June 30, 2015 Fuller

The Genomics Virtual Laboratory (GVL) funded through Nectar, is taking the information technology out of bioinformatics, providing biologists with easy access to a suite of genomics tools and resources.

In 2003 the international Human Genome Project announced the first sequence map of a human genome, spending 13 years and US$3 billion to do it.

Since that time there has been a revolution in genome sequencing technology, so that what was once accessible only to a mega project is now easily within the reach of an average research lab.

New sequencing facilities at the Garvan Institute of Medical Research, for example, are able to sequence 150 whole human genomes every three days, at a cost to Australian researchers of less than $2,000 per genome.

This accessibility has fuelled massive growth in genomics research. Genomics is transforming every field involving the biology of organisms, from medicine to agriculture.

Keeping pace with the growth of genomics data

However, the proliferation of genome sequencing—at ever-higher resolutions—has created a bottleneck: large numbers of biologists who want to analyse genomes but who until now did not have access to the tools or infrastructure to do it.

Before the Genomics Virtual Laboratory (GVL), biologists working with genomics needed to be part of a team that included information technology specialists and bioinformaticians in order to set up the technology environment and make sense of the data from the analysis.

“There was a whole, traditional set of things you needed to do before you could start the analysis. Get funding, buy hardware, install it, load software, test, fail, test, set up Galaxy, have a systems administrator to run it, and all of that,” says Ron Horst, Project Manager for the Genomics Virtual Lab at The University of Queensland.

Once the environment was set up, managing the data for analysis was also an issue.

“The sequencing data would be shipped back to researchers from sequencing centres by UPS or DHL, just on a hard drive,” says Dr Igor Makunin, Research Fellow at The University of Queensland’s Research Computing Centre.

When Nectar called for proposals for virtual labs, researchers at The University of Queensland, the Victorian Life Sciences Computation Initiative (VLSCI), the Garvan Institute, and CSIRO, had the idea to create the GVL, to take the IT out of bioinformatics and make genomic data analysis more accessible to biologists.

The GVL provides access through a web portal to a growing suite of genomics analysis tools that biologists can start working with immediately, with no setup required. Data can be analysed easily on the Australian Research Cloud. The GVL also provides a workbench for reproducible results and tutorials to help biologists learn analysis techniques.

Empowering biologists to do genomic analysis

Dr Chanyarat Paungfoo-Lonhienne at The University of Queensland’s Institute for Molecular Bioscience is one of the new generation of biologists working with genomics.

She works with UQ’s Sugarcane Ecogenomics Research Group, aiming to understand more about the microbes in the soils and the roots of sugarcane plants and how these affect the plants’ growth and health. Ultimately, the research could lead to more sustainable practices for growing this important Australian crop, using less fertiliser.

Using the GVL, Dr Paungfoo-Lonhienne has been able to undertake genomic analysis she would not have been able to do on her own without it.

“I am a biologist,” she says. “I don’t know about Linux or languages like Python, and running most of the genomics software requires you to know these things. With the GVL, it’s a web-based tool. It helps me to overcome those problems.

“Instead of spending time trying to learn how to install software and use a command line interface, I can focus on the goals I want to achieve. It makes everything easy for biologists like me.”

Dr Paungfoo-Lonhienne is preparing a manuscript for publication, using results she achieved with the GVL.

“We have some good results from using the GVL. I’m writing them up at the moment, and hopefully we can submit the manuscript before the end of the year. I’m very pleased,” she says.

A dedicated learning centre

The tutorials available through the GVL have also proved very popular.

“The dedicated learning centre we’ve developed has become a bit of a hit internationally,” says Dr Makunin. “It has hundreds of users from around the globe, ranging from Tufts University in the US to countries like Kazakhstan.”

The GVL at the Peter MacCallum Cancer Centre

The largest cancer research group in Australia is also using the GVL.

The GVL is providing a user-friendly platform which enables researchers at the Peter MacCallum Cancer Centre to explore their data and perform routine and well established bioinformatics.

Because they are spending less time on these tasks, the bioinformatics team can focus on the more challenging and complex problems required for novel discoveries.

Having the facility in the cloud also allows Petermac researchers to collaborate easily with external parties and to access their data no matter where they are.

“This is the best exemplar of this kind of platform in the world,” says Associate Professor Andrew Lonie, Head of the Life Sciences Computation Centre at VLSCI.

“Few countries are able to do what we’re doing, which is to provide genomics capability to the masses on common infrastructure.”

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