London School of Hygiene and Tropical Medicine

Michael Gaunt

Lecturer and Wellcome Trust Junior Research Fellow Michael Gaunt of the London School of Hygiene and Tropical Medicine performing phylogenomic calculations on tropical disease killers on an Xserve G5 cluster.

The Science

With the sequencing of many higher eukaryotes completed, some researchers have turned their focus to the genomes of eukaryotic parasites. How do hosts, carriers, and the parasites themselves interact at a genetic level to produce diseases like Malaria, African Sleeping Sickness, and Chagas disease. Chagas disease alone kills more people each year in Latin America than HIV/AIDS.

Lecturer and Wellcome Trust Junior Research Fellow Michael Gaunt and his colleagues at the London School of Hygiene and Tropical Medicine use comparative genomics, or phylogenomics, to better understand the genetic mutations and inheritance mechanisms (for example, Gaunt et al Nature 421:936-9), and, ultimately, to find vaccine and drug targets in the fight against these parasites.

The Technology

“Genomics has changed everything,” says Gaunt. “We need substantial computational power to run both our software pipelines and microsimulations. But before we had benchmarked the PowerPC G5 processor, several systems were slower than a standard desktop system. The applications didn’t scale.” The Apple Workgroup Cluster, because of its integrated software and powerful hardware architecture, was immediately faster.

“This thing can really fly,” says Gaunt. “I was quite struck at just how quick it could move. I routinely perform 2-8,000 hour calculations, and on a system this fast, it’s not that hard. It’s not a big thing for the machine to do.”

The raw horsepower of the system enables the researchers to do things they had not before been able to do. “Without this type of power, these calculations would be completely infeasible,” says Gaunt.

Management has been a breeze, too. “Overall the administration is not really an issue,” says Gaunt. “I wasn’t brought up in UNIX administration, but it wasn’t hard to administer this cluster.” The system doesn’t distract the scientist from his research. “I still spend almost all of my time on research, not administration,” he says.

The BioTeam, makers of iNquiry and Apple’s partner in building the Apple Workgroup Cluster for Bioinformatics, won rave reviews from Gaunt: “I was very impressed by the BioTeam folks. They were there for us every step of the way.”