Cloud computing pilot boosts biomedical research

20.09.2010

CSC – IT Center for Science Ltd offers cloud computing service to the Institute for Molecular Medicine Finland (FIMM) to boost the performance of FIMM’s advanced biomedical software environment. The service utilizes the high-speed data transmission link between Meilahti and Otaniemi established in June.

Biomedical sciences have become data and computationally intensive disciplines. Many research groups and institutions have set up their own local computational resources - usually compute clusters and storage solutions. However, often these resources become insufficient as the need for computing grows over time.

Many countries, including Finland, have set up supercomputer and data centers to satisfy this kind of demand. The current way of accessing the resources often implies that one size has to fit all. The users of the local compute clusters and storage solutions would like to migrate their tasks to a new more efficient environment, but this has not been a trivial task. Cloud computing is a technology that can offer a solution for exactly that.

"Cloud interface to high-performance computer clusters and storage in order to encapsulate scientific software environments aims to improve biomedical institutes' access to ICT centers' resources", says Tommi Nyrönen who leads the development at CSC. In practical terms this means that the FIMM’s compute cluster has seemingly doubled its size with half of the processors provided by CSC’s cloud. The arrangement utilizes the high-speed data transmission link between Meilahti and Otaniemi established in June.

End user experience is important

Technological transparency is important for the end user experience. The users of the FIMM compute cluster can carry on their work as normal, except for shorter waiting times.

Samuli Ripatti is one of the researchers at FIMM whose group pilots the infrastructure. Work of Ripatti's group on the genetic mapping of the Finnish population has attracted global attention. "The goal for our research is identifying the genetic components of metabolic traits such as cholesterol levels and obesity and heart disease using unique biomedical sample collections of Finland. From our perspective, use of the cloud compute cluster did not require changes in the way the we work. We simply see that the local cluster is able to run our statistical data analysis pipeline faster, and we can thus extend our analysis to both larger datasets in terms of genomic coverage and sheer number of people – and towards higher level data-analyses." 

Technical experts from both CSC and FIMM participated in building of CSC’s cloud computing infrastructure and its use to extend FIMM compute cluster. In particular, Timo Miettinen from FIMM and Olli Tourunen from CSC were instrumental in making this endeavor a success. Extension of FIMM compute cluster is nevertheless just the beginning of cloud computing on CSC’s computational resources. It is envisaged that cloud computing will be useful also for other purposes.

Part of European biosciences infrastructure development

The cloud pilot demonstrates a distributed infrastructure solution between three national organizations. It is a stepping stone to be scaled as a European infrastructure targeted for biomedical sciences. CSC – IT Center for Science Ltd., Institute for Molecular Medicine Finland FIMM, and The National Institute for Health and Welfare work together in a national spearhead project Biomedinfra.fi funded by the Academy of Finland. The goal is a significant role for Finland in three European biomedical sciences research infrastructures that are currently being developed. The focuses are biobanks (BBMRI), utilization of biomedical research information (EATRIS), and biological data resources and bioinformatics (ELIXIR).

Contact :

Tommi Nyrönen, Development Manager, CSC – IT Center for Science, Ltd., tommi.nyronen at csc.fi tel. +358 50 381 9511

European research infrastructure projects on bioinformatics:

BBMRI: Biobanking and Biomolecular Resources Research Infrastructure (biobanks) http://www.bbmri.eu
EATRIS: European Advanced Translational Research Infrastructure in Medicine (utilization of research information) http://www.eatris.eu
ELIXIR: European Life Sciences Infrastructure for Biological Information (biological data resources and bioinformatics) http://www.elixir-europe.org

CSC

CSC - IT Center for Science Ltd. is a non-profit limited company administered by the Ministry of Education, Science and Culture. Having core competences in modeling, computing and information services, CSC provides versatile IT services, support and resources for academia, research institutes, and companies. The Funet communication links provide research workers with Finland's widest selection of scientific software and databases and Finland's most powerful supercomputers.