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.

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 including the CLC Genomics Workbench, Ingenuity Pathway Analysis and Ingenuity Variant Analysis.
  • We are also happy to provide consulting services and advise you on the experimental design of your research project.

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 and whole genome 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 and for the School of Life and Environmental Sciences.

  • Introduction to DNA sequence analysis on Galaxy
  • Introduction to RNA sequence analysis on Galaxy
  • Intermediate to DNA sequence analysis on Artemis (coming soon)
  • Introduction to RNA sequence analysis on Artemis (coming soon)
  • Introduction to CLC Genomics Workbench on Artemis (coming soon)
  • Pathogen genomics for global health
  • Introduction to microbial genomics on Galaxy

View our training courses, slides and schedule for more information.

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.

Bioinformatics pipelines

  • Read quality checking
  • Reference mapping
  • Denovo assembly
  • Genome annotation
  • Variant calling
  • Genome comparison and phylogeny
  • Differential expression

CLC Genomics Workbench

CLC Genomics Workbench is a comprehensive suite of bioinformatics tools packaged into a user-friendly graphical environment. The Workbench is also backed by a dedicated server and will be connected with the Artemis HPC in 2018. 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 11 university licenses using the Sydney Informatics Hub PPMS. Please note, if you are using a license which someone else has booked, the SIH can terminate your session, so please do use the booking system.

Please email our bioinformatics technician at sih.info@sydney.edu.au for more information on CLC Genomics Workbench or to request a free trial.

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 University has one IPA license that is available free of charge to Sydney University students, researchers, and affiliates and can be booked using the Sydney Informatics Hub PPMS. Log into IPA at https://www.qiagenbioinformatics.com/product-login/.

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

Please email our Bioinformatics Technician at sih.info@sydney.edu.au for more information on IPA.