BIO Community Grid
Establishing a Nordic bioinformatics grid infrastructure
Nordic countries are planning to establish a new grid infrastructure for bioinformatics. With a Nordic bioinformatics grid infrastructure heavy computational tasks can be performed faster and more efficiently. The project is funded by Nordic Data Grid Facility.
The available amount of data in bioinformatics is huge. One way to characterize for example protein function is to perform large-scale analyses on the available data. These analyses are to an increasing extent dependent on fast computers. The demands are similar for most bioinformatics groups within the Nordic countries and it therefore makes sense to coordinate common efforts. Presently, bioinformatics resources are available within each country but with limited coordination between the countries. With a Nordic bioinformatics grid infrastructure heavy computational tasks can be performed faster and more efficiently.
Upon each new release of the databases and new genomes, the bioinformatics community wishes to perform these analyses as quickly as possible. There are compute intensive jobs also in the areas of structure prediction and protein dynamics. A grid solution is then an efficient way to make enough number of processor units available.
There are several challenges involved with the establishment of a Nordic bioinformatics grid infrastructure. First, there are large amounts of data that need to be synchronised between the nodes. Second, several of the bioinformatics programs need to be rewritten/optimised for a grid environment. Furthermore, compatibility issues and standardised protocol for input/output need to be considered.
Initial participants in the project are Linköping University (Sweden), Stockholm University (Sweden), SNIC (Sweden), NSC (Sweden) CSC (Finland) and Bergen Centre for Computational Science (Norway). Further groups might be added during the project.
The Nordic Bioinformatics Grid-project is a result of the proposal presented in the Nordic Computational Grand Challenge Survey. The Survey was a joint project by the supercomputer centers in Finland, Denmark, Norway and Sweden. The main goal of the survey was to identify outstanding problems in science whose solution will greatly benefit from the use of large-scale e-Infrastructure (i.e., infrastructure for computational science that includes large computational resources, storage devices, and high-speed networks).
Principal Investigator
Bengt Persson
Professor of Bioinformatics
Linköping University & Karolinska Institutet. Sweden
e-mail: bpnATifm.liu.se
Other contact person from participating countries:
Olli Tourunen, CSC, Finland
olli.tourunenATcsc.fi
Inge Jonassen, Bergen, Norway
ingeATii.uib.no.
Additional information:
Nordic Data Grid Facility: http://www.ndgf.org/
Presentation of the Bioinformatics Grid at the Finnish Supercomputing Days:
Nordic computational challenges:
http://www.csc.fi/english/csc/news/news/computational_challenges_2007_3_19
Copyright NDGF