Barcelona Supercomputing Centre (BSC-CNS Barcelona, Spain)
Organisation and Competences: Barcelona Supercomputing Center (Center Nacional de Supercomputación (BSC-CNS)) is the Spanish National Supercomputing Center. The mission of BSC is to investigate, develop and manage information technology in order to facilitate scientific progress. BSC provides access to MareNostrum (~100 TF machine) to a large community of users. BCS-CNS is not only a supercomputing services centre, but also a research center with 125+ researchers in all levels of supercomputer design and several application areas (engineering, life sciences and earth sciences).
Role: BSC will be involved in WP4, and will lead subtask 4.1.1 From the life science department at BSC, we plan to devote coordinated efforts from two different groups. The group of computational genomics (leaded by David Torrents) and the group of INB (leaded by Josep LLuis Gelpí). Both groups combined have the potential of developing and applying strategies of data storage and management adequate to specific functional needs associated to large sequencing data. The computational genomics group is already applying different de novo assembly strategies for different genomic scenarios. For example, within the International Cancer Genome Consortium, we are contributing in the Spanish initiative with the storage and management of sequenced genomes and their assembly to locate structural variations. The combination of our experience and the computing facilities allocated at the BSC (MareNostrum: 10,000 CPUs and Altix with 2.5 Tb of RAM memory), will allow us to be involved and push the following tasks: - Initial
sequencing data gathering, storage and management for BSC internal use relative to WP4 tasks and for the rest of partners. -Development and evaluation of best strategies for de novo and reference based genome assembly. Particular emphasis and attention will be focused in large memory requirement issues due to the unusually large genome size of Pines. - Generation of genome assemblies and evaluation of the quality of each assembly by using expression data and homologous gene information.
Staff members' profile:
Dr. David Torrents- PhD, is ICREA Research Professor and group leader in the Department of Life Sciences at the Barcelona Supercomputing Center (BSC). Dr. Torrents obtained his undergraduate degree in Biochemistry (1995) and his PhD in Molecular Biology (2000, with the highest qualification: PhD extraordinary prize) from the University of Barcelona. Stay of 6 years at the EMBL in Heidelberg into the Peer Bork's group of bioinformatics as an EMBO postdoctoral fellow. Dr. Torrents actively participated and co-coordinated sections of the primary analysis of several eukaryotic genomes as part of the corresponding international sequencing consortia providing primary digestion and annotation of functional elements in sequenced genomes. Valentí Montcunill, member of Torrents group will also participate as a computer scientist.
Prof. Josep Lluis Gelpí- is professor at the university of Barcelona and leading the Computational Bioinformatic Node of the National Institute of Bioinformatics hosted by the BSC. He has got a wide and extensive experience in generating and managing large datasets.