GOALS - July 2015

2015
Goals
Author

Sam White

Published

July 2, 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.

Miscellany

Goal(s):

  • 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

Status:

  • 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.

Miscellany

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.