07 February 2014

python, ecolunch, shiny, and Qubit

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February 3 - 7 notes

Yikes - to celebrate the approach of the year anniversary of my open lab notebook I let a month slip by without updates. During this time I’ve been cranking on all cylinders as well as dealing with home business. Finally taking the time to transcribe my notes from this time to digital.


  • Working on presentation for EcoLunch. Using slidify
  • Biology seminar - Jessica Hellman
  • Meeting w/Jessica
    • discussed ecological genomics and my results


Given strong correlations in expression, should analyze expression on colonies together!



  • Continuing work on EcoLunch
  • Meeting with Tim Hunter at Microarray facility
    • for RNA samples, should check with Qubit given inconsistent Nanodrop and Bioanalyzer results
    • look at Nanodrop traces - is there salt contamination?
    • DGE - Covaris sonicator for DNA fragmentation at library prep stage
    • RADseq - Caliper XT for size selection. or do gel extraction
  • meet with Grace - feed Pogos


Performed AmPure Bead PCR Purification on double digest DNA samples. 300ul round bottom PCR plates sit on top of magnetic plate. Beads make ring at bottom. Easy and quick protocol.


Working all week on EcoLunch presentation.

Developed shiny R web app to display expression levels of specific transcripts by search term. Slick.


Transcriptome presentation!

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