ARES – a GÉANT Open Call project aims to add​ress urgent genome data set challenges

6/11/2014

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A GÉANT Open Call project, ARES, (Advanced networking for the EU genomic Research) aims to create a novel Content Distrib​​ution Network (CDN) architecture to support medical and research activities, making large data sets accessible to healthcare practitioners for better patient care.

 

Cambridge, UK | 06 November 2014

“It is expected that in the next few years all newborns will have their whole genomes sequenced, with medicine increasingly built upon genome processing, it is evident that managing genomic data will shortly be a very serious problem.”  (O’Driscoll, Daugelaite & Sleator 2013). 

The objective is to de​​sign and deploy scalable network service architectures that allow quick, efficient delivery of genomic processing results to support European medical and research needs.  It will make use of both Cloud Computing and Content Distribution Network architecture services in addition to open source software packages. 

​Says Gianluca Reali, Coordinator, ARES:

“Genomic data is being generated at a significantly higher rate than the deployment rate of the network resources that can handle them – a very serious problem. We realised that doctors and genomic scientists in thousands of hospitals and research centres will not be able to quickly d​ownload and process the files they need to treat patients, without existing data networks creating bottlenecks.

So we applied for the GÉANT Open Call funding, to try and address this time-critical need. Genome science simply will not support healthcare practically and effectively without an innovative and unique infrastructure.   

The GÉANT network allows many ARES collaborators to work together, and provides us with the infrastructure we need to gain a deeper understanding of network problems related to sustainable increases in the use of genomes for diagnostic and research purposes. 

The infrastructure is the ideal environment to identify management policies of genomes and their auxiliary files. In particular, looking at efficiency, resiliency, scalability, and QoS in a distributed environment - using a multi-user CDN approach.”​

ARES is a collaboration between students and researchers at the University of Perugia (UoP) and th​e Polo d'Innovazione di Genomica, Genetica e Biologica SCARL​

​​​A serious and urgent issue

As we enter an era of genomics-based healthcare, critical decisions are increasingly genetically informed and personalised to each patient.  In addition, it is expected that public health, business and academia will soon want to access DNA sequences more frequently, as well as industries such as biology, food and medicine. ​

But with one sequenced human genome file equal to about 3.2 GB, the immense computer required to process this data as part of very large data sets, is seeing data growth in orders of magnitude. The Catalog of Human Genetic Variation (1000 Genomes), for example, is 464 TB for just 1000 samples.  

This growing interest in genome data, coupled with the increasing speed of DNA sequencing and dramatic lowering of costs allows study in much greater depth, which in turn requires a more powerful infrastructure.

The future of ARES

The results will provide the GÉANT network with a strong example of the advantages of an advanced CDN service and  demonstrates a platform that has potential for other computational and storage intensive data uses. 

Their next steps will be to perform a comprehensive set of experiments on the proposed novel CDN concept on genomic data sets.

​​Michael Enrico, Technical Coordinator for the GÉANT project: 

“ARES is innovating an infrastructure that is likely to assist genomic doctors and researchers at potentially thousands of hospitals and clinics across Europe, supporting ground-breaking research, such as studying particular gene mutations.  In doing so, they will be contributing a new CDN solution for our European users, that has the potential to be rolled out across the GÉANT network as a service.”

To find out more about ARES and to read recent research papers, please visithttp://www.geant.net/opencall/Applications/Pages/ARES.aspx​.

GÉANT Open Calls

As part of the GÉANT Innovation Programme, the GÉANT Open Call projects bring in fresh ideas and support new uses of the network. There are 21 projects within the Open Call initiative, each aligned to one of the GÉANT project’s joint research activities within its innovation programme. All Open Call projects sit within one of four subject areas:

  • Applications and Tools – supporting advanced research activities and projects.
  • Authentication – helping support secure end-to-end authentication of systems and people.
  • Network Architecture and Optical Projects – studying future networking systems./li>
  • SDN - exploring Software Defined Networking potential to meet new networking demands.

The power of the GÉANT network and those of its National Research and Education Network partner networks comes from the applications researchers use across them. By developing innovative uses for the network, barriers to research can be broken down and collaboration across Europe is increased. These activities have been designed to investigate how the GÉANT network can support advanced research activities and projects.

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Further press information:
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