Tag Archives: coding

Wednesday 11/06/13

Posted on November 6, 2013 by admin

8:30a – 12:20a Morning tasks give Jeff deep-seq prep’d sample 4 (F3) to run as qPCR standard All analysis tasks on Cajal and all split-dax running from Monet completed. Restart Monet to install new 4Tb HDs: ProBox5 & 6. Move … Continue reading →

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Monday 11/04/13

Posted on November 4, 2013 by admin

8:40a – 12:50a Goals Cell culture check cells. Probably all need to grow at least another day or two Show BB the contaminated cultures for teachable moment. Cell staining ~ 3-4 pm start hot washes for Y RNA vs DNA … Continue reading →

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Saturday 11/02/13

Posted on November 2, 2013 by admin

9:00a – 12:00p remotely. 12:00p – 12:00a Goals Coding Add to ChromatinCropper export labeled overview fig, object centroid and bounding box in original coordinates (for computation of distance to lamina) direct measure of distance to lamina New functionalities for ChromatinCropper … Continue reading →

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Friday 11/01/13

Posted on November 1, 2013 by admin

10:00a – 9:15p Coding ChromatinCropper Current version not saving vlists! (molecule lists specific to ROI). need more display images in analysis. Data analysis: H:\2013-09-24_F6-405\splitdax Savefolder: ‘C:\Users\Alistair\Documents\Research\Projects\Chromatin\Data\2013-11-01_coloredRegions’ SplitDax System now checks filesize of the new daxfile. If expected size = actual … Continue reading →

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Ph Project To Do

Posted on October 30, 2013 by admin

Goals: Counts co-localized vs. not co-localized in Mutant vs Wildtype Psc knockdown and imaging More numbers for Ph in Ph-Wt and Ph in Ph-M Modeling: a. get correct random walk behavior from polymer model b. reproduce data trend with ka … 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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Thursday 10/24/13

Posted on October 24, 2013 by admin

8:40a – 6:20p, 11:30p – 12:55a Goals Fix Ph model — neigbhors of neighbors in situs day 2 Cell Staining Hot washes (20 min, 2x 9 min in oven + 1 min switch) 1x SSCT cold wash PBT wash 45 … Continue reading →

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Tuesday 10/22/13

Posted on October 22, 2013 by admin

8:30a – 10:30p Goals Ph simulations: time and optimize? Ph simulations: add Ph-Flag species Analyze qPCR data chromatic warp computations for Bogdan Banff report RNA prep/ clean up RT reaction cast gels with Bogdan test RT reaction qPCR analysis for … Continue reading →

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Wednesday 10/16/13

Posted on October 16, 2013 by admin

10:00am – 11:00pm Coding finishing up addition of cross-correlation based drift correction for global and local region data to ChromatinCropper GUI Mentoring Bogdan finds that samples which gave extra bands on PCR failed T7 reaction. Other samples gave good (~1000ng/uL) … Continue reading →

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