Accelerating life science research


The application of high-performance computing could have far-reaching implications for bioinformatics and life sciences researchers, as Robert Roe discovers


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ife science researchers are tasked with progressively complex simulations. Tis increasing complexity requires considerably more computational


power, which is why some scientists are turning to the use of high-performance computing to accelerate their simulations. Tis explosion in the number of potential


users and research topics is forcing HPC providers to re-think the way they offer HPC to life science researchers. At the same time, researchers are facing unprecedented growth in the data they are handling, forcing many of them to explore new avenues to accelerate life science research. Jorge Balcells, director of technical


services at Verne Global, highlighted the increased demand for HPC: ‘Te trend that we are seeing in our customers is simply an exponential increase in the granularity of data that is being processed. Tat exponential increase directly correlates with an increase in the demand for power.’ Te increase in the power requirements


when moving from small to large scale computing are fairly obvious, but being able to support a cluster at existing premises can be a difficult challenge, as Balcells explains: ‘You are seeing a big push towards cloud-based HPC; it is an evolution, but a forced evolution because the resources that you need to power a data centre are scarce in large metropolitan areas.’


THE TREND THAT WE ARE SEEING IN OUR CUSTOMERS IS SIMPLY AN EXPONENTIAL INCREASE IN THE GRANULARITY OF DATA THAT IS BEING PROCESSED


22 SCIENTIFIC COMPUTING WORLD Tere are other options for deploying cloud-


based HPC. Larger facilities may have the resources to set up their cluster, although this requires considerable technical knowledge. Another option would be to co-locate with other like-minded facilities or collaborators. Again this requires considerable resources, but they can be split between multiple research centres limiting the initial investment. In 2014, the data centre provider, Infinity,


secured a five-year framework agreement with Janet, the UK’s national research and education network, provided by Jisc. Te creation of a Jisc data centre to support the requirements for academic research was the first example of its kind in the UK. Te initial Jisc partners are University College London (UCL), Kings College London, Te Sanger Institute, Te Francis Crick Institute, Te London School of Economics and Political Science (LSE) and Queen Mary University of London (QMUL). One of the largest concerns for genomics


and the wider life science industries is the amount of storage needed to support research over the long term. One Biomedical research facility, Te Scripps Institute (TSRI), recently deployed DDN’s end-to-end data management solutions, including its SFA7700X file storage system using DDN’s WOS object storage archive, to support fast analysis and cost-effective retention of research data produced by cryo-electron microscopy (Cryo-EM). TSRI uses advanced microscopes, next-gen


digital cameras and sophisticated soſtware pipelines to shed light on new treatments for Alzheimer’s, Parkinson’s, Lou Gehrig’s and Huntington’s diseases while identifying new ways to combat HIV, Ebola and Zika. DDN’s storage enables TSRI to harness about 30TB of data generated each week by Cryo-EM while scaling an active archive for widespread collaboration and content distribution.


According to Jean-Christophe Ducom,


HPC manager, information technology services at TSRI, Cryo-EM has become the biggest producer of data, yielding four times more output than the institute’s genomics workflows. ‘DDN helps us give scientists what they want—unlimited storage capacity and easy access to data that holds the secret to life- saving discoveries.’ If setting up a cluster seems like a step too


far, then there are options for cloud-based HPC that allow researchers to send large-scale batch jobs to remote computing facilities. However, as Balcells highlights, not every data centre is the same, and the cost of power can be considerably different from one location to another. Verne Global’s data centre is located in


Iceland and uses only renewable energy from geothermal and hydroelectrical power plants located in the country. However, the placement of this data centre is not purely for ecological reasons. ‘We chose the site aſter a lot of due diligence


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