progress on the genomics virtual laboratory - andrew lonie
DESCRIPTION
The Genomics Virtual Laboratory (GVL) project, funded by NeCTAR, is building scalable infrastructure, workflow platforms and community resources for Australian genomics researchers. At this stage, the GVL comprises: a prototype workflow management system based on the Galaxy framework, a bioinformatics toolkit (for command-line users), and a visualisation service based on the UCSC Genome Browser, all implemented on the NeCTAR Research Cloud; and a developing set of tutorials and exemplar workflows targetted at common high throughput genomics tasks. In this talk I will demonstrate GVL capabilities and discuss progress and the GVL roadmap.TRANSCRIPT
Andrew Lonie1 & Michael Pheasant2
1 Victorian Life Sciences Computation Initiative, University of Melbourne2University of Queensland
Progress on the Genomics Virtual Laboratory
What is the Genomics Virtual Lab?
NeCTAR funded nationally distributed platform for genomics, built on the Research Cloud and RDSI
What is the Genomics Virtual Lab?
What did I promise today?
Demonstrate GVL capabilities and discuss progress:
1. scalable infrastructure on the Research Clouda. workflow management system based on Galaxyb. a bioinformatics toolkit (for command-line users)
2. a visualisation service (UCSC Genome Browser)3. a developing set of tutorials and exemplar workflows
Workflow platforms
Cluster-on-the-cloud
Use the public GVL, or roll your own
Building a GVL
http://usecloudman.orgCloudman = Middleware for building, distributing and managing cloud-based platforms, especially Galaxy
Building a GVL image
Tutorials and workshops
genome.edu.au
Progress and timelines
Dec 2012Prototype at Qld (UQ) and Vic (UoM)
● Galaxy● UCSC browser + databases● Bioinformatics cluster-on-the-cloud● Initial tutorials and exemplars
Jun 2013Production at Qld (UQ) and Vic (UoM), prototype @ other Research Cloud nodesData coordination centres, data catalogues
Dec 2013Additional workflows and tutorialsAdditional nodes
Jun 2014Operations (support centres - subscriptions)
Making the GVL possible
Go8 Universities● The University of Queensland● The University of Melbourne● Monash University● The University of Sydney● The University of Western Australia
Medical Research Institutes● The Garvan Institute of Medical
Research● Victor Chang Cardiac Research Institute● Baker IDI Heart and Diabeties Institute● Peter MacCallum Cancer Centre
eResearch Agencies● Queensland Facility for Advanced
Bioinformatics (QFAB)● Queensland Cyber Infrastructure
Foundation (QCIF)● Life Sciences Computation Centre
(LSCC) at the VLSCI● Victorian eResearch Strategic
Initiative (VeRSI)
National Agencies● NeCTAR, DIISRTE● CSIRO● EMBL Australia● Bioplatforms Australia (BPA)● Australian Genome Research Facility
(AGRF)● Australian National Data Service
(ANDS)