# Bioinformatics
Ira Cooke (ira.cooke@jcu.edu.au) : Metagenomics, RNASeq
Roger Huerlimann (ROGER.HUERLIMANN@OIST.JP) : Metagenomics
Matt Field (matt.field@jcu.edu.au) : Genomic Variants
Ulf Schmitz (ulf.schmitz@jcu.edu.au) : Networks and Functional Enrichment
Siyuan Wu (thaddeus.wu@jcu.edu.au) : Networks and Functional Enrichment
Always refer to the official JCU timetable at https://timetable.jcu.edu.au for the most up to date timetable information. In this subject you will learn through a combination of online lectures, live lectures and live computer workshops.
Each week we will have two live lectures, at 8am (sorry) on Tuesday and Wednesday. The first of these lectures will usually cover background theory and the second will usually be a live code demonstration or a discussion of coding-related topics.
On Thursdays at 10am we will have a three hour computer workshop session. These computer workshops are crucially important because they will allow you to work on the assignments while having access to tutors for one-on-one advice.
| Activity | Scheduled Time | Location |
|---|---|---|
| Revision | Regularly. Your choice | Youtube & LearnJCU |
| Theory lecture | Tuesdays 8am | 034-011C (TSV); Online via LearnJCU |
| Coding lecture | Wednesdays 8am | 004-132 (TSV); Online via LearnJCU |
| Computer workshop | Thursdays 10am-1pm | 300-001; |
This subject places a strong emphasis on practical skills. These are assessed through coding assignments (available as part of weekly tutorial sessions) and through your major assignments.
The process of accessing, completing and submitting these assignments follows a best practice workflow for doing reproducible bioinformatics research. Assistance with this process is available during practical sessions. We have also prepared this guide for reference in case you forget one of the steps.
Details of assessment items and relative weightings are provided in the subject outline available on the subject LearnJCU site. As we progress through the subject this page will be updated with live links to all tutorials and assignments.
| Tutorial | Week Released | Guide | Github Classrooms Link | Expected Outputs |
|---|---|---|---|---|
| Unix Fundamentals 1 | Week 2 | Guide Unix Fundamentals | Github Invite Link | |
| Unix Fundamentals 2 | Week 3 | Guide: Loops and Variables | Github Invite Link | |
| R Fundamentals | Week 4 | Guide: R fundamentals | Github Invite Link | |
| Tidyverse 1 | Week 5 | Guide: Tidyverse 1 | Github Invite Link | Expected Outputs |
| Tidyverse 2 | Week 6 | Guide: Tidyverse 2 | Github Invite Link | Expected Outputs |
| Genomic Features and Alignments | Week 8 | Guide: Genomic Features | Github Invite Link | Expected Outputs |
| Variants | Week 10 |
In this subject you will complete 2 major assignments. All students complete the first assignment (Metagenomics). Students of BC3203 must complete the RNASeq assignment (optional for BC5203). Students of BC5203 must complete the independent project.
| Assignment | Guide | Report Template | Github Classrooms Link |
|---|---|---|---|
| Metagenomics | Guide | Report Template | Github Invite Link |
| RNA-Seq | Guide | Report Template | Github Invite Link |
| Independent Project | Guide | Report Template | Github Invite Link |
To see a full list of all your assignment repositories, login to github and then visit the following link
http://github.com/JCUBioinformatics
Command notes for coding lectures are available from the links below
| Lecture | Week | Topic | Link |
|---|---|---|---|
| Coding Lecture 1 | 1 | Intro to Unix | Code |
| Coding Lecture 2 | 2 | Working with NGS Data (FastQC) | Code |
| Coding Lecture 3 | 3 | Intro to R | Code |
| Coding Lecture 4 | 4 | Tidyverse & QIIME | Code |
| Coding Lecture 5 | 5 | Tidyverse 2 & QIIME | Code |
| Coding Lecture 6 | 6 | Genomic Features | Code |
Throughout this subject you will build familiarity with the unix command line and with programming (using R). If you haven’t encountered these previously, we strongly recommend you complete some online tutorials as preparation for the subject.
The recommended textbook for the R components of the subject is R for Data Science by Garrett Grolemund, Mine Cetinka-Rundel and Hadley Wickham. The entire book is available for free online at https://r4ds.hadley.nz/
There are huge numbers of online resources available for learning the command line. One of my favourites is the Grymoire by Bruce Barnett. It is a good balance between being too hard/easy and written in an entertaining style. It is highly recommended if you want to deepen your knowledge of the unix text system (awk, sed, grep).
This linux zine by Julia Evans. Contains a lot of stuff that is not relevant to this subject. Look for “unix permissions”, “pipes”, “asking good questions”, “man pages”
This handy command line reference contains many of the commands you need to know for this subject plus many many others
To complete the tutorials and assignments for this subject you will need access to a computer with a unix-like command line interface. To make sure everyone has access to the same environment we have setup an RStudio web server with everything you need.
This is available at https://rstudio.bioinformatics.guide .
You will receive an email from the subject coordinator with a username and password to access this service.
Note: Web based rstudio seems to work best using the google chrome browser.
If you are willing to put in some effort you can set up everything on your own personal computer. This is relatively easy on macOS or Linux but is also possible (with some effort) on windows. If you choose to do this you will need to be fairly self sufficient as your instructors will not have time to troubleshoot installation issues.
Please see this guide for setting things up on your own computer.
In this subject you will regularly encounter new commands or functions. Cheat sheets help you to remember commands you know and can sometimes also help you discover new commands or functionality you weren’t aware of.
We recommend you download the cheat sheets below. If you find them useful you may want to print them out and bring them along to tutorial sessions.
If a guide is missing or you have a question not covered please email the subject coordinator to request it.