Semester 2 2024
Coordinator:
Instructors:
Teaching assistants:
Course Contact Dave Adelson
Lectures and practicals will be delivered face to face. If you are unwell, please think of others and do not attend.
Lectures: Monday 9AM, Napier, LG29
Practical 01: Monday 11am-1pm, Ingkarni Wardlii 218
Practical 02: Friday 11am-1pm, Ingkarni Wardlii 218
| Week | Monday | Lecture | Monday Practical | Friday Practical |
|---|---|---|---|---|
| 1 | 22/7 | Intro to Bioinformatics (Dave) | Introduction to VMs/Introduction to R (1) | Introduction to R (1.5) (Steven/Dave) |
| 2 | 29/7 | Statistics (Steven) | Statistics worksheet (Steven) | Introduction to R (2) (Steven) |
| 3 | 5/8 | Evolutionary Processes (Dave) | Stats Test Introduction to Bash (1) (Steven/Anna) | Introduction To Bash (2) (Anna) |
| 4 | 12/8 | Next-generation sequencing (Dave) | Evolution test Scripting in Bash (1) (Dave) | Scripting In Bash (2)(Dave) |
| 5 | 19/8 | Alignment Process (Dave) | NGS test Evolutionary Processes (1) (Dave) | Evolutionary processes (2) (Dave) |
| 6 | 26/8 | Alignment Process (Dave) | No test Alignment/NGS (1) (Dave) | Alignment/NGS (2) (Zhipeng) |
| 7 | 2/9 | Reproducible Science (David L) | Alignment test (Zhipeng)/ Coding comments (David L) | Reproducible Science (1) (David L) |
| 8 | 9/9 | Version Control (David L) | Version Control (David L) | Local Version Control (David L) |
| - | 16/9 | Mid-Semester Break | ||
| - | 23/9 | Mid-Semester Break | ||
| 9 | 30/9 | Ancient DNA (Yassine) | GitHub Repositories (David L) | Version control test/ GitHub Intro (David L) |
| 10 | 7/10 (PH) | Public Holiday 7/10 No lecture | Public Holiday No practical | aDNA (Yassine/Shyam) |
| 11 | 14/10 | Transcriptomics - Gene Expression (Zhipeng) | Transcriptomics - DE analysis (1) (Zhipeng) | Transcriptomics - DE analysis (2) (Zhipeng) |
| 12 | 21/10 | Transcriptomics - assembly (Zhipeng) | Transcriptomics - assembly (1) (Zhipeng) | Transcriptomics - assembly (2) (Zhipeng) |
| 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 9/08/24 |
| Assessment 2 | Bash Scripting & Statistics | Friday 23/08/24 | ||
| Assessment 3 | Evolutionary processes | Friday 30/08/24 | ||
| Assessment 4 | Alignment/NGS | Friday 13/09/24 | ||
| Assessment 5 | Version Control | Friday 18/10/24 | ||
| Assessment 6 | Transcriptomics | Friday 01/11/24 | ||
| Tests (x6) | 10% for all quzzes combined | 10% for all quizzes combined | ||
| Major Project topic acceptance/confirmation | Differential gene expression | N/A | 10% of total mark | Friday 13/09/24 |
| Major Project | Differential gene expression | N/A | 20% of total mark | Friday 08/11/24 |
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).