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 Bioinformatics 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 14 national nodes delivering national bioinformatics capability, organised around six Key Areas: Data, Tools, Compute, Standards, Training and Platforms, mapped to expertise in medical and biosciences domains.

EMBL-ABR Nodes

Bioinformatics support

The Sydney Informatics Hub provides a wide range of project support and services in bioinformatics. 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.

Bioinformatics project support: Pipelines and analysis support

We develop global best practice data processing and analysis bioinformatics pipelines and execute these, on researchers data, at scale on National HPC facilities, University of Sydney’s Artemis HPC, and on Commercial Cloud. We engineer bioinformatics pipelines to maximise the efficiency and minimise run times and costs for HPC and Cloud facilities. Our high-throughput pipelines for model and non-model organisms include:

  • small germline variant calling
  • somatic variant calling
  • structural variant and indel calling
  • transcriptome assembly

We assist with bioinformatics analyses such as:

  • Read and assembly quality checking
  • Metagenomics (WGS and 16S)
  • Metatranscriptomics
  • Genome wide association studies
  • Single cell
  • Differential expression
  • Comparative genomics
  • Phylogenetics
  • Short and long read de novo assembly
  • Genome annotation

We also assist with

  • sensitive/protected and big data management lifecycles
  • best practices and advise on the experimental design for next generation sequencing studies.
  • 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

Grant support

We assist with developing budgets and draft University in-kind contribution estimates for computing, data storage, and data analysis services for grant applications.
We assist with preparing and reviewing project proposals for computing resources grants, including the National Computational Merit Allocation Scheme, Intersect HPC Allocation Scheme, Microsoft Azure and AWS Cloud Research grants.

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.

SIH-led training courses:

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

Training partner courses that SIH facilitate:

  • EMBL-ABR: Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow
  • EMBL-ABR: Introduction for phylogenetic trees for beginners
  • EMBL-ABR: UCSC Genome Browser: a full-featured genomic data system
  • Galaxy Australia: Differential Gene Expression from Bacterial RNA-seq Data
  • Galaxy Australia: Genome Assembly
  • Galaxy Australia: Finding genetic variants in bacterial sequence data
  • Galaxy Australia: 16S Metagenomics

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.