Training and Events

Our experts have all been involved in developing and delivering workshops here and overseas for many years now. Workshops are delivered on-site or may be run in-house for your group. Many of the training materials were developed for use on Galaxy Australia and these are used in our formal workshops and are also available for use to deliver your own workshops or for self-directed learning and for conducting your own research.


All our upcoming workshops and events for building bioinformatics careers are listed below. See also:

Resources for researchers and students as recommended by the Parkville Bioinformatics Training Group

We’re interested to hear from any Melbourne precinct research group or individual researchers and students about training needs: please email the Parkville Bioinformatics Training Group with your suggestions or requests.


UPCOMING ONLINE MELBOURNE BIOINFORMATICS WORKSHOPS in 2020

All our trainer-led workshops are now delivered online and are FREE for all researchers and students from the University of Melbourne and its affiliated research institutes.

Due to the very high local demand and popularity of these workshops, we are limiting access for 2020 to researchers and students from the University of Melbourne and its affiliated research institutes.

Registrants must use an eligible institutional email address to gain admission to these trainer-led workshops.

Please note that all the materials used in these workshops are freely available online and are designed to be used for for self-directed learning. Click on toolbox above to find the directory of materials.Air Jordan

March 23, 2021 - 1-5pm
online via Zoom

Workshops

Structural variant calling using long read data – new

Learn how to identify structural variants in genomes using Galaxy

Presenter: Grace Hall

Overview

Structural variations are involved in many aspects of medicine and biotechnology. Their importance in various diseases, including cancer, and their relevance to microbial evolution has made the field a prominent area of research.

The advent of long read technology has recently enabled more accurate analysis of structural variants (SVs), invigorating the field and permitting numerous discoveries in the last half-decade.

In this training workshop you will gain an introduction to structural variation calling using long read data. We will discuss what structural variants are, their importance in medicine and biotechnology, and how they are identified and visualised using modern online bioinformatics tools. We will also touch on the interpretation of our SV calls, by calculating performance metrics for our SV caller, sniffles.

Learning Objectives

This workshop will cover all major steps to bioinformatics analysis. We will discuss the initial data, the SV calling pipeline, visualisation of results, and interpretation and communication of our findings.

Theory behind SV types, their role in medicine and biotechnology, long read technologies, and read alignment will also be communicated.

There is currently no ‘best practice’ for SV calling. We will use a workflow consisting of read alignment with minimap2, SV calling with sniffles, text reformatting of VCF files with awk, and visualisation with circos to perform our analysis.

Benchmarking will be performed on our SV caller – sniffles – to estimate its accuracy, precision and recall. This performance information will be vital as we switch to a human read set, as will permit better interpretation of the results we obtain.

Tools used: Galaxy: minimap2, sniffles, awk, circos

Prerequisites & requirements

This workshop does not require any programming experience but familiarity with Galaxy and Galaxy workflows, or completion of the online “Introduction to Galaxy” workshop is required. You will write one line programs using awk to reformat your variant calls, but this code will be provided and explained.

This is a hands-on workshop and attendees must provide their own laptops for the workshop with the following software pre-installed.

  • Web browser (Firefox or Chrome recommended)
  • Zoom (Version 5 or greater)

Most workshops are FREE for all researchers and students from the University of Melbourne and its affiliated institutes only (refer ‘Members’ section).


March 25, 2021 - & Friday 26, 12:30-4pm both days
online via Zoom

Workshops

Using Containers in Bioinformatics workshop

Are you wondering how your bioscience research could benefit from workflow containerisation? Containers enable you to package up an application and its dependencies and encourage reproducibility, portability and shareability of computational workflows. This workshop explores the merits, advantages and limitations of applying containers in bioinformatics.

This introductory online workshop is offered nationally free of charge by the Australian BioCommons and Pawsey Supercomputing Centre. Melbourne Bioinformatics is contributing experts to facilitate from the University of Melbourne.

Places are limited. Applications close 5pm AEDT Monday 15 March 2021.