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Marine Genomics

Welcome

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 ()

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 start be sure to work through the github setup guide

The module uses two template repositories. Each one already contains numbered RMarkdown files for your notes and every folder that the instructions use, so you won’t need to make any folders yourself.

Recommended git and github workflow for this module

  1. Setup your account on the rstudio server so that it can connect with github using these instructions
  2. Complete workshops 1-3 as instructed above. In workshop 1 you will make your own repository on github from the mb5370-workshops template and clone it into an RStudio project, and you’ll use this project for workshops 1-3. Those workshops are just for you to learn and will not be assessed.
  3. Make your own repository on github from the bbd-metagenome template. You will use this repository to document your work in workshop 4.
  4. Work through workshop 4. Take notes as you go in the numbered RMarkdown files. When you are done with the analyses go back over your notes and write it up for inclusion as part of your ePortfolio. Detailed instructions on what is expected are provided on LearnJCU for this item.