Andrew Lonie
COLLABORATING INSTITUTIONS | TYPE/ROLE |
| Melbourne Bioinformatics | LEAD INSTITUTE |
| University of Melbourne | MEMBER INSTITUTE |
| VicNode | MEMBER INSTITUTE |
| University of Queensland | MEMBER INSTITUTE |
| Queensland Cyber Infrastructure Foundation (QCIF) | COLLABORATOR |
Bioplatforms Australia contract, with additional funding from Nectar, both funded by NCRIS
Over ten years after the sequencing of the human genome, in 2013 the National eResearch Collaboration Tools and Resources project (Nectar) funded this project, led out of the University of Queensland by Ron Horst, with partners from the VLSCI (now Melbourne Bioinformatics), the Garvan Institute and CSIRO. With the exponential growth in genomic data being generated, the Australian-made GVL was built to make genomic data analysis more accessible to biologists. It has successfully achieved this goal and continues to serve the research community in many ways.
The Genomics Virtual Lab is a computational workbench providing a highly accessible cloud-based genomics analysis environment preconfigured with best practice genomics tools and supplemented with comprehensive tutorial materials and protocols, managed services and user support.
There are now large installations at Monash, Melbourne and Queensland universities, with more planned for Western Australia, New South Wales and Tasmania. Adopted both locally and overseas, the GVL has already been recognised as a quality platform to help address the shortage of bioinformatics expertise around the world and manage the complex, multiple-layered data analysis tasks confronting life scientists today.
The GVL works as both a research and training tool, with life scientists able to undertake self-directed training to then translate this knowledge to their own data. It is also being used to deliver content in the Masters of Science (Bioinformatics) at the University of Melbourne.
As part of the work being undertaken to extend the reach of the GVL, our experts have carried out performance analysis testing of GVL-based clusters on the Nectar cloud.
Australian-made Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud, in PLOS ONE, 26 October 2015. Recognition of the value of the Australian-made Genomics Virtual Laboratory (GVL) was boosted further this week with its publication on 26 October in PLOS One. Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud outlines how a team of Australian […]
Building upon three existing NCRIS-funded capabilities, the Nectar Research Cloud, RDS data services and the Genomics Virtual Laboratory (GVL), RDS Omics empowers the modern biologist to go from raw data to complex, collaborative, downstream analyses without the need to purchase expensive compute or pay for scarce bioinformaticians. Modern biology is being revolutionised by high-throughput molecular […]
In mid-March Melbourne Bioinformatics’ resident Galaxy guru, Simon Gladman, attended the ELIXIR Galaxy community meeting in Freiburg, Germany for the official launch of the https://usegalaxy.eu/ server and to announce the upcoming this new Galaxy Australia server – https://usegalaxy.org.au. With NCRIS funding, we are partnering with QCIF to extend and update the service model for Galaxy across Australia […]
2 November 2017 In a Victoria University report published this week which set about measuring the return on investment on Australia’s Virtual Laboratories (VLs), which provide digital interfaces, tools and data to online research communities, it has been reported that they are generating a return on investment of up to 138 times their cost. Estimating […]
Last month the GVL was trialled by colleagues in New Zealand (NZ) who were interested in its use for both research and training in bioinformatics. Aleksandra Pawlik, Research Community Manager, New Zealand eScience Infrastructure, wrote afterwards: We’re ending the first of the scheduled training workshops and indeed it was a great idea. GVL removes all […]
The Australian-made Genomics Virtual Laboratory keeps on producing outcomes for Melbourne Bioinformatics. Yesterday (10 May 2018) co-authors Enis Afgan (ex-VLSCI, now Johns Hopkins University), Andrew Lonie (Melbourne Bioinformatics), James Taylor (Johns Hopkins University) and Nuwan Goonasekera (Melbourne Bioinformatics) submitted this paper to Cornell University’s arXiv, which outlines how to launch complex applications (typical for bioinformatics) across various […]
The ongoing evolution of services behind the GVL, including Galaxy Australia, saw a number of solid outcomes for our teams at Melbourne Bioinformatics and QCIF throughout May to August. Galaxy Community Conference Key Galaxy developer Simon Gladman and UQ’s Derek Benson attended the Galaxy Community Conference held in Portland, Oregon from 25-30 June 2018. Simon […]
The GVL is now being tailored for the specific needs of researchers in microbiology. Read CLIMB story in microGVL project page. For a full explanation of what this means for UK public health and how our microGVL plays its part, read Prof Mark Pallen’s 27 July 2016 blog from the PHGfoundation.