Training and Events

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

Access all our Training Documentation.

Any of our upcoming workshops and events for building bioinformatics careers will appear here below. Sign up to our newsletter for regular updates and also go the the listing at EMBL Australia Bioinformatics Resource where you can select training options from listings worldwide.

Science Gateways webinars are hosted and posted here on a range of subjects of interest, including bioinformatics eg. iTasser, Python etc. Science gateways are online interfaces that give researchers, educators, and students easy access to specialised, shared resources that are specific to a science or engineering discipline. You can sign up there for regular updates.

OTHER MELBOURNE PRECINCT TRAINING OPPORTUNTIES

We are also interested to hear from any Melbourne precinct research group or individual researchers and students about training needs, please email the Communications Team with your query.


September 26, 2017 - 1.30-4.30pm
Melbourne Bioinformatics Boardroom, 187 Grattan Street, Carlton, VIC 3053 Australia

Workshops

Introduction to High Performance Computing

Using High Performance Computing (HPC) resources such as Melbourne Bioinformatics in an effective and efficient manner is key to modern research.  This workshop will introduce you to HPC environments and assist you to get on with your research.

In particular you will learn:

  • What is HPC?
  • Loading software modules
  • Submitting jobs
  • Selecting job queues
  • Monitoring your job’s progress
  • What resources can I request?
  • Selecting appropriate resources

Prerequisites: You will need a basic understanding of Unix, or you should have attended an ‘Introduction to Unix’ workshop in the past. All participants are required to bring their own laptop computers.

LAST RUN: May 3, 2017
NEXT SESSION: October 2, 2017

September 26, 2017 - 9.30am-12.30pm
Melbourne Bioinformatics Boardroom, 187 Grattan Street, Carlton, VIC 3053 Australia

Workshops

Introduction to Unix

Knowledge of the Unix operating system is fundamental to being productive on HPC systems such as those offered by Melbourne Bioinformatics. This workshop will introduce you to the fundamental Unix concepts by way of a series of hands-on exercises.

In particular you will learn how to do the following things:

  • Log into a Unix machine remotely
  • Organise your files into directories
  • Change file permissions to improve security and safety
  • Create and edit files with a text editor
  • Copy files between directories
  • Use command line programs to manipulate files
  • Automate your workflow using shell scripts

The workshop is facilitated by experienced Unix users who will be able to guide you through the exercises and offer assistance where needed. The workshop is intended for beginners with no prior experience in Unix. Attendees are required to bring their own laptop computers.

LAST RUN: May 3, 2017
NEXT SESSION: October 2, 2017

October 2, 2017 - 9:30am - 12:30pm (AEST)
Melbourne Bioinformatics Boardroom, 187 Grattan Street, Carlton, VIC 3053 Australia

Workshops

Introduction to Unix

Knowledge of the Unix operating system is fundamental to being productive on HPC systems such as those offered by Melbourne Bioinformatics. This workshop will introduce you to the fundamental Unix concepts by way of a series of hands-on exercises.

(more…)

LAST RUN: May 3, 2017

October 2, 2017 - 1:30-4.30pm (AEST)
Melbourne Bioinformatics Boardroom, 187 Grattan Street, Carlton, VIC 3053 Australia

Workshops

Introduction to High Performance Computing

Using High Performance Computing (HPC) resources such as Melbourne Bioinformatics in an effective and efficient manner is key to modern research.  This workshop will introduce you to HPC environments and assist you to get on with your research.

(more…)

LAST RUN: May 3, 2017

October 3, 2017 - 1.30pm-4.30pm
Melbourne Bioinformatics Boardroom, 187 Grattan Street, Carlton, VIC 3053 Australia

Workshops

Introduction to Galaxy and the GVL

Galaxy is an open source, web-based platform for accessible, reproducible, and transparent computational biomedical research. It allows users without programming experience to easily specify parameters and run individual tools as well as larger workflows. It also captures run information so that any user can repeat and understand a complete computational analysis. Finally, it allows users to share and publish analyses via the web.

This beginners workshop will introduce Galaxy’s interface, tool use, histories, and workflows and get new users of the Genomics Virtual Laboratory up and running.

This is a hands-on workshop and attendees should bring their own laptops.

LAST RUN: May 4, 2017

October 4, 2017 - 1.30-4.30pm
Melbourne Bioinformatics Boardroom, 187 Swanston Street, Carlton, VIC 3053, Australia

Workshops

RNA-Seq Differential Gene Expression Analysis using Galaxy and the GVL

In this tutorial we will cover the concepts of RNA-Seq differential gene expression (DGE) analysis using Galaxy: an open, web-based platform for accessible, reproducible, and transparent computational biomedical research.

Participants with no previous Galaxy experience are strongly recommended to attend the “Introduction to Galaxy” workshop first.

Attendees are required to bring their own laptop computers.

LAST RUN: May 4, 2017

October 5, 2017 - 1:30pm-4.30pm (AEST)
Melbourne Bioinformatics Boardroom, 187 Grattan Street, Carlton, VIC 3053, Australia

Workshops

Variant Calling with Galaxy & the GVL for beginners

In this tutorial we cover the concepts of detecting small variants (SNVs and indels) in human genomic DNA using a small set of reads from chromosome 22. The tutorial is designed to introduce the tools, datatypes and workflow of variant detection. We will align reads to the genome, look for differences between reads and reference genome sequence, and filter the detected genomic variation manually to understand the computational basis of variant calling.

(more…)

LAST RUN: May 5, 2017

October 9, 2017 - 1.30pm-4.30pm
Melbourne Bioinformatics, 187 Grattan St, Carlton

Workshops

Containerised Bioinformatics: Docker and other tools for reproducible analysis

Containerisation is a method of bundling an application or pipeline with all its dependencies, from language runtimes like Python and R to the operating system itself. This technology has already revolutionised web development by providing a simple way to run web applications a in precisely controlled environment, regardless of which computer system they are running on. This workshop will explain how these advantages can be easily applied to bioinformatics analysis, to ensure 100% reproducibility of your work, along with easy distribution of your pipelines to other users without the need for complex installation.

This workshop will teach you:

  • What containerisation is, and why you might use it in bioinformatics
  • What some common containerisation tools are, and when to use each of them
  • How to find and run containers built by other people
  • How to run containers on HPC systems (like Melbourne Bioinformatics)
  • How to build your own application into a container (containerisation)
  • How to use containers as elements of a bioinformatics pipeline
  • How to distribute your container online

This workshop is aimed at anyone with basic Unix command-line experience.

Attendees are required to bring their own laptop computers.


October 10, 2017 - 1:00pm - 5:00pm (AEST)
Melbourne Bioinformatics Boardroom, 187 Grattan Street, Carlton, VIC 3053, Australia

Workshops

Open source science with Git and GitHub

Learn how to keep a record your code’s evolution over time using the git version control system, used by companies and open-source projects worldwide. Git allows you to easily maintain snapshots of your code as you make changes, keep multiple parallel versions of your code, and collaborate with others.

(more…)

LAST RUN: May 23, 2017

October 23, 2017 - 1.30-4.30pm
Melbourne Bioinformatics, 187 Grattan St, Carlton

Workshops

Introduction to long-read genome assembly

New genome sequencing technologies are producing much longer reads. This workshop combines an introductory presentation to introduce the theory of de novo genome assembly with hands-on practice. It will cover long-read technologies and data types, and provide an overview of genome assembly methods. You will use command-line tools to perform long-read assembly and short-read polishing of bacterial genome data.

Prerequisites:

This workshop requires a familiarity with Unix and genomics concepts.

Workshop attendees must bring a laptop.