Bioinformatics

The central dogma of molecular biology - that is, how genetic information is used to create an individual organism - is key to understanding many aspects of life sciences including human and animal health, species evolution, diversity, agricultural improvement and conservation. Since the emergence of new high throughput technologies that have the ability to produce terabytes of data, scientists have had to come up with solutions on how to manage and analyse this wealth of data giving rise to the bioinformatics field.

Subscribe to the University of Sydney’s bioinformatics mailing list.

EMBL-Australian Bioinforamtics Resource: SIH NODE

EMBL Australia Bioinformatics Resource (EMBL-ABR) is a distributed national resource supporting local, national and international collaborations, infrastructure projects, coordinated training, and networks to life science researchers in Australia. It was set up as a collaboration with the European Bioinformatics Institute (EMBL-EBI) to maximise Australia’s bioinformatics capability.

SIH is one of 13 national nodes, organised around six Key Areas: Data, Tools, Compute, Standards, Training and Platforms, mapped to expertise in biosciences domains.

EMBL-ABR Nodes

Bioinformatics support

The Sydney Informatics Hub provides a wide range of support and services in bioinformatics. We provide support and training for:

  • The proper and secure management of your data.
  • Data visualisation and quality control.
  • How to effectively use the University’s Artemis HPC and Research Data Storage systems for large datasets.
  • Specialist software and online platforms including QIAGEN’s CLC Genomics Workbench. Ingenuity Pathway Analysis and Galaxy Australia.
  • Popular open source software
  • We are also happy to provide consulting services and advise you on the experimental design of your research project.

Bioinformatics pipelines

We can assist you with:

  • Read quality checking
  • Reference mapping
  • De-novo assembly
  • Genome annotation
  • Genome wide association studies
  • Variant calling
  • Genome comparison and phylogeny
  • Differential expression
  • Single cell sequencing

Support and training is free for all staff and students from the University of Sydney. Fill in the assistance form. We will be in touch to arrange an initial meeting to discuss your project.

Training courses

SIH deliver a range of bioinformatics training courses open to University of Sydney research staff, students and affiliates. We deliver training in next generation sequencing analysis and in the use of specialist bioinformatics software on Artemis, HPC and on the Genomics Virtual Lab. We can also deliver courses and content as part of internal or external collaborative training programs. For example, we have delivered bioinformatics workshops as part of training programs for NSW Health, Westmead Institute for Medical Research and for various Faculties/Schools across the University.

  • Introduction to DNA and RNA sequence analysis on Galaxy
  • Introduction to RNA sequence analysis in R
  • Introduction to Single Cell RNA sequence analysis (10X Genomics)
  • Next Generation Sequencing Analysis on Artemis
  • Introduction to microbial genomics on Galaxy
  • Galaxy Australia Training Series
  • Introduction to CLC Genomics Workbench on Artemis
  • Pathogen genomics for global health

View our training courses, slides and schedule for more information and get notified on upcoming training courses by subscribing to our training mailing list.

Bioinformatics Software

The University has licenses for several specialist commercial bioinformatics software. SIH will soon be providing a suite of bioinformatics pipelines to process and analyse high-throughput next generation and whole genome sequencing data on Artemis, HPC.

CLC Genomics Workbench

CLC Genomics Workbench is a comprehensive suite of bioinformatics tools packaged into a user-friendly graphical environment. You can perform a range of analyses on next generation sequencing data and create customisable workflows for studies in genomics, transcriptomics, epigenomics and metagenomics.

Since May 2018, the CLC Genomics Workbench is integrated with the University’s high performance computer, Artemis. This will provide users with even more processing power and higher throughput.

The user guide on using CLC Genomics on Artemis can be downloaded here.

CLC is offered at a heavily discounted rate subsidised by the University. Single licences are currently $750 (incl. GST) for a 6 month or $1,500 (incl. GST) for a 12 month subscription. A single license may be shared amongst a research group, however only one user from the group can use the license at any one time. Subscribers can book one of 5 university licenses using the Sydney Informatics Hub PPMS. Licenses include access to the Microbial Genomics Modules. Bookings are essential in order for you to use a license, to ensure fair use amongst CLC Genomics Workbench users.

Please email our bioinformatics technician at sih.info@sydney.edu.au for more information on CLC Genomics Workbench or to request a free 4-week trial. You can also read more about what it does on QIAGEN’s website.

Ingenuity Pathway Analysis

Ingenuity® Pathway Analysis (IPA®) is a powerful analysis and search tool that uncovers the significance of ‘omics data and identifies new targets or candidate biomarkers within the context of biological systems. IPA has broadly been adopted by the life science research community and is cited in thousands of articles for the analysis, integration, and interpretation of data derived from ‘omics experiments, such as RNA-seq, small RNA-seq, microarrays including miRNA and SNP, metabolomics, proteomics, and small scale experiments.

The QIAGEN Bioinformatics website has a set of training resources. The most popular webinars are:

The University has one IPA license that is available free of charge to Sydney University students, researchers, and affiliates. Users are required to book their sessions using the Sydney Informatics Hub PPMS. Please email our Bioinformatics Technician at sih.info@sydney.edu.au to get access to IPA.

Alternatively, please see Sydney University’s Ingenuity Pathway Analysis User Setup Guide.

Software available through the Westmead Institute for Medical Research

The Westmead Institute for Medical Research offers subsidized access to propreitary bioinformatics software to members of the University of Sydney or Westmead Institute for Medical Research. Software currently include:

  • Metacore
  • Partek

Please contact the Advanced Genomics Specialist at the Westmead Institute for Medical Research for more information.