A Practical Bioinformatics Workbench for the 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 researchers built the GVL to take the ‘IT’ out of bioinformatics.
Adopted both locally and overseas, and rolling out to more centres over 2015/16, the GVL has already been recognised as an aid to address the severe shortage of bioinformatics expertise around the world and manage the complex, multiple-layered data analysis tasks confronting life scientists today.
The GVL workbench is an accessible cloud-based genomics analysis environment with comprehensive tutorial materials and protocols, managed services and user support. There is a common platform for data analysis, tool development, and training, with a powerful interface for managing these services and resources.
Large installations at Monash, Queensland, Melbourne and Western Australian Universities and Australia’s largest cancer research group at the Peter MacCallum Cancer Centre will likely soon be followed by Sydney, Deakin, New South Wales and Tasmania Universities.
Although it is available on the OpenStack-based Australian Research Cloud and the Amazon Web Services cloud, the principles, implementation and build process are designed to be cloud-agnostic, making it readily available to research groups around the world.
Co-author, Enis Afgan, moved from VLSCI to Johns Hopkins University this year and is now lead architect & co-developer for Galaxy on the Cloud infrastructure with two of the top ranking universities in the world: Johns Hopkins, and MIT (through the Broad Institute), to be used by their associated life science researchers and companies.
“The US-based Galaxy project is working closely with the Australian GVL and Nectar to pilot an instance of the GVL on Jetstream, the US equivalent of Australia’s Research Cloud,” says Enis Afgan.
“The GVL is the best exemplar of this kind of platform in the world,” says Assoc Prof Andrew Lonie, Director, VLSCI and EMBL Australia Bioinformatics Resource. “It places Australia, and the participating Australian institutions, in an enviable leadership position on the world stage.”
“I have just returned from a visit with EMBL people in Europe where there has been genuine interest in using the GVL, particularly as a training resource for bioinformatics. It is important that we showcase these assets Australia has to bring to global collaborative projects which are developing around genomics, to take our place amongst the action,” says Andrew Lonie.
In other developments, three VLSCI bioinformaticians are working at the Doherty Institute to develop a ‘microGVL’ to apply microbial genomics technologies to investigations into infectious diseases and food-borne outbreaks and for use as a training tool.
Now the UK’s Cloud Infrastructure for Microbial Genomics (CLIMB) project, funded to build the UK’s microbial genomics capabilities across four-sites in Birmingham, Warwick, Cardiff and Swansea, is keen to roll out the microGVL on its cloud-based infrastructure to deliver training for microbial medical bioinformatics. Public Health England is also deploying it internally for training and for running their bacterial surveillance pipeline.
More generally, the GVL has been used for workshops from South Africa to the USA:
“Thanks for your help and for making this incredible resource available. I couldn’t teach this lab without it”, writes Nick Kaplinsky, Department of Biology, Swarthmore College, Pennsylvania, USA. (The workshop was part of a genomics course Nick teaches at Swarthmore.)