysseySimulate150K_BYKp3

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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