BC3203

# Bioinformatics

Lecturers

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

Lecture and Tutorial Times

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;

Assessment

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 Guide: Variants Github Invite Link  

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

Learning Resources

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

Where to start

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.

Diving deeper into R

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/

Diving deeper into the command line

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

Computational Resources

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.

Cheat Sheets

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.

Guides for common tasks

If a guide is missing or you have a question not covered please email the subject coordinator to request it.