Training and Events

This workshop is offered by Research Platform Services, and the trainer is Lev Lafayette.

Are you a life science researcher with desktop system that isn’t adequate for your big datasets or the complex research problems? It’s time to learn more about High Performance Computing (HPC). The University of Melbourne HPC system, Spartan, is freely available to researchers.

This introductory course will provide an introduction to the Linux command line and give you an overview of  Spartan. You’ll learn how to write Slurm script so you can submit data or task parallel jobs, with plenty of “hands-on” examples of running with research applications. (more…)

This workshop is offered by Research Platform Services, and the trainer is Lev Lafayette.

Job submission scripts in Slurm allocate resources and computation in batch mode. Job submissions can be made more powerful and flexible with a working knowledge of shell scripting and more advanced Slurm commands.

This workshop covers advanced Linux commands, regular expressions and regex tools, various shells, the use of variables, loops, conditional statements, the incorporation of shell scripting knowledge in job submission scripts, and autogenerating scripts with heredoc. (more…)

This beginners workshop will explain how containerisation can be used in bioinformatics analysis.

Overview

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. (more…)

This workshop is offered by the University of Melbourne’s Research Platform Services.

Registrations via Eventbrite open on 21 May 2019.

Overview

Software development is a central part of bioinformatics, but for many reasons software quality is not always prioritised, leading to problems in maintenance, usability and reproducibility. Adopting software engineering best practices at the beginning of a project can address these problems, but this is often not done due to lack of time and/or experience. This workshop covers the essentials of good programming practices and provides you with tools and knowledge to build high quality bioinformatics software from the outset. We will introduce a tool for quickly creating new software projects with important features and infrastructure already included. You will use this tool to initialise a new project including a fresh repository on GitHub.

Target audience

Bioinformaticians with beginner to intermediate level of programming experience who want to apply good software engineering practices in their daily work. Experience with the Unix command-line is assumed. Basic familiarity with Python (or similar languages) is an advantage.

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This workshop introduces the analysis of RNA-seq count data using R. This will include reading the data into R, quality control and preprocessing, and performing differential expression analysis and gene set testing, with a focus on the limma-voom analysis workflow. (more…)

In this workshop, you will be learning how to analyse 10X Chromium single-cell RNA-seq profiles using R. This will include reading the count data into R, quality control, normalisation, dimensionality reduction, cell clustering and finding marker genes. The main part of the workflow uses the package. You will learn how to generate common plots for visualising single-cell data, such as t-SNE plots and heatmaps. This workshop is aimed at biologists interested in learning how to explore single-cell RNA-seq data generated by the 10X platform.

This workshop is presented by Dr Yunshun Chen from Walter Eliza Hall Institute of Medical Research (WEHI). Dr Chen is a statistical bioinformatician and a senior post-doc at WEHI Bioinformatics Division. He is one of the authors and the main maintainer of the edgeR package. He has extensive experience in RNA-seq gene expression and single-cell RNA-seq analyses. (more…)

This workshop introduces the analysis of RNA-seq count data using R. This will include reading the data into R, quality control and preprocessing, and performing differential expression analysis and gene set testing, with a focus on the limma-voom analysis workflow. (more…)

The inaugural Victorian Cancer Bioinformatics Symposium (VCBS) aims to bring together those with an interest in the application of bioinformatics in cancer research and clinical practice.

High-profile invited speakers include:

Prof Shannon McWeeney, Oregon Health Sciences University, Portland, USA
Prof Cristin Print, University of Auckland, New Zealand
Prof Vanessa Hayes, Garvan Institute, Sydney, Australia
A/Prof Mark Cowley, Children’s Cancer Institute of Australia, Sydney, Australia

There’ll be opportunities for attendees from all career stages and professional roles to give talks at this event. The symposium will also include a poster session and an evening networking event.

See registration website for updates and details.