BIOTECH-7005-BIOINF-3000

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* TOC
{:toc}

## Biotech 7005/Bioinf 3000: Frontiers of Biotechnology: Bioinformatics and Systems Modelling
{:.no_toc}

Semester 2 2025 - Provisional Timetable

**Coordinator:**
- Jessica Webb

**Instructors:**
- Jessica Webb
- Anna Sheppard
- Steven Delean
- David Lawrence
- Stevie Pederson
- Bastien Llamas
- Chelsea Matthews
- Alexander Stuart

__*Course Contact*__
Jessica Webb
- Email: Jessica.webb@adelaide.edu.au
- Phone: N/A
- Office: Molecular Life Sciences Rm 4.11

### Contact Hours

Lectures: Monday 9AM, Physics, 103
- 28 July — 27 Oct

Practical 01: Monday 11am-1pm, Ingkarni Wardlii 218
- 28 July — 27 Oct

Practical 02: Friday 11am-1pm, Ingkarni Wardlii 218
- 1 Aug — 31 Oct

### 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][2] (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][7] (Stevie) | [Alignment/NGS (1)] (Chelsea)  | [Alignment/NGS (2)] (Chelsea)             |
| **7**    | 8/9        | [Ancient DNA][11] (Bastien) | *Alignment test* / [aDNA][12] (Bastien)  | [Transcriptomics - DE analysis] (1) (Stevie)  |
| **8**    | 15/9       | [Transcriptomics][8] (Stevie)  | [Transcriptomics - DE analysis] (2) (Stevie)    | *Gene expression test* / [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, recording)  | [Coding comments] (David L) |[Reproducible Science] (1) (David L)  |
| **11**   | 20/10      | Version Control (David L, recording)  | [Version Control - Git Intro] (David L)  | [Version Control - Git Advanced] (David L) | 
| **12**   | 27/10      | NO LECTURE | *Version control test*/[GitHub Intro] (David L) | [GitHub Advanced] (David L)  |

[1]: http://biotech7005.services.adelaide.edu.au/01-bioinformatics.slide
[2]: Lectures/02-statistics.html
[3]: http://biotech7005.services.adelaide.edu.au/03-evoprocess.slide
[4]: http://biotech7005.services.adelaide.edu.au/04-sequencing.slide
[5]: http://biotech7005.services.adelaide.edu.au/05-alignment.slide
[6]: http://biotech7005.services.adelaide.edu.au/05-alignment.slide
[7]: Lectures/transcriptomics1-lecture1.html
[8]: Lectures/transcriptomics1-lecture2.html
[9]: Practicals/VCF_Analysis/Week_8_Practical-VCF_Analysis.md
[10]: Practicals/Transcriptome_Practical/Transcriptome_assembly.md
[11]: https://github.com/University-of-Adelaide-Bx-Masters/BIOTECH-7005-BIOINF-3000/blob/master/Lectures/ancient_DNA_lecture.pdf
[12]: https://university-of-adelaide-bx-masters.github.io/BIOTECH-7005-BIOINF-3000/Practicals/ancient_DNA_practical/aDNA_prac.html

[Introduction to VMs]: Practicals/AWS_RONIN_connection.md
[Introduction to R]: Practicals/R_Practicals
[Introduction To Bash]: Practicals/Bash_Practicals/1_IntroBash.md
[Scripting In Bash]: Practicals/Bash_Practicals/2_BashScripting.md
[Evolutionary processes]: Practicals/evolutionary_prac/evolutionary.md
[Alignment/NGS (1)]: Practicals/NGS_Practicals/1_NGS_Practical1.md
[Alignment/NGS (2)]: Practicals/NGS_Practicals/2_NGS_Practical2.md
[Variant Calling practical]: Practicals/VCF_Analysis/Week_8_Practical-VCF_Analysis.md
[Graphical analyses]: https://github.com/kortschak/graphprac/
[DE gene tutorial]: Tutorials/Tutorial10_DE_analysis.pdf 
[Statistics worksheet]: Tutorials/Wk2_Statistics.html
[Coding comments]: Practicals/Code_comments_practical/code_comments.html
[Reproducible Science]: Practicals/reproducible_science_practical/reproducible_science_practical.html
[Version Control - Git Intro]: Practicals/version_control_git_intro/version_control_git_intro.html
[Version Control - Git Advanced]: Practicals/version_control_git_advanced/version_control_git_advanced.html
[GitHub Intro]: Practicals/github_intro/github_intro.html
[GitHub Advanced]: Practicals/github_advanced/github_advanced.html
[Transcriptomics - DE analysis]: Practicals/Transcriptome_Practical/Transcriptomics_DE.md
[Transcriptomics - assembly]: Practicals/Transcriptome_Practical/Transcriptomics_assembly.md

## Assessment

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

| **Assessment - All Students**                                 | **Subject**                |  **UG Weight**  | **PG Weight** | **Due Date**          |
|--------------------------------------------------------------|-----------------------------|-----------------|------------|-----------------------|
| [Assessment 1](Assignments/Assignment1.md)                   | R programming               |  90% for all assignments combined           | 60% for all assignments combined         | Friday 15/08/25     |
| [Assessment 2](Assignments/Assignment2.md)                   | Bash Scripting & Statistics |              |         | Friday 29/08/25     |
| [Assessment 3](Practicals/evolutionary_prac/evolutionary.md) | Evolutionary processes      |              |          | Friday 05/09/25  |
| [Assessment 4](Assignments/Assignment4.md)                   | Alignment/NGS               |              |          | Friday 19/09/25  |
| [Assessment 5](Assignments/Assignment5_transcriptome_assembly.md)      | Transcriptomics   |              |          | Friday 18/10/25     |
| [Assessment 6](Assignments/Assignment6.md)                   | 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 19/09/25
| [Major Project](Assignments/major_project.md)                     | 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:

- [ ] Answered all the questions?
- [ ] Followed naming conventions for Assessments?
- [ ] **Attached an assessment coversheet?** (Available [here](COVERSHEET.md)).
	- This is a course requirement. See the [Academic Honesty Policy](http://www.adelaide.edu.au/policies/230/). **Failure to attach a coversheet to your submission will incur a 5 point penalty for the assignment.** 
- [ ] 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 your 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 (As specified on MyUni)?

### Major Project (20%) - Masters Students Only

In this course, next-generation sequencing (NGS) datasets/protocols will used for the [Major Project](Assignments/major_project_2024.md).  *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).

## Useful Links

[How To Ask Questions The Smart Way](http://www.catb.org/esr/faqs/smart-questions.html)

[How to write a good bug report](https://musescore.org/en/developers-handbook/how-write-good-bug-report-step-step-instructions)

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