GOALS – July 2015

Before we check out this month’s goals, let’s have a quick review of last month’s goals and which, if any, I was able to accomplish:

 From June 2015:

Geoduck Reproductive Development Transcriptomics

Done. Data from this was received 20150629.

BS-Seq Illumina Data Assembly/Mapping – C.gigas larvae OA

Little progress. No response from Univ. of Oregon. However, it seems that Mac has been having a similar issue with libraries constructed using Epigentek kits. She has contacted Illumina and Epigentek for help.

Geoduck & Olympia Oyster Genome Sequencing

No progress. Purchasing personnel (both departmental and university) appear to have had difficulty contacting BGI. I have put both purchasing personnel in contact with the BGI rep (Frank Hu), so things are starting to progress. Still not certain why they were unable to accomplish this.



  • Migrate Wikispaces notebook to this notebook
  • Add to GitHub code pages
  • Flesh out/create README files on server(s)
  • Lab cleanup tasks
  • Assist on Jonathan’s Capstone project
  • Establish go-to location for lab personnel questions
  • Teach Unix shell at Software Carpentry


  • Migrate Wikispaces notebook to this notebook – Minimal progress
  • Add to GitHub code pages – Updated “Commercial Protocols”, improved wget command for offline notebook backups
  • Flesh out/create README files on server(s) – Some progress, but mostly on the notebook backups and newly received transcriptomic data. No progress on older directories.
  • Lab cleanup tasks – Partial progress. Autoclaved multiple bags of old autoclave trash.
  • Assist on Jonathan’s Capstone project – Improved my time management working with Jonathan, but his sequencing results are a bit odd and he needs guidance on how to manipulate, and comprehend, what the data means.
  • Successfully taught both the shell and GitHub at Software Carpentry.


O.lurida RNA Isolation and Reverse Transcription

Need to isolate RNA from a set of Jake’s mechanically-stressed oyster tissue. Need to clarify with Steven if we want the 1hr post-mechanically stressed to “match” with the 1hr heat shock samples that were previously processed, or if we want the 24hr post-mechanically stressed samples.


Need to address short-falls from the EH&S annual lab inspection. Most are minor, easily addressed issues and won’t take much time (e.g. print lab safety signs in color). The various computer tasks still stand: notebook migration from Wikispaces to this notebook, transitioning lab resources from Wikispaces to GitHub, creating/updating “readme” files for directories on our servers, etc. Lab organization goals: improve -80C organization and create an online inventory of the -80C, establish an online inventory of lab supply locations (i.e. thermometers can be found in FTR209, Drawer #02), general clean up.


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