GVL: Taking the ‘IT’ out of Bioinformatics

GVL: Taking the ‘IT’ out of Bioinformatics
June 8, 2016 Karen Mecoles

“This is the best exemplar of this kind of platform in the world, few countries are able to do what we’re doing”

— Associate Professor Andrew Lonie, Director VLSCI

It took 13 years and US$3 billion to map the first human genome sequence, as part of the Human Genome Project in 2003. Since then, revolutionary genome sequencing technology has transformed all fields of biological research, from medicine to agriculture, allowing the average researcher to conduct large-scale projects from their lab.

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

This accessibility has fuelled massive growth in genomics research, however, the proliferation of genome sequencing – at ever-higher resolutions – has created a bottleneck, with a large number of biologists looking analyse genomes, without the tools or infrastructure to do so.

The Genomics Virtual Laboratory (GVL) funded through Nectar was established by researchers at The University of Queensland, the Victorian Life Sciences Computation Initiative (VLSCI), the Garvan Institute, and the CSIRO, to provide biologists with an online suite of genomics tools and resources.

Ron Horst, Project Manager for the Genomics Virtual Lab at The University of Queensland says that prior to GVL biologists working in genomics would have to collaborate closely with information technology specialists and bioinformaticians to analyse and make sense of their data.

“Our goal for GVL was to take the ‘information technology’ out of bioinformatics,” Mr Horst said. “Traditionally, before a researcher could even start their analysis, they would have to get funding, buy hardware, install it, load software, test, fail, test, set up Galaxy, and have a systems administrator to run it.

“Then there were issues with managing the analysis, with data being shipped back and forth to researchers from sequencing centres on hard drives, it certainly wasn’t ideal.”

Overcoming these barriers, the GVL provides an easy to access web portal with a growing suite of genomics analysis tools, allowing biologists to start analysing their data immediately using the Nectar Cloud.

The GVL also provides a workbench for reproducible results, and tutorials to help biologists learn the key analysis techniques they need to support their research.

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 thanks to the GVL.

Working with The University of Queensland’s Sugarcane Ecogenomics Research Group, which aims to understand more about microbes in the soil 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,” Dr Paungfoo-Lonhienne said.

“By using the GVL I have been able to undertake genomic analysis that I would not have been able to do on my own without it.

“I am a biologist,” she says. “I don’t know about Linux or coding languages like Python, and running genomics software requires you to know these things.

“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,” she said. “It makes everything easy for biologists like me.”

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

“We have some good results, which I’m writing up at the moment, Dr Paungfoo-Lonhienne said. “Hopefully we can submit a manuscript before the end of the year, I’m very pleased.”

The tutorials available through the GVL have also proved very popular with researchers in Australia and internationally, with hundreds of users from around the globe logging on to analyse their data, from Tufts University in the United States to research groups in Kazakhstan.

The largest cancer research group in Australia, the Peter MacCallum Cancer Centre is now also using the GVL as a user-friendly platform for their genomics analysis.

According to Associate Professor Andrew Lonie, Director, VLSCI and EMBL Australia Bioinformatics Resource, the GVL is enabling researchers at Peter MacCallum to explore their data and perform routine, well-established, bioinformatics with ease.

“Because they are spending less time on these tasks, the bioinformatics team at Peter Mac can focus on the more challenging and complex problems required for novel discoveries,” Associate Professor Lonie said.

“Having this facility in the Cloud also allows Peter Mac’s researchers to collaborate easily with external parties and to share and access data remotely.

“This is the best exemplar of this kind of platform in the world, few countries are able to do what we’re doing,” he continued. “The GVL provides genomics capability to the masses on a common infrastructure, allowing more efficient research, collaboration and faster outcomes.”

For more information, or to access the Genomics Virtual Lab, go to:https://genome.edu.au.