Alistair's Lab Notebook

10:00 am

Goals

• prep some slides for rotation meeting discussion
• work on figures for project 2
• revise manuscript and figures for chromatin paper

Project 2

• dispatching data analysis needed for next figures

Manuscript

• working on draft

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

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.

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

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?

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.