Tag Archives: coding

Sunday 05/19/13

Posted on May 19, 2013 by admin

10:30 A – 10:00 P, 11:00 P – 12:15 A Probe extraction Previous test gel, suggesting some samples at least have probe: Run denaturing gel at 100 uL scale 95 minutes. Cut out smallest band over 50 bp. sample loading … Continue reading →

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Friday 04/05/13

Posted on April 5, 2013 by admin

9:00 A – 8:00 P, 9:00 P – 10:45 P General (8:00 A allergy test) STORM analysis Getting images of relative background levels in 3-Cy5 vs 405-cy5 Drift correction makes sparse images look horrible (even the rather long integration of … Continue reading →

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Tuesday 04/02/13

Posted on April 2, 2013 by admin

9:45A – 5:00P, 8:00P – 10:00P Modeling Exploring parameter space of site-interaction-number models. Bursty regime: fraction of time in the transcribing state is low (kon/(kon+koff)) Transcription rate in the on phase cooperativity noise Most obvious at low induction In general … Continue reading →

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Saturday 03/23/13

Posted on March 23, 2013 by admin

11:00 A Cell culture Moved cell to 28C incubator observe substantial cell debris in dish (dead cells from heat shock?) Genomics Installing OligoArray2.0 http://berry.engin.umich.edu/oligoarray2/ Need to install legacy BLAST. Installed. Need to install OligoArrayAux: http://mfold.rna.albany.edu/?q=DINAMelt/OligoArrayAux. Error with database in2 = … Continue reading →

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Saturday 03/16/13

Posted on March 16, 2013 by admin

11:00 A – 7:00P Kinetic modeling STORM Analysis Switching is indeed failing on BX-C 2/20 data. Sad we still don’t have this basic data with enough depth yet. S3 cell data shows plenty of blinking out at 58 and 90K … Continue reading →

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Friday 03/15/13

Posted on March 15, 2013 by admin

9:50 A – 8:30 P Goals Write SDB abstract. OligoPaint prep * Run probe design * Order probes 3. Chromatin color region selection * write script to chose genomic regions based on size, color, and color-confidence score. Genomics Probe Design … Continue reading →

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Wednesday 03/13/13

Posted on March 13, 2013 by admin

10:00 A – 9:30P, 11:00P – 12:55 A STORM Finish O/N run on STORM2 STORM Analysis Launch Analysis of all fab7 data collected on STORM2 — now running on Cajal in small batches. Finish configuring local repo on TUCK to … Continue reading →

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Tuesday 03/12/13

Posted on March 12, 2013 by admin

10:00A – 11:15P STORM Finish O/N STORM run on STORM2 Finish O/N STORM run on STORM3 Installing mount and sliders on STORM4 to allow for 3D imaging Lessons: Final appeture (removed for alignment) front-back position chosen to minimize the size … Continue reading →

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Monday 03/11/13

Posted on March 11, 2013 by admin

10:00 A Group meeting (Eileen) see notes Journal club: High salt recruits aversive taste pathways STORM Hal crashed on STORM3 at 10:11A (still 34 locations acquired). sent STORM3 error report to Hazen (see email record) STORM2 run seemed to finish … Continue reading →

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Friday 03/08/13

Posted on March 8, 2013 by admin

10 A – 11:00 P Transcription models Finished derivation from yesterday on multiple binding wrote up in Review, started extension to cooperativity Markov Chains in TeX write like chemical equations with mhchem package Use Tikz drawing package Named Graphs (Tikz … Continue reading →

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