eRSA services in use: Cluster in the Cloud, Nectar Cloud and HPC
The software and Nectar Cloud resources I have been able to use through eRSA have been incredibly useful, especially for the population analyses.
Marine biologist Dr Claudia Junge has had a fascination with the ocean since she first went scuba diving at the age of 14. So after studying biology in Germany and undertaking a PhD at the University of Oslo, Norway, she decided to discover the deep seas of the South.
An ARC Research Associate in the School of Biological Sciences at the University of Adelaide, Dr Junge is using eR SA and the Nectar Cloud to power her research into Australia’s dusky shark and bronze whaler shark populations. Dr Junge is working with a multidisciplinary team of researchers as well as multiple government and industry partners to find out how many genetic stocks of dusky and bronze whaler sharks there are in Australia, in order to sustainably manage the species.
After extracting DNA from shark tissue samples, Dr Junge then uses next-generation sequencing (NGS), applying a method that involves cutting the genome into smaller fragments at specific recognition sites.
“Because of this, I end up with thousands of single nucleotide polymorphisms (SNPs) across the whole genome,” Dr Junge said.
“To run bioinformatic analyses on so many SNPs and samples you need a number of resources and it’s just not possible to have all of these on your desktop computer – this is where eRSA really comes in handy.”
“Once I have extracted the genetic information, such as levels of gene flow, we then work with modelling researchers, and the chemistry information our collaborators have found, to parameterise species specific spatially explicit population models.
“The software and Nectar Cloud resources I have been able to use through eRSA have been incredibly useful, especially for the population analyses, because you need specific programs, which they’re always willing to install.
“I have datasets that include over 10,000 SNPs for up to 300 different individuals and just one of these analyses can take 150 hours, not to mention that I then have to do this in replicates of 20 for 10 different settings – if I even attempted to do this on a desktop it would take forever.
“It’s great that researchers like me can use eRSA’s resources – I use the cluster in the cloud to access a high-performance computing cluster that uses virtual machines – it makes my life a lot easier and so much faster to get the results I need.”
The long-term result of Dr Junge’s research will be better fisheries management.
“As both species are fished in Australia – bronze whalers predominately in South Australia and dusky sharks predominately in Western Australia – and only produce very few offspring, compared to most commercially fished species, our studies are also important in ensuring that Australasian stocks are not being overfished.”
Contrary to previous studies, results from Dr Junge’s project have already shown that dusky shark populations around Australia are made up of the same genetic stock.
“We found that dusky sharks being fished in Indonesia belonged to the same genetic stock as our Australian samples,” Dr Junge said.
“This is important for fisheries management to keep in mind, particularly when making sustainability agreements interstate and internationally.
“Interestingly, bronze whaler sharks in Southern Australia are also very mobile and seem to be connected genetically.
“But from what we can tell, samples from Western Australia and also from around the Great Australian Bight are somewhat different, genetically, from the southern and eastern side of Australia as well as New Zealand.”
This research was supported under the Australian Research Council’s Linkage Projects funding scheme (project LP120100652).