RDisk
A Reconfigurable and Parallel Architecture for Browsing Genomic Databases
Context
Scanning the genomic database is a common task, daily performed by thousands
of researchers for extracting new knowledge from this huge amount of
data. Today, this represents tens of Gigabytes. Tomorrow, according to the
genomic data exponential growth, the volume of information to manipulate will
reach Terabytes.
RDisk System
We propose a 48 parallel disk system whose originality is to attach
reconfigurable computation capabilities near the disk for providing on-the-fly
data filtering. Speed-up is provided both by accessing tens of disk in
parallel and by hardwiring efficient FPGA filters.
Applications
- BLAST-like search
- Motif search (see WAPAM implementation on Ouest Genopole)
- Content-based image search
To learn more...
- D. Lavenier, S. Guyétant, S. Derrien, S. Rubini,
A reconfigurable parallel disk system for filtering genomic banks,
ERSA'03, Engineering of Reconfigurable Systems and Algorithms , Las Vegas, Nevada, USA, 2003.
(pdf)
- S. Guyetant, M. Giraud, L. L'Hours, S. Derrien, S. Rubini, D. Lavenier, F. Raimbault,
Cluster of re-configurable nodes for scanning large genomic banks,
Parallel Computing, 31 (1) 2005.
(link)
- S. Guyétant,
Architecture parallèle reconfigurable pour le filtrage
de banques de données non structurées ; application à la génomique
Thèse de l'université de Rennes 1, décembre 2004
(lien)
- M. Giraud, S. Guyétant, D. Lavenier,
Encodage Linéaire d'automates pondérés. Filtrage de motifs génomiques et application sur l'architecture prototype R-disk,
TSI,24(6), 2005.
(lien)
Gallery