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Semester 2 2019
Coordinator:
- Dan Kortschak
Instructors:
- Dan Kortschak
- Nathan Watson-Haigh
- Steve Pederson
- Jimmy Breen
Course Contact Dan Kortschak Email: [email protected] Phone: 08 8313 0928 Office: Braggs 2.60
Lectures: Thursday 1pm, Barr Smith South, 3022
- 1 Aug — 8 Aug
- 12 Aug ‡ (Monday 4pm, Hughes 309 Lecture theatre)
- 22 Aug — 29 Aug
- 2 Sep ‡ (Monday 4pm, Hughes 309 Lecture theatre)
- 12 Sep — 19 Sep
- 10 Oct — 31 Oct
Tutorials: Thursday 9am-11am, Benham, G25
- 1 Aug — 8 Aug
- 12 Aug ‡ (Monday 9-10am, Benham, G25)
16 Aug ‡ (Friday 4-5pm, Ligertwood, 113)- 22 Aug — 29 Aug
- 2 Sep ‡ (Monday 9-10am, Benham, G25)
- 6 Sep ‡ (Friday 4-5pm, Ligertwood, 113)
- 12 Sep — 19 Sep
- 10 Oct — 31 Oct
Practicals: Monday 11am-1pm, Mawson, G12 Computer Suite
- 29 Jul — 16 Sep
- 14 Oct — 28 Oct
| Week | Monday | Lecture | Practical | Tutorial |
|---|---|---|---|---|
| 1 | 29/7 | Introduction to Bioinformatics* (Dan) | Introduction to R (1) (Steve) | Discussion |
| 2 | 5/8 | Evolutionary Processes* (Dan) | Introduction to R (2) (Steve) | Continue practical |
| 3 | 12/8‡ | Statistics (Steve) | Introduction To Bash (Steve) | Evolution test |
| 4 | 19/8 | Alignment Process* (Nathan) | Scripting In Bash (Steve) | Stats Test Statistics worksheet |
| 5 | 26/8 | Alignment Process* (Nathan) | Evolutionary processes (Dan) | |
| 6 | 2/9‡ | Next-generation sequencing* (Dan) | NGS data practical (1) (Steve) | Alignment test |
| 7 | 9/9 | Genome assembly (Lloyd) | NGS data practical (2) (Steve) | NGS sequencing test |
| 8 | 16/9 | Transcriptomics (Nathan) | RNAseq practical (Jimmy) | Genome assembly test |
| - | 23/9 | Semester Break | ||
| - | 30/9 | Semester Break | ||
| 9 | 7/10 (PH) | Systems Biology (Ville) | No practical (PH) | Transcriptomics test |
| 10 | 14/10 | Introduction to Systems Biology* (Dan) | Graphical analyses (Dan) | |
| 11 | 21/10 | Epigenetics* (Jimmy) | Systems biology test | |
| 12 | 28/10 | The Future — wooooooo* (Dan) | Wrap-up (Jimmy/Dan/Steve) Q&A |
‡ Lectures and tutorials at special times. * Slides not visible outside UofA network.
| Assessment | Subject | Weight | Due Date |
|---|---|---|---|
| Assessment 1 | R programming | 6% | Tuesday 13th August |
| Assessment 2 | Bash Scripting & Statistics | 6% | Monday 2nd September |
| Assessment 3 | Evolutionary processes | 6% | Monday 9th September |
| Assessment 4 | NGS data practical | 6% | Monday 23rd September |
| Assessment 5 | RNAseq practical | 6% | Monday 30th September |
| Assessment 6 | Graphical analyses | 6% | Monday 28th October |
| Tests | 9% | ||
| Project | Complete Dataset | 15% | Monday 4th November |
| Exam | 40% |
Have you:
- Answered all the questions?
- Followed naming conventions for Assessments?
- Attached an assessment coversheet? (Available here).
- This is a course requirement. See the Academic Honesty Policy.
- Identified the work as yours?
- Emails should have the course and assessment task names.
- Documents should be named with your name, the course name and the assessment task.
- Printed documents should have you name and the course and assessment task in the text/footer/header.
- Used appropriate electronic communication with assessors?
- Emails should have a meaningful subject.
- Handed in the assignment before the due time (Friday tutorial 9am)?
In this course, the following next-generation sequencing (NGS) datasets/protocols will be in detail:
- Whole genome sequencing/Resequencing
- Transcriptome Sequencing (RNAseq)
- DNA Methylation/Bisulfite Sequencing
- Enrichment/Capture sequencing (Methyl-capture, ChIPseq, RIPseq)
- Metagenomics/Microbial profiling
Each of these NGS approaches uses similar programs and analysis approaches, such as quality control (quality and sequencing adapter trimming), genome alignment, and downstream visualisation and statistical methods. For the major project, you will take a published dataset and complete all the analysis tasks (from raw data to final results) during the course.
You have the freedom to choose any dataset you would like before we start week 5's practical (NGS data practical), or choose from four datasets that we have chosen. You will be asked assessment questions on your data during practical assessments throughout the semester, and a final report will be due the week before the end of semester (Week 12)