Bioinformatics Spring School 2020

Bioinformatics Spring School 2020

About

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.

When and where?

This is an in-person event.

Cost?

This event will only cost your time (there isn’t a $ charge).

Is this for me?

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.

Curriculum

Bioinformatic topics

DNA variant calling from next generation sequence data

Genotype-by-sequencing analysis (RAD-Sequencing)

RNA-sequencing differential expression analysis

Environmental DNA analysis

Computational Topics

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.

Introduction to the Unix command line (Bash)

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:

Introduction to R

Analysis portions of the workshops will be performed using R. As such we will provide a brief introduction to R. This will include:

Introduction to working in a high performance computing environment

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:

Introduction to version control using git

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:

Apply

We ask that you commit to the entire week.

This workshop will require participants to provide their own laptop (we will have a limited number of machines to lend)

Expressions of interest are now CLOSED

N.B. Due to COVID-19 travel restrictions please only apply if you are located in New Zealand or meet the entry criteria

Applications close 5pm 27 October NZT, successful applicants will be notified by the 30th October.

Any queries please email carpentries@otago.ac.nz