mb5370

Marine Genomics

Welcome to the genomics module of MB5370, techniques in marine science. This website serves as the handbook for the module and contains detailed instructions for each of the computer workshops. All of the instructions on this website assume that you are logged in to the class rstudio server. If you did not receive an email with a username and password for this server please contact the module coordinator (ira.cooke@jcu.edu.au)

Teaching Staff

Module coordinator: Ira Cooke

Tutors: Mikhail Nazareth, Maddison Howells, Sophie Renton, Fernando Mejia-Gonzalez

Contributors: This module was developed by Ira Cooke with help from Matt Field, Peter Cowman, Yui Sato, Andrew Calcino, Sally Lau and Julia Hung.

Workshops

Github for the Marine Genomics Module

There are some special setup instructions for working with github and git in the genomics module. Before you get started on the workshops be sure to work through the github setup guide

Recommended git and github workflow for this module

  1. Complete workshops 1-3 as instructed above. There is no need to make github repositories for these. Those workshops are just for you to learn and will not be assessed.
  2. Setup your account on the rstudio server so that it can connect with github using these instructions and create a repository on github. You will use this repository to document your work in workshop 4.
  3. Work through workshop 4. Take notes as you go using RMarkdown. When you are done with the analyses go back over your notes. Ensure that they follow a logical sequence. Remove any trivial commands, code experiments that didn’t work out, or anything not relevant to the final analysis. You can make these notes in RMarkdown using the github_document output format. When you knit your document you can then add any files created by the knitting process to git and push them to github.