Monthly Archives: June 2011

Tuesday 06/14/11

Posted on June 14, 2011 by admin

9:30 A — 7:00P, 8:00P — 11:00P working on hb-variation figures Revised discussion of gap-shadows paper again.  sent to ML. # reorganize directory: mRNA counting , enhancer modeling, etc rerun MP02 data on alternate threshold settings, no change in transcript … Continue reading →

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Monday 06/13/11

Posted on June 13, 2011 by admin

9:30 A – 7:00P, 8:00P – 11:30P Biophysics meeting.  Discussed having faculty list skills per lab. Meeting with Sunney Xie Finish Confocal run, 12 embryos by 2:00P. BAC 11 early rescue line died out :(. phone discussion with Xiaowei Zhuang. … Continue reading →

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Sunday 06/12/11

Posted on June 12, 2011 by admin

3:00P – 6:40P, 8:30P – 11:00P Confocal, MP02 ON (13 embryos finished, 10P-4P) Working on figures from hb-heterogeneity analysis. New confocal run, setup 12 MP01 embryos, 10P-scanning.

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Saturday 06/11/11

Posted on June 11, 2011 by admin

9:15 A — 12:00P, 8:30P – 9:30P, 10:30P- 11:30P Aligning hb-gradient data based on matching endogenous profiles. check mCD8 cloning plates — colonies don’t look good, check insert concentration and try ligation again. set-up MP02 ON confocal

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Friday 06/10/11

Posted on June 10, 2011 by admin

10:45 A – 8:40 P Updates to Biophysics website for basic demo of wordpress capabilities: stacked pages, RSS publications, RSS awards, Events calendar (10:45-12:30) Ligating dGFP-mCD8 cloning Lab meeting 2p – 4p Plate cells, incubating at 37C, 5:00P. Analyzing hb-data. … Continue reading →

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Thursday 06/09/11

Posted on June 9, 2011 by admin

10:00A – 2:30P, 11:00P – 12:30A Meeting with Brian to get Biophysics WordPress site up. Reconfiguring Biophysics webpage. plugins and images need to be uploaded by FTP — should be fixable. Comments not easy to remove.

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Wednesday 06/08/2011

Posted on June 8, 2011 by admin

10:45 A — 4:00P, 8:30P-10:00P FTP site and MYSQL database installed for new biophysics site. Slow copy speed (still copying files to GRAID) is due to file number and Mac finder, not hardware problem.  Recommended solution use command line copy. … Continue reading →

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Tuesday 06/07/2011

Posted on June 7, 2011 by admin

10:30A – 7:00P, 8:00P – 10:20P Moved mRNA counting controls to independent script in new project mRNA_counting.  Streamlined upload steps and memory demands. Running double-label analysis on full size image (and testing timing for precise z-specification). profiling and improving speed … Continue reading →

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mRNA counting control

Posted on June 6, 2011 by admin

  Double labeling, raw image (left), and competition labeling, raw image (right)                         Images are max-projects through the z-dimension.  hatches mark dotfinder located centroids.  Yellow stars mark mRNA transcripts found … Continue reading →

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Monday 06/06/11

Posted on June 6, 2011 by admin

9:40 A -7:00P, 8:00P – 9:50P Finish ON confocal of pnr and tup Confocal of C80-hets 22C slide (only 12 properly staged embryos with the transgene). Rewrite dotfinder.m to process and pass all original image data to CheckDotUpDown.m, making the … Continue reading →

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