Genomics Repository

The repository enables researchers to add large datasets to their personal workspace and use standardised workflows to run on the University's Phoenix High Performance Computing (HPC) system. Once Phoenix has analysed the data, output file/s will be returned to the researcher's workspace for downstream analyses.

Incremental backups of the Genomics Repository are performed daily with full backups being performed monthly.

Academic Staff

The Genomics Repository is largely utilised by Researchers for approved University of Adelaide research data processing.

HDR Students

Higher Degree Research Students can utilise the Repository under the approval and supervision of their supervisor.

There are multiple layers of responsibility for the Genomics Repository.

Users of the Repository

When you agree to use the Repository you will need ensure your use of it is for University of Adelaide purposes, unless you have prior approval from the Bioinformatics Hub team. All users of Repository are required to clean and maintain their own data that is analysed. You can choose to share the data that is stored in the Repository, to enable other researchers to access the same datasets rather than having duplications.

Business Owner

For governance, approvals, investment in or feedback on the Genomics Repository, please contact the Bioinformatics Hub.

Phone: +61 8 8313 1207 (ex. 31207)
Email: bioinf_hub@adelaide.edu.au

Service Owner

If you are having issues with the technology infrastructure of the Genomics Respository, eg if it is not working, you should contact the Information Technology and Digital Services (ITDS) Service Desk (see the Additional support section details below).

The Genomics Repository has been designed to:

• Provide a secure and backed up storage for genomics data (daily incremental backups and monthly full backups)
• Enable researchers to safely store, analyse and share large genomic dataset
• Centralise the store of large genomics datasets, reducing the need to store them in multiple locations
• Set reminders to trigger archiving raw data (manual)
• Allow data to be exported
• Allow other researchers the ability to re-use genomic data and workflows to enable additional outcomes to be found from a single dataset
• Provide a facility for ‘processing genomics pipelines’ including:
  • An analysis Workflow Description Language
  • Workflow repository allowing workflows to be shared
  • Building workflows
  • Manage processing time/costs (Reporting purpose only)
  • Directly accessing and using Phoenix HPC for compute.

The Genomics Repository has extensive data storage capabilities (200 TB) enabling researchers to store and process data in a timely manner with the assurance of regular data backup. The ability to share datasets within the repository enhances the capability of collaboration across research groups. Bioinformaticians and non-computational researchers benefit from this critical platform capability that can be utilized without specialist data processing knowledge. The repository facilitates the reproducibility of complex datasets within the University This Genomics repository supports the ability to provide completely reproducible data processing workflow that can be included in high-quality research outputs.

Log into the Genomics Repository

The Genomics Repository is one of a number of different research computing options available to researchers at the University. Guidance on selecting the most appropriate option for you research can be found here: High Performance Computing Options.

The following resources are available if you'd like to learn more:

• User guide (subject to change with system improvements)
• Presentation about the Genomics Repository
• Component diagram
• Workspace lifecycle diagram
• Cleaning your workspace (data lifecycle)
• Simple data movements diagram

Workflow Description Language (WDL)

• WDL makes it straightforward to define analysis tasks, chain them together in workflows, and parallelize their execution. Learn more
• CWL to WDL tool: Visit Github
• WDL workshops: Workshop information in Google Drive
• Language specification: Learn more
• Slide deck about Common Workflow Language.

A genome is an organism's complete set of DNA stored in long molecules of DNA called chromosomes. In order to study the genome of an organism, high-throughput genome sequencing technologies have been developed that produce a large amount of data. Other sequencing approaches, such as the sequencing of genes from the genome that are expressed (RNA-seq or transcriptome sequencing), can also be carried out using these sequencing approaches allowing researchers to study many elements of the organism's genetic system at low cost.

The Genomics Repository will enable the university to centralise and simplify genomic data storage, analysis and collaboration. The goal is to provide bioinformaticians and non-computational researchers with the tools they need to perform their research without specialist data processing knowledge as there are pre-prepared processing commands available in the repository. This will result in a more efficient preparation and execution of data analysis, allowing for completely reproducible data processing workflow that can be included in high-quality research outputs. Additionally, by enabling a system where genomic data is centralised in a backed up storage repository, researchers will now be able to re-use genomic data with University collaborators enabling additional outcomes to be found from a single dataset.

The Genomics Repository is free to use. You will not incur any costs or ongoing charges.

To request access to the Genomics Repository, contact the Bioinformatics Hub between 9am and 5pm, Monday - Friday.

Phone: +61 8 8313 1207 (ex. 31207)
Email: bioinf_hub@adelaide.edu.au