Protected: project 2, planning

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Sunday 08/31/14

10:00 am – 11:30 pm

Project 2

Chromatin

  • need to fix multichannel drift correction in new version of ChromatinCropper

ClearlyDriftCorrectionError

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Protected: project 2 update:08/31/14

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Protected: chromatin draft figures

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Saturday 08/30/14

10:50 am – 11:00 pm

Tasks

  • video editing for XZ?
  • Finish revisions to BW Essay. Send to XZ.
  • Start working on review
  • project 2, design next 2 set of experiments

Review

  • reading and editing paper.
  • finished reading and making notes.
  • still need to assemble notes into a coherent review essay.

Discussion with Bogdan

  • will share data on Cajal

Literature

  • Stark’s totally awesome genome scale enhancer screen, finally in print.
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Friday 08/29/14

9:30 am – 10:30 pm

Chromatin project

  • some further questions
    • can we find a fundamental unit of yellow that is (more) self-interacting if we go to smaller internal sizes?
  • working on figure layout

Meetings

  • project 2 meeting
  • ice bucket challenge for Xiaowei
  • discussing project goals with Jeff

Literature

  • interesting article on chromatin state dynamics in blood development
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Protected: project 2 update: 08/28/14

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Thursday 08/29/14

9:00 am – 11:30 pm

chromatin project

  • working on figures
  • trying to lay out story — let’s formulate this as a presentation first.
  • I think the volume/pixel scaling and the Rg scaling actually provide some different information. Moreover they lend themselves to emphasize different parts of the data
    • the ‘getting denser’ is most obvious from the ‘volume’ data
    • shape changes that don’t affect density could still cause Rg to decrease (e.g. becoming more symmetrical).
    • these are also different forms of data in the pixel vs vector representations
    • Rg data makes a better statistic for comparing against other models (like the random walk).

Project 2

  • working on data analysis

Cell culture

  • growing really slowly :(.

Communication

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Wednesday 08/27/14

9:30 am – 11:30 pm

Chromatin project

  • working on figures to compare internal vs intact blue scaling (see post).

Project 2

  • analyzing new data (see post)

Other

  • poster session in Naito
  • new CRISPR/Cas9 transgenic targeted insertion toolkit being developed by Perrimon lab. Looks very cool.
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Tuesday 08/26/14

10:00 am – 11:30 pm

Writing

  • some revisions to BWF proposal in response to vague comments from XZ.
  • finalize and submit reviewer comments for recent manuscript (review due Wed)

STORM

  • Re-aligning STORM2
  • re-aligned backport optics
  • 561 and 647 beams are no longer aligned prior to backport optics (too much tweaking of the mirrors in front of the lasers…)
  • Tried to balance brightness and flatten field. Upper portion of 647 channel is still a bit dim.
  • Improved alignment of quadview somewhat (less of the field of view is cut off. These shutters and lens controllers are getting pretty sticky…

Chromatin Spot Data collection

  • multiple spots for G10 spots from chrX.
  • Maybe 2 months in culture has been a bit too long for these guys.
  • Started new cells from frozen stock. Seem to be growing alright.

Data analysis

  • Analyzing black domains
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