Training and Events

In this tutorial we cover the concepts of RNA-seq differential gene expression (DGE) analysis using a simulated dataset from the common fruit fly, Drosophila melanogaster. (more…)

This is a detailed hands on tutorial on the UCSC Genome Browser which will provide beginners with an introduction to the UCSC Genome browser and how to use it to ask a wide variety of biological questions such as investigating variants, gene expression and epigenetics.

A selection of tools in the browser will be demonstrated including; in silico PCR, BLAT, and sessions. Example RNAseq data (BAM files) will be provided to demonstrate how to upload your own data to make custom tracks for use within the browser. You will also learn how to navigate the Table browser to retrieve genomic positions for targets of interest and create and load a custom bed file. (more…)

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…)

Overview

This is a detailed hands on tutorial illustrating the use of a number of popular websites in analysis of protein protein interactions networks (PPI). In addition to detailed exploration of BioGRID and IntACT other relevant webtools for exploring PPI data will be briefly explored (Eg GeneMania, String). Towards the end of the workshop you will learn how to import downloaded PPI data into Cytoscape for analysis of networks. Note that this workshop will not cover Cytoscape in detail, but it will get you started…

Learning Objectives

Learn about the main online data resources for PPI data and how to use them.

Learn about important differences in high and low throughput methods for generating interaction data and how to curate them

Important data standards for interaction data (IMEx)

Know how to retrieving large and small PPI data networks and import them into Cytoscape for analysis.

Requirements

The workshop is aimed at bench researchers with no coding/programming skills who wish to learn how to utilise online data and resources to refine their biological research questions and discovery.

All participants are expected to have a good understanding of molecular Biology.

What you need:

• A charged lap top (a mouse is also handy for selecting)

• access to Uniwireless/Eduroam

• Web browser (Firefox recommended)

• Installation of Cytoscape 3 on your computer (its free) (https://cytoscape.org/)

Upcoming events:

• (Fully booked) Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow
  Wednesday 25 September 12.00-4.00pm & Thursday 26 September 12.00-4.00pm AEST
• Phylogenetic trees for beginners
  18 October (Part A: Presentation/ hands-on exercises) & 4 December 2019 (Part B: Q&A relating to participants’ real life data problems)