Harvard Medical School
Advancing Structural Biology Research
Group B Streptococcus Alpha-C protein: Group B Streptococcus (GBS) is the leading cause of neonatal pneumonia, sepsis, and meningitis. The alpha C protein is a surface-associated protective antigen found on many Ia, Ib, and II GBS isolates. The crystal structure of a 169 amino acid N-terminus alpha C protein is shown.
If necessary, Gohara adds, “I can push the modifications back over to the Linux side once they’ve been tuned and tested.” Right now, however, the inclination is to stay on Mac OS X.
Maintaining the Cluster with Desktop Tools
To check the cluster and to install security updates or patches on the head node, Gohara uses Apple’s server administration tools, and particularly its remote monitoring tools.
“Every now and then if I want to log into the systems directly or back something up, I’ll use Apple Remote Desktop,” he says. “I’m not an IT person, but I found that maintaining our cluster took very little of my time. That’s partly because the tools are very convenient and easy for a non-professional administrator to use, and I don’t have to leave my desk to do most tasks. I can sit at my workstation doing my normal work while applying updates or running maintenance tasks on the cluster.”
Gohara says Harvard itself has an Apple Care contract for ongoing hardware and software support. “But we rarely use the service,” he says. “The systems have been very stable considering the amount of use they get.”
Money in the Bank
A major benefit of employing the Xserve G5 cluster, says Gohara, is its impact on the lab’s research budget. “We have very limited budgets,” he points out. Given current budgets, the performance and the ease of administration make Xserve and OS X the best fit.
What’s more, the ability of researchers to renew grants or apply for new ones depends, in part, on how much work can be accomplished. “A lot of the structural biology research going on here and elsewhere involves solving large structures requiring long computations,” says Gohara. “In many cases, structure determination is a key component of applying for, and renewing, grants. Having hardware that performs well and allows us to do our work efficiently all come into play when it comes to maintaining or acquiring new funding.”
Moving Toward a Single Environment
SGI and Linux have been the dominant platforms in structural biology research for the last decade, so labs like Hogle’s had to maintain two separate types of hardware in addition to Macs and PCs on the desktop.
“Minimizing unnecessary time and effort spent on system maintenance is an important consideration in a research setting. Every hour we spend on administration is an hour we can’t spend on research.”
“Now our users can do almost everything on a single machine, without ever having to switch to another platform,” Hogle says. “They can check email, write grants, and at the same time in the background, have a CNS job running — or any other application for scientific computing. It’s all there.”
Best of all, there is no performance cost for this single-platform ease of use; quite the contrary. The electron microscopy and x-ray crystallography people are starting to use the Xserve cluster instead of the one originally set up for them, often seeing increases of three to ten times the performance of the earlier cluster computer.
Gohara would like to see a single computing environment — Mac OS X — for all structural biology research.
“For certain computing tasks, you have to be right on the edge,” he says, “but at the same time, we need a stable environment to get the most out of applications and make sure everything is properly compiled and tested. Of the platforms we do support, one is no longer maintained by the distributor and the other doesn’t offer enough standardization to be a complete out-of-the-box solution.” Apple and OS X provide the performance researchers need along with manageability and cross-platform interoperability.
