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From bench science to supercomputer
New UB visualization lab is one of the few in the nation to bridge the gap
By ELLEN GOLDBAUM
Contributing Editor
A new laboratory with state-of-the-art graphics workstations at UB is providing a rare commodity: a way to bridge the gap between bench science and supercomputing through molecular modeling and bioinformatics tools.
The UB Laboratory for Molecular Visualization and Analysis (LMVA) is one of a handful of such facilities in the nation, providing a critical service to researchers at UB and its affiliated research partners. The LMVA provides the computer tools to individual scientists that allow them to use UB's Center for Computational Research (CCR) in the most efficient and effective way possible.
"UB is home to one of the leading academic supercomputing facilities in the country," said Gerald Koudelka, professor of biological sciences and director of the LMVA. "To get the most out of that facility, scientists need to refine their molecular models as much as possible before submitting them to CCR. They need to gain experience writing jobs, submitting them and interpreting the output. That's what our new facility will allow them to do."
At other institutions, he continued, scientists are left to grapple with these issues on their own, often having to spend huge amounts of money from their individual grants to obtain these computational tools for their own labs. With the new lab, which officially opened last month, Koudelka said researchers pay a "ridiculously low" fee of $250 per grant. Forty-three researchers already have signed up to use the lab.
Koudelka and Robert Straubinger, professor of pharmaceutics in the School of Pharmacy and Pharmaceutical Sciences, founders of the LMVA, decided that the smartest use of resources would be to obtain the best hardware and software available for molecular visualization and make it available to the entire university.
Koudelka noted that the new facility would not be possible without the Science and Engineering Node Services (SENS), which provides computing support to faculty and students in engineering and the sciences.
"SENS provides excellent support for UNIX," said Koudelka. "There is no better place for this kind of operation than at UB."
Scientists who are using the LMVA work in a range of areas, many of which relate to determining the structure and function of proteins and nucleic acids implicated in diseases and to the design of new molecules that can inhibit them. Projects focus on such areas as topical antimicrobial and anti-inflammatory agents, agents for reversing multi-drug resistance in cancer and infectious diseases, design of compounds that have anti-addictive effects and vaccine design.
"The Laboratory for Molecular Visualization and Analysis is an advanced computational facility designed to help faculty and their students create models of how molecules interact," said Jaylan Turkkan, vice president for research. "This facility should speed research in drug discovery and help identify causes of diseases, and allow faculty to train students in the most advanced computers and software available today."
The laboratory also is the basis for curricula being designed as part of the new professional master's degree programs in chemical biology—the so-called "bench lab behind bioinformatics" that combines computational training with extensive laboratory experience—and computational chemistry, the study of atomic and molecular structure, which can speed drug design through the use of automated libraries of chemical compounds. Development of the programs is being funded by a grant from the Alfred P. Sloan Foundation.
Koudelka explained that, contrary to popular belief, research in bioinformatics and related scientific fields is not conducted entirely on supercomputers.
"All bench-level experiments first have to be tested and retested so that the data are in the best possible form before they are submitted to the CCR," he said.
The new lab provides the high-end computational tools that allow scientists to do that.
"I like to think of this lab as training the bench-level 'army,'" said Koudelka. "These are the weapons for the 'infantry.'"
The lab's "weapons" feature major commercial and open-source software on high-performance graphics computing platforms, enhanced servers and gigabit-rate networking hardware that provides Internet II-level connections to CCR and to UB's New York State Center for Engineering Design and Industrial Innovation, the lab's graphics partner.
The LMVA evolved from a collaboration of UB scientists involved in the cross-disciplinary Center for Advanced Molecular Biology and Immunology (CAMBI), the School of Pharmacy and Pharmaceutical Sciences, the Department of Chemistry in the College of Arts and Sciences and the Science and Engineering Node Services (SENS).
It was made possible by an initial equipment grant from the National Institutes of Health, which then led to further support from the National Center for Research Resources and gifts from Hewlett-Packard (HP) and Sun Microsystems Inc.