About¶
Tip
Expressions of interest have closed for 2025 and successful applicants have been emailed.
Bioinformatics Spring School 2025 is a week long training event for researchers, supported by Genomics Aotearoa (GA) and Research Education Advanced Network New Zealand (REANNZ).
We will combine talks from researchers and hands on computational workshops (influenced by The Carpentries), covering example bioinformatic workflows. The exact topics will be decided by the organisers based on submitted Expression of Interests.
This event is organised by:
- Dr Chloe Van Der Burg (Genomics Aotearoa)
- Matt Bixley (REANNZ)
- Professor Mik Black (Biochemistry)
- Dr Murray Cadzow (Research and Teaching IT Support)
- Dr Ludovic Dutoit (Zoology)
Cost?¶
This event itself will only cost your time (there isn't a $ charge) and lunches will be provided. Attendees will need to fund all other travel related expenses.
When and where?¶
- 9:30 - 16:30, 17-21 November 2025
- University of Otago, Dunedin, New Zealand
- This is an in-person event.
Preliminary Schedule:¶
Info
The workshop content is in a draft state and (mostly) available to look through already if you follow the links.
Monday:¶
- Introduction to an HPC environment
- Introduction to Unix Shell
- Indigenous genomic data considerations
| Time | Session |
|---|---|
| 09:30 | Welcome |
| 10:00 | Intro HPC |
| 10:30 | Break |
| 10:50 | Unix Shell |
| 12:15 | Lunch |
| 13:00 | Unix Shell cont |
| 14:40 | Break |
| 15:00 | Indigenous Genomic Data |
| 16:30 | Done |
Tuesday:¶
- Introduction to Genomic Variant Calling
- Common genomic data formats
- an example variant calling pipeline using common tools
| Time | Session |
|---|---|
| 09:30 | Talk |
| 10:00 | Genomic Data Carpentry |
| 10:30 | Break |
| 10:50 | Genomic Data Carpentry |
| 12:15 | Lunch |
| 13:00 | Genomic Data Carpentry |
| 14:40 | Break |
| 15:00 | Genomic Data Carpentry |
| 16:30 | Done |
Wednesday:¶
- Introduction to Genome Assembly
- How to assemble a genome using long reads
- Using the scheduler
- Plotting and data manipulation in R
- Creating plots with ggplot
- Data manipulation with the Tidyverse
| Time | Session |
|---|---|
| 09:30 | Genome Assembly |
| 10:30 | Break |
| 10:50 | Genome Assembly |
| 12:15 | Lunch |
| 13:00 | R |
| 14:40 | Break |
| 15:00 | R cont |
| 16:30 | Done |
Thursday:¶
| Time | Session |
|---|---|
| 09:30 | Talk |
| 10:00 | RNAseq |
| 10:30 | Break |
| 10:50 | RNAseq |
| 12:15 | Lunch |
| 13:00 | RNAseq |
| 14:40 | Break |
| 15:00 | RNAseq |
| 16:30 | Done |
Friday:¶
- Reproducibility tasters
- Version control with Git
- Reproducible documents with Quarto
- Virtual environments
| Time | Session |
|---|---|
| 09:30 | Talk |
| 10:00 | Version Control |
| 10:30 | Break |
| 10:50 | Version Control cont. |
| 12:15 | Lunch |
| 13:00 | Quarto |
| 14:40 | Break |
| 15:00 | Virtual Environments |
| 16:30 | Done |
I'm interested! How do I apply?¶
Expressions of interest have closed for 2025.