---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2015-07-02 16:44:14+00:00
layout: post
slug: goals-july-2015
title: GOALS - July 2015
categories:
  - 2015
  - Goals
---

Before we check out this month’s goals, let’s have a quick review of [last month’s goals](https://robertslab.github.io/sams-notebook/posts/2015/2015-06-01-goals-june-2015/) 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](https://github.com/sr320/LabDocs/issues/117). 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](https://genefish.wikispaces.com/Jonathan%27s+Notebook)

    
  * 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](https://genefish.wikispaces.com/Jonathan%27s+Notebook) – 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.


