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Virtual lab for genomics researchers trials around Australia
Dr Christina Hall, VLSCI, and Dr Nuwan Goonasekera, VeRSI
The Genomics Virtual Laboratory (GVL) project, under development at the University of Queensland, the VLSCI's (Victorian Life Sciences Initiative) Life Sciences Computation Centre and the Garvan Institute, with funding from the NeCTAR program, is building scalable infrastructure, workflow platforms and community resources for Australian genomics researchers.
At this stage of development, the GVL comprises:
- A prototype workflow management system based on the Galaxy framework.
- A bioinformatics toolkit (for command-line users).
- A visualisation service based on the UCSC Genome Browser. These components are all implemented on the NeCTAR Research Cloud.
- A developing set of tutorials and exemplar workflows targeted at common high-throughput genomics tasks.
Further components under development include a scientific collaboration framework portal, and support for genomic datasests of national significance, such as the Framework Datasets, funded by Bioplatforms Australia.
The GVL is currently in pilot phase and is being trialed at several biomedical research institutes around Australia; it is also being used extensively for training and education in high-throughput genomics in Melbourne, Brisbane and Sydney. A working GVL is expected to be available for the Australian life-sciences community in the second half of 2013.
VeRSI and the GVL
VeRSI’s primary involvement in the GVL has been in contributing to the development of technology and software infrastructure to enable the GVL’s on-demand compute platform. This has been mainly through extending the CloudMan software to support cluster management on the NeCTAR cloud.
CloudMan is a cluster-management software that dynamically scales a compute cluster’s size up or down depending on system load, allowing for efficient use of available computing resources in cloud environments. VeRSI has contributed to the following areas of CloudMan’s functionality:
- Porting CloudMan to run on the NeCTAR Research Cloud.
- Improving CloudMan’s management of Galaxy services.
- Improving CloudMan’s support for multiple file systems.
- Rewriting CloudMan’s user interface to be easier to use (a screenshot of the new user interface is provided below).
A screenshot illustrating the CloudMan cluster management platform being used to manage the GVL infrastructure
VeRSI has also contributed to other supporting tools within the GVL infrastructure, such as software libraries for provisioning clusters and automating bioinformatics pipelines. The most notable is the BioBlend library (Sloggett, Goonasekera and Afgan – BioInformatics 2013). This is a simple Python-based library for interacting with CloudMan and Galaxy that allows the dynamic instantiation of CloudMan-based infrastructure and the subsequent scripting of Galaxy-based workflows.
VeRSI actively continues to contribute to the project, and is currently helping to test and improve the scalability of the GVL.
VeRSI is also working on eResearch Tools for the Australian Research Community with the Australian Synchrotron and other NeCTAR projects. To find out more, please visit our NeCTAR project web page.