Wednesday 03/12/14

Posted on March 12, 2014 by admin

8:00a — 12:00a

Research Organizing

  • launched matlab-functions repository: a private repo with all my common functions.
  • Better for hosting on github, managing between computers, and sharing with lab members.
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Ph project manuscript to do

Posted on March 12, 2014 by admin
  1. Add Pc to figure 1 (all Pc, not just Ph associated Pc)
    • Follow same layout of 3 panels, confocal, STORM, stats.
  2. Fig 6 diameter as a function of Ph-ML concentration.
  3. Modeling supplement: detailed description and chemical equations
  4. Fig 3. fix the scalebars and fix the different blacks. Remove text on scalebar. send as illustrator.
  5. Fig 2. losing black lines.
  6. Big ‘clusters’ in PhM data.
  7. Send FISH-STORM images
  8. analyze PSC-PH data
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Protected: project2 update

Posted on March 12, 2014 by admin

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Protected: project 2 update 03/10/14

Posted on March 10, 2014 by admin

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Thursday 03/06/14

Posted on March 6, 2014 by admin

11:00a

Maintenance stuff

  • moved 2013-10-07_F09 and 2013-10-09_F01V2 from proRAID to ProBox1 to make room for more Ph datasets on ProRAID1
  • deleted these files from ProRAID. Now moving all Ph datasets from ProRAID2 onto ProRAID1 (another 1.3 TB. some of these could use compression still).
  • automatic analyze on arrival didn’t reset wait-times, consequently failed to keep launching analysis throughout the night. Fix and start running.

Robert Singer Visit

  • meet at Balskus Lab at 12:10p

Chromatin Project

  • Set up PCRs
  • 25 uL Phusion + 20 uL ddH2O + 1 uL 1:50 library + 2.5 uL 10uM Forward + 2.5 uL 10uM ReverseT7
  • regions selected
    • C01 chr2L:10203488-10443191__Y_240kb_TAD_G-gaps
    • C02 chrX:16351360-16440669__K_90kb_Disco_TAD
    • C03 chr3R:17205633-17399201__BLUE_200kb_lbe-Tin_cluster
    • C04 chrX:15953918-16160086__BLUE_200kb_disco
    • C05 chr3R:3953538-4054361__BLUE_100kb_grn
    • C06 chr2R:1593366-1640664__BLUE_47kb
    • C07 chr3R:11833445-11870730__BLUE_37kb_pnr_GATAe
    • C08 chr2R:5080631-5092410__BLUE_12kb
  • PCR failed (Gel failed?)
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Wednesday 03/05/14

Posted on March 5, 2014 by admin

8:10a – 11:30p

To do

  • Call Russell House to check for reservations for Thursday
  • write code for on the fly data transfer
  • debug Hal based splitdax and bead integration.

Computer

  • copying 2013-12-28_PhWtPh, 2013-12-29_PhMPh, 2013-12-31_PhWtPh from ProBox6 to ProRAID

Project2,

Coding (general use stuff)

Automatic detection and analysis

  • wrote new scripts (could/should be functions)
  • AnalyzeOnArrival_140305.m
  • SplitOnArrival_140305.m
  • CopyOnArrival_140305.m
  • CopyAndAnalyzeOnArrival_140305.m

Chromatin Project

  • discussion with Bogdan
  • new library arrived
  • diluted both primer sets
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Protected: project2 update

Posted on March 5, 2014 by admin

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Tuesday 03/04/14

Posted on March 4, 2014 by admin

8:30a – 9:45a, 2:00p – 11:45p

computer stuff

  • Copying files extremely slow. 335 Gb copy from ProBox 1 less than half done
  • computer seems to have taken the night off. Splitdax was on like 115 of 136 at midnight and is now only on 128 of 136.
  • canceled
    • 2013-12-28_PhWtPh, 2013-12-29_PhMPh, 2013-12-31_PhWtPh from ProBox6 to ProRAID
    • 2014-01-30_PhMPh and 2014-01-30_PhWtPh from AlistairRAID2 to ProRAID
  • still copying 2014-01-09_PhM from ProBox1 to ProRAID. extremely slow. This folder needs some splitdax action too.

(cross-country skiing, 9:45a – 2:00p)

RC computing

  • Bug fix: remote queue commands need to begin with #!/bin/bash not #!/bin/bash/.
  • Fixed cufflinks file

    #!/bin/bash

    #SBATCH -n 1

    #SBATCH -t 1440

    #SBATCH -p general

    #SBATCH –mem=6000

    #SBATCH -o /n/home05/boettiger/out

    #SBATCH -e /n/home05/boettiger/err

    module load centos6/cufflinks-2.1.1.Linux_x86_64
    cufflinks –max-bundle-frags 90900900 -G /n/holyscratch/zhuang_lab/boettiger/gencode.v18.annotation.gtf /n/holyscratch/zhuang_lab/boettiger/IMR90.sam > /n/holyscratch/zhuang_lab/boettiger/outputCufflinks.txt 2> /n/holyscratch/zhuang_lab/boettiger/errorsCufflinks.txt

ChromatinCropper

  • Found Bug!! props2D.mainArea*pixelSize should have been props2D.mainArea*pixelSize^2! For the most part this should just be a linear rescaling of the data.
  • fixed bug, reran data. As expected, more-or-less a linear rescaling. Some adjustments due to sparicity of localizations results in minor relative shifts.
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Monday 03/03/14

Posted on March 3, 2014 by admin

9:30a – 12:05a

Project 2

  • Out of disk space on Tuck and temp drive.
  • analyzing data, team meeting, writing new code, and more stuff: see project post.

The little things

  • passage Kc cells, replace cell media
  • make new STORM imaging buffer

Ph Project

  • image all negative control coverslips on STORM2
  • two fields of view per condition. 50K frames in general.

File shuffling

  • (delete from source folder after transfer is complete).
  • 2014-01-09_PhM from ProBox1 to ProRAID
  • 2013-12-28_PhWtPh, 2013-12-29_PhMPh, 2013-12-31_PhWtPh from ProBox6 to ProRAID
  • 2014-01-30_PhMPh and 2014-01-30_PhWtPh from AlistairRAID2 to ProRAID
  • let’s consolidate all Ph project folders onto ProRAID instead of the numerous proboxes and AlistairRAID2. Recently added chromatin imaging data on ProRAID can move to appropriate chronological record on ProBoxes
  • need to clean up ProBox7 and need to clean up 2 color images — including the Ph data.
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Protected: project2 troubleshooting

Posted on March 3, 2014 by admin

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