Tag Archives: coding

Sunday 12/29/13

Posted on December 29, 2013 by admin

9:00a – 12:15a Goals Write to Ajaz about new plans Read in _oligo.txt files and analyze probe distributions STORM G1-G2 Start analysis of F12-G01 and F12-G11 data continue work on STORMrender Manual Literature Reading Kieffer-Kwon et al Cell 2013. link … Continue reading →

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Sunday 12/22/13

Posted on December 22, 2013 by admin

9:45a – 11:50p Goals align 750-647 G1 double stains matlab-storm STORMrender update menu options for feducial drift correction to allow finding the bin file of feducial data using the browser (oops, this was already the default for an empty input, … Continue reading →

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Friday 12/20/13

Posted on December 19, 2013 by admin

10:00a – 12:45a STORM imaging need images of 715 beads to align A750 and A647 channels Making new 715 bead slide at 1:20,000. If this looks good we can try a 2-color bead slide as well. trimming the tape so … Continue reading →

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Wednesday 12/18/13

Posted on December 18, 2013 by admin

10:30a – 8:15p, 12:00p- 1:00a Meeting with XZ prepping slides (see notes) Test probes synthesis analyze tomorrow Coding matlab-storm Work with Jeff to restructure startup / installation need to update readme need to update all global variables to new conventions … Continue reading →

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Friday 12/13/13

Posted on December 13, 2013 by admin

10:45a – 12:15a Notebook backed up notebook updated wordpress Z-calibration cross correlation doesn’t improve curve alignment visibly — curves are fundamentally a bit different no spatial structure evident Ph Project reviewing simulation results saved as simulationName_2.eps to file Test new … Continue reading →

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Thursday 12/12/13

Posted on December 12, 2013 by admin

10:45a – 11:00p Ph Simulations Troubleshooting extra along bonds. Oops, actually just resulted from plotting the wrong attachment matrix for the given position list. Simulations ran at subsaturating Ph — more total sites than available Ph. Hence there is a … Continue reading →

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Protected: project 2 update 12/10/13

Posted on December 10, 2013 by admin

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Protected: Saturday 11/30/13

Posted on November 30, 2013 by admin

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Wednesday 11/27/13

Posted on November 27, 2013 by admin

Goals Sequencing analysis plots of coverage uniformity per probe set plots of failed probe vs. purity using new indexed method (or maybe just a length cut-off) Ph Project restart simulations Genomics start building library 4 (on Monet) start building library … 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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