Tag Archives: STORM

Protected: Saturday 11/30/13

Posted on November 30, 2013 by admin

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Monday 11/25/13

Posted on November 25, 2013 by admin

9:10a – 11:45p Meetings Lab Meeting: private notes Journal Club: notes Mentoring Meeting Bogdan will explore length dependence in Blue domains BXC ~ 1900 nucleosomes — feasible scale for simulation Polymer simulations Bogdan attempting to get GPU accelerated openMM working … Continue reading →

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Sunday 11/24/13

Posted on November 24, 2013 by admin

10:00a – 11:00a, 3:00p – 5:00p, 7:00p-12:30p Goals Deep Seq Analysis Analyze distribution along probe region of copy number variation Analyze sequence dependence of copy number variation If a sequence contains a deletion, do we also have that same sequence … Continue reading →

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Saturday 11/23/13

Posted on November 23, 2013 by admin

10:00a – 11:00p STORM2 Helping Guipeng and Ruobo get set up on STORM2. Cell staining prepping cells for hybridizaton. last row (4 coverslips) forgot to add last rinse of PBS. Cells dried out. Coverslips tossed. cells into formamide, ready for … Continue reading →

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Friday 11/22/13

Posted on November 22, 2013 by admin

9:45a – 11:50a (remotely) 12:00p – 7:10p Genomics A549 whole cell data finished running cufflinks. Bottom half of genes are empty / all have zero FKPM (chr12 on). attempting to run cufflinks 2.1 centos6 version on cytosol BAM file directly … Continue reading →

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Tuesday 10/29/13

Posted on October 29, 2013 by admin

9:30a – 10:00p Other Goals Spoke broke. Pick up repair between 4p-6p. Presentation Prep working on slides for Rowland Center Talk. STORM Finish O/N imaging of E08 (75kb R) Set up imaging of E10 (100kb Y) Mentoring HC genes for … Continue reading →

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Sunday 10/27/13

Posted on October 27, 2013 by admin

5:30p – 10:15p STORM Record z-calibration scans for STORM4 Imaging E1 (200 kb green) cells on STORM4 Chromatin modeling Found small bug in Bogdan’s code which prevents condensation This seems to now to work as expected. Data copying data from … Continue reading →

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Saturday 10/26/13

Posted on October 26, 2013 by admin

10:00a – 8:00p Banff report (working remotely) Trimming scientific progress section (whole report needs to fit in 4 pages) added more participant comments into all sections (I think this is more meaningful the organizer summaries). STORM4 Record chromatic bead data. … Continue reading →

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Friday 10/25/13

Posted on October 25, 2013 by admin

10:00a – 9:00p Ph Meeting (10:30-1:00p) More numbers simple fig for on rate / off rate model descrimination need more bio-info trends Psc knockdown Mentoring Discussing Random Walk simulation algorithms explaining existing model code presented stripped down model code for … Continue reading →

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Tuesday 10/15/13

Posted on October 15, 2013 by admin

11:00am – 12:30p Fly work Flip stocks terminate bottle stocks Coding working on ChromatinCropper added user controls added drift correction options changed display changed export / save data methods STORM STORM of G5-P2-Cy3 with G4-P1-405 Little/no signal in Cy3 channel … Continue reading →

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