Bioinformatics Spring School 2020 is a week long training event for researchers, supported by Genomics Aotearoa and the New Zealand eScience Infrastructure (NeSI).
We will combine talks from researchers and hands on computational workshops (influenced by The Carpentries), covering example workflows of DNA variant calling, genotyping by sequencing (GBS), RNAseq analysis, and environmental DNA (eDNA).
This event is organised by Murray Cadzow, Ngoni Faya and Ludovic Dutoit.
This is an in-person event.
This event will only cost your time (there isn’t a $ charge).
REGISTRATION IS CLOSED
This event is designed to give researchers (including students - 4th year and above) the opportunity to learn about and practice some bioinformatic skills. We’ll be covering bioinformatic workflows such as:
along with computational topics such as:
This week long event is designed to be an immersive experience so we ask that you commit to the entire week. We have chosen to interleave the computational topics throughout the week so that we can build on them throughout the entire week, so this ensures participants have the key knowledge at the right time.
The underlying workshop content is extremely similar to previous workshops run by Genomics Aotearoa so if you’ve already attended the Genomic Data Carpentry and RNAseq workshops you will have already covered the majority of the content.
These topics will be integrated into the bioinformatics workshops and built upon across the week with the goal of demostrating a best practices workflow approach to Bioinformatics analysis.
Many bioinformatic programs will only operate in a Unix command line environment, as such we need to provide an introduction to working in this environment which will cover:
Analysis portions of the workshops will be performed using R. As such we will provide a brief introduction to R. This will include:
We’ll be making use of the New Zealand eScience Infrastructure (NeSI), which is the national provider of high performance computing for researchers, to run our analysis and as part of this we’ll cover:
Running programs on the command line gives us the opportunity to save the commands used in scripts that we can reuse later on. It’s important that as we develop these scripts that we have a machanism to track the changes made. Git is a program that enables us to track the changes we make and see the differences between previous versions. The introduction to version control will cover:
| Time | What |
|---|---|
| 09:30 | Welcome |
| 10:00 | Introduction to NeSI |
| 10:45 | Break |
| 11:10 | Introduction to BASH |
| 12:15 | Lunch |
| 13:00 | Keynote - Phil Wilcox |
| 14:00 | Introduction to BASH cont. |
| 14:45 | Break |
| 15:00 | Introduction to R |
| 16:30 | End of Day |
| Time | What |
|---|---|
| 09:30 | Speaker |
| 10:00 | DNA variant calling |
| 10:45 | Break |
| 11:00 | DNA variant calling cont. |
| 12:15 | Lunch |
| 13:00 | DNA variant calling cont. |
| 14:30 | Break |
| 14:45 | DNA variant calling cont |
| 16:30 | End of Day |
| Time | What |
|---|---|
| 9:30 | Speaker |
| 10:30 | Data101: From raw data to individual samples files |
| 11:00 | Break |
| 11:15 | Calling SNPs de-novo |
| 12:15 | Lunch |
| 13:00 | Calling SNPs de-novo, discussion |
| 13:30 | Calling SNPs with a reference genome |
| 14:30 | Break |
| 15:00 | Evolutionary Genetics basic toolbox (Population structure, Phylogenetic tree) |
| 16:30 | End of Day |
| Time | What |
|---|---|
| 09:30 | Speaker |
| 10:00 | RNAseq |
| 10:45 | Break |
| 11:00 | RNAseq cont. |
| 12:15 | Lunch |
| 13:00 | RNAseq cont. |
| 14:30 | Break |
| 14:45 | RNAseq cont. |
| 16:30 | End of Day |
| Time | What |
|---|---|
| 09:30 | Symposium |
| 10:30 | Break |
| 10:45 | Experimental Design |
| 11:00 | QC and Denoising/Clustering |
| 12:15 | Lunch |
| 13:00 | Taxonomy Assignment |
| 14:30 | Afternoon Tea |
| 14:45 | Statistical Analysis |
| 16:15 | Course Summary |
| 16:30 | End of Day |