Published on 11-Sep-2011
The two sequencing machines in use in the King's College London and NIHR Biomedical Research Centre's genomics facility collectively generate up to 50 billion base pairs of usable DNA sequence data every 10 days. The HPC system can reduce the time necessary to analyze this data 20-fold or more, reducing the time for analysis from days to hours.
Medical researchers at the National Institute for Health Research and King's College London needed high performance computing capabilities to more quickly analyze, store and archive vast quantities of data.
IBM® System x® iDataPlex® combined with IBM BNT® RackSwitch G8124 10 Gigabit Ethernet switches helped reduce the time necessary to analyze data; thus reducing the time needed for analysis from days to hours.
This IBM HPC system provides higher computing power, energy efficiency, a high-performance storage system and a 20-fold reduction in analysis time.
Medical researchers at the National Institute for Health Research and King's College London used IBM System x iDataPlex high performance computing with IBM BNT RackSwitch G8124 10 Gigabit Ethernet to more quickly analyze, store and archive vast quantities of data.
Don Lokuadassuriyage, Cluster Administrator at King’s College London
Charles Ferland, BNT Vice President, IBM System Networking, EMEA
Don: Biomedical Research Centre, we are here focused mainly on providing translational medicine which means you know what we find in the lab we take it back to a clinical environment and to enable patients to find cures for diseases. So hopefully identify the genes, which probably leads to a clinical trial, which probably leads to finding some medication or preventing people from getting that specific disease, so benefits to human kind. The problem we had was we have four genomic sequences that provides a lot of data, for example fifty billion base pairs of useful DNA, every ten days, and that's about 500 gigabytes per sample. Within a week we can produce at least 2 terabytes worth of data. We had to find a place to store the DNA data and process it and archive it so in case of emergency we had something to go back to.
Most of the software tools are run on the cluster access data that’s stored on separate storage solution. So we need fast interconnects between the two systems so we utilize the IBM Switch to provide ten gigabytes per second connectivity between the nodes and the storage.
Charles: The IBM system networking product provides a very low latency that means the actual servers and the actual application can communicate with each other a lot faster and that improves the user experience and means quicker results to your research date.
Don: With the old desktop base systems it took over ten days to analyze one flow cell worth of data and now it takes less than twenty three hours. So in terms of identifying genes that cause diseases or other factors, it’s very fast. Hopefully after identifying a disease causing gene that can be translated back into patient care so you can provide cures for example cancer or osteoporosis and they can make medication hopefully to prevent the activation of those genes within individuals and hopefully cure existing individuals as well. So having a fast network backbone means you can get the data faster, it’s much more reliable and it saves time.
Charles: What we’re doing with IBM system Networking is connecting these different components in the data centre and making sure we have the optimal communication between all of them. Making sure we have the fastest response time, accelerating the application performance and making sure that the user experience is always optimal.
Products and services used
IBM products and services that were used in this case study.
System Networking, System x: iDataPlex
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