CSIRO Galaxy Bioinformatics Portal: A user friendly GUI for bioinformatics on HPC infrasructure

Mr Joel Ludbey1

1CSIRO, Camberwell, Australia


The talk will have two basic themes. One being focused around the features and usability of the Galaxy portal and how it can benefit bioinformaticians. The second being focused around the specific deployment and configuration we have at CSIRO and how it exposes the HPC infrastructure without compromising the benefits of a workflow tool such as Galaxy.

While HPC is particularly suited to bioinformatics it can be troublesome to get over the hurdle that is the CLI particularly if you do not have a technical background. The galaxy portal aims to remove this hurdle and hide away the HPC components behind a simple point-and-click interface that facilitates the creation of reproducible and portable workflows.

Galaxy usability and benefits:

– What is galaxy?

– Why would I want to use galaxy?

– Benefits and features of galaxy?

– Galaxy and CSIRO HPC

– Simple demonstration of a basic workflow using local and remote jobs

Galaxy deployment and configuration

– How is galaxy configured in CSIRO

– How does the HPC infrastructure fit into all this

– Automated deployment using ansible

– Why did we do things this way, could we do better


Joel Ludbey has been operating as a part of the IM&T SC group since 2008, starting as a distributed systems administrator for CSIRO under the Australian Research Collaboration Service (ARCS) joint venture which was responsible for providing eResearch services to the Australian research community. While he has held several system administration focused roles within IM&T SC he is currently operating as the Scientific Workflow Specialist for the IM&T SC User Services group and is the primary technical support and architect of the CSIRO Galaxy portal . A role that aims to aid researchers in the creation, implementation and optimisation of scientific applications and workflows utilising CSIRO’s computational facilities and external partner resources.


AeRO is the industry association focused on eResearch in Australasia. We play a critical coordination role for our members, who are actively transforming research via Information Technology. Organisations join AeRO to advance their own capabilities and services, to collaborate and to network with peers. AeRO believes researchers and the sector significantly benefit from greater communication, coordination and sharing among the increasingly different and evolving service providers.

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