iSGTW Feature - An orange in the emergency room: grids join the race against viral epidemics

Feature - An orange in the emergency room: grids join the race against viral epidemics

The race to stay one step ahead of evolving plant viruses is one that requires new and innovative methodologies.
Images courtesy of Alessandro Lombardo

Have you ever seen an orange in the emergency room? Have you ever diagnosed a tomato on a computer?

These things have been reality in Sicily for a long time. Biologists at the University of Catania, Italy, are involved in the PI2S2 project, studying the virulence and spread of plant viruses using bioinformatics applications created for grid computing.

The testbed viruses-cucumber mosaic virus, tomato yellow leaf curl virus, tomato yellow leaf curl sardinia virus, tomato spotted wild virus and citrus tristeza virus-are, at least from an economic point of view, the causal agents of some of the most important plant pathologies in the Mediterranean region.

Forewarned is forearmed

To help farmers withstand possible epidemic events, researchers are using grids to explore new and innovative bioinformatic approaches, studying the factors involved in viral spread and virulence, the structural genomic features, and building a database to help detect possible "host-jumps."

High performance distributed workstations will soon become essential in bioinformatic computing, since new sequencing techniques and reducing costs are producing a vast amount of information that can no longer be handled using traditional methods.
Images courtesy of Alessandro Lombardo

Ten years computing in one month

Applications already grid-enabled include programs that provide a complete workflow for aligning multiple pair-wise sequences as well as tools for constructing phylogenetic networks, detecting recombination events and predicting secondary structures using a genetic algorithm.

Thanks to the elevated speed afforded by grid computing, scientists can analyze entire viral genomes, or a very high number of sequences, in a "reasonable" time, cutting previous times by approximately a factor of ten. Hence, researchers have started down a new road, encompassing a future vision: the integrated know-how of agronomists, molecular biologists and IT experts.

This work was carried out in the context of the PI2S2 project managed by the COMETA Consortium. PI2S2 is financed by the Italian Ministry of University and Research, under its "Programma Operativo Nazionale 2000-2006", and aims to create an e-infrastructure in Sicily that connects to those already existing in Italy and in the rest of the world. The COMETA e-infrastructure is distributed over seven sites with more than 2000 CPU cores and 250 TB of disk storage.

The COMETA e-infrastructure is an Enabling Grids for E-sciencE collaborating project and was showcased at the recent EGEE User Forum.

- Muoio Annamaria, INFN-Catania; and Alessandro Lombardo, Science and Technology Park of Sicily