Semester 2 2025 - Provisional Timetable
Coordinator:
Instructors:
Course Contact Jessica Webb
Lectures: Monday 9AM, Physics, 103
Practical 01: Monday 11am-1pm, Ingkarni Wardlii 218
Practical 02: Friday 11am-1pm, Ingkarni Wardlii 218
| Week | Monday | Lecture | Monday Practical | Friday Practical |
|---|---|---|---|---|
| 1 | 28/7 | NO LIVE LECTURE Intro to Bioinformatics (recording) | Introduction to VMs/Introduction to R (1) (Steven) | Introduction to R (1.5) (Steven) |
| 2 | 4/8 | Statistics (recording) | Statistics worksheet (Steven) | Introduction to R (2) (Steven) |
| 3 | 11/8 | Evolutionary Processes (recording) | Stats Test / Introduction to Bash (1) (Steven/Chelsea) | Introduction To Bash (2) (Chelsea) |
| 4 | 18/8 | Next-generation sequencing (recording) | Evolution test / Scripting in Bash (1) (Chelsea) | Scripting In Bash (2)(Chelsea) |
| 5 | 25/8 | Alignment Process (recording) | NGS test / Evolutionary Processes (1) (Alex) | Evolutionary processes (2) (Alex) |
| 6 | 1/9 | Alignment Process (recording), Transcriptomics - Gene Expression (Stevie) | Alignment/NGS (1) (Chelsea) | Alignment/NGS (2) (Chelsea) |
| 7 | 8/9 | Ancient DNA (Bastien) | Alignment test / aDNA (Bastien) | Transcriptomics - DE analysis (1) (Stevie) |
| 8 | 15/9 | Transcriptomics - assembly (Stevie) | Gene expression test / Transcriptomics - DE analysis (2) (Stevie) | Transcriptomics - assembly (1) (Stevie) |
| - | 22/9 | Mid-Semester Break | ||
| - | 29/9 | Mid-Semester Break | ||
| 9 | 6/10 (PH) | Public Holiday 6/10 No lecture* | Public Holiday 6/10 No Practical * | Transcriptomics - assembly (2) (Stevie) |
| 10 | 13/10 | Reproducible Science (David L) | Coding comments (David L) | Reproducible Science (1) (David L) |
| 11 | 20/10 | Version Control (David L) | Version Control (David L) | Local Version Control (David L) |
| 12 | 27/10 | NO LECTURE | Version control test/GitHub Repositories (David L) | GitHub Intro (David L) |
| Assessment - All Students | Subject | UG Weight | PG Weight | Due Date |
|---|---|---|---|---|
| Assessment 1 | R programming | 90% for all assignments combined | 60% for all assignments combined | Friday 15/08/25 |
| Assessment 2 | Bash Scripting & Statistics | Friday 29/08/25 | ||
| Assessment 3 | Evolutionary processes | Friday 05/09/25 | ||
| Assessment 4 | Alignment/NGS | Friday 20/09/25 | ||
| Assessment 5 | Transcriptomics | Friday 18/10/25 | ||
| Assessment 6 | Version Control | Friday 07/11/25 | ||
| Tests (x6) | 10% for all tests combined | 10% for all tests combined | ||
| Major Project topic acceptance/confirmation | Differential gene expression | N/A | 10% of total mark | Friday 20/09/25 |
| Major Project | Differential gene expression | N/A | 20% of total mark | Friday 14/11/25 |
Note that the Major Project topic accepotance and assignment only apply to Masters level students. Undergraduates do not do a Project.
Have you:
In this course, next-generation sequencing (NGS) datasets/protocols will used for the Major Project. Note that these data sets have not been provided yet and that the major project assignment document has not been finalised yet
You will be assigned a unique dataset and carry out quality control (quality and sequencing adapter trimming), genome alignment, feature counting, normalising and removal of noise transcripts followed by differential gene expression analysis and downstream visualisation and statistical methods. For the major project, we will assign part of a published dataset and you will complete all the analysis tasks (from raw data to final results).