Nectar microGVL – helping control food poisoning outbreaks

Nectar microGVL – helping control food poisoning outbreaks
November 23, 2016 Karen Mecoles

Accurately predicting the source of contaminated food in a food poisoning outbreak to potentially save lives and prevent serious illness – that’s just one practical real world challenge that Nectar’s microGVL is helping address.

microGVL – the microbial Genomics Virtual Laboratory is a leading genomics activity representing best practice in international microbial research and public health outbreak investigations.

Simon Gladman

Simon Gladman, Research Scientist and Lead Developer, microGVL

“The microGVL enables best practice outbreak analysis across the world” according to Mr Simon Gladman, Research Scientist and lead developer of the microGVL, based at the Victorian Life Sciences Computation Initiative hosted at the University of Melbourne. “Our user base includes highly esteemed research teams from across the globe including scientists based in Australia, USA, NZ, UK and many other countries.”

Rapidly increasing demand for an accessible microbial genomics analysis platform was the catalyst for establishing the microGVL. Significant reductions in the cost of whole genome sequencing over the last five years have resulted in a dramatic increase in the volume and size of the datasets produced – datasets that are simply infeasible to process on standard desktop computing environments.

Traditional analysis of this information was highly resource intensive and required access to expensive specialised super computers and a team of supporting IT staff – resources that were simply beyond the capabilities of many labs.

With funding from Nectar and BioPlatforms Australia, the team of VLSCI expert bioinformaticians built the microGVL as a cloud-based turnkey solution for microbial genomics researchers. The microGVL is a machine image that runs on compute nodes hosted in the Nectar research cloud, and comes pre-installed with the software tools and interfaces required by bioinformaticians and research scientists to undertake statistical and computational-based analysis.

“Operating the microGVL in the Nectar virtual cloud environment has many benefits. Firstly it negates the need for expensive computer hardware and specialised IT support staff. More importantly, it removes the complexity for researchers by providing a convenient interface between researcher data and specialised analysis tools. Researchers can simply access the VL via the user-friendly web-based launch page, securely load their data, select a tool… and their analysis is quickly up and running.”

The microGVL offers 100+ tools accessible via the web browser based Galaxy system – the GUI interface for accessing bioinformatics tools, Rstudio for statistical analysis, Jupyter Notebook for interactive Python programming, and a virtual desktop that provides a Linux machine interface as well as direct command line access to over 200 additional tools.

End users range from research labs at the University of Melbourne’s Dental School and Department of Microbiology and Immunology through to large biotechnology programs such as the International Wheat Genome Sequencing Consortium and public managed services that run up to 15000+ jobs each month.

The microGVL is also an exemplar for international collaboration with interactions across a team of international researchers from UK, Canada and Australia hosting reciprocal visits to refine the list of analysis tools. Since its official release in February 2016, the microGVL and its tools have also been showcased at numerous international conferences.

International collaboration has been further extended by multiple projects leveraging the lessons learned from the microGVL project. The technology has been ported to the prestigious UK Cloud Infrastructure for Microbial Bioinformatics (CLIMB) project, the Amazon cloud via AWS, with another genomics virtual laboratory deployment currently underway in South Africa. There are also plans to provide microGVL access to members of the European Elixir project.

“The microGVL has a bright future as a key component in the Nectar research cloud – our focus is now on increasing the number of tools to meet the future needs of our extensive user base. Thanks to Nectar, we’ve provided a highly-utilised resource that was specifically developed to meet the specialised needs of bioinformaticians”.

Reducing the duration, severity and burden of illness from pathogen outbreaks such as Listeria and Salmonella – that’s one of the best real world outcomes that Australian research can deliver.

Author: Loretta Davis

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