BIOTECH-7005-BIOINF-3000

Biotech 7005/Bioinf 3000: Frontiers of Biotechnology: Bioinformatics and Systems Modelling

Semester 2 2025 - Provisional Timetable

Coordinator:

Instructors:

Course Contact Jessica Webb

Contact Hours

Lectures: Monday 9AM, Physics, 103

Practical 01: Monday 11am-1pm, Ingkarni Wardlii 218

Practical 02: Friday 11am-1pm, Ingkarni Wardlii 218

Timetable (Provisional)

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 (Steven) 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) No test Alignment/NGS (1) (Chelsea) Alignment/NGS (2) (Chelsea)
7 8/9 Reproducible Science (David L) Alignment test (TBD)/ Coding comments (David L) Reproducible Science (1) (David L)
8 15/9 Version Control (David L) Version Control (David L) Local Version Control (David L)
- 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 * GitHub Repositories (David L)
10 13/10 Ancient DNA (Bastien) Version control test/ GitHub Intro (David L) aDNA (Bastien)
11 20/10 Transcriptomics - Gene Expression (Stevie) Transcriptomics - DE analysis (1) (Stevie) Transcriptomics - DE analysis (2) (Stevie)
12 27/10 Transcriptomics - assembly (Stevie) Gene expression test Transcriptomics - assembly (1) (Stevie) Transcriptomics - assembly (2) (Stevie)

Assessment

Assessment Schedule & Weighting (Not all assignments in final form yet.)

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 Version Control     Friday 18/10/25
Assessment 6 Transcriptomics     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.

Assessment Checklist

Have you:

Major Project (20%) - Masters Students Only

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

Differential gen expression analysis (RNAseq)

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).

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