MENLO PARK, Calif.—Late last year, SRI International, an independent nonprofit research and development organization, launched its new Center of Excellence in Computational Biology, which aims to conduct collaborative research in symbolic systems biology, synthetic biology and bioinformatics to advance knowledge of biological systems and accelerate drug discovery and development.
"Because the center will make the first strides to formally synthesize three of the most revolutionary disciplines of early 21st century biology, it is poised to break new ground and improve the quality and reach of biomedical research," predicts Dr. Patrick Lincoln, who has served as the director of SRI's Computer Science Laboratory for seven years and will now also serve as director of the Center of Excellence in Computational Biology.
Explaining how the three disciplines differ, Lincoln says the goal of systems biology is to model life by understanding how it naturally emerges from biological components such as genes. The goal of synthetic biology is to create logic machines by integrating components into higher-order genetic networks using mathematical modeling. And symbolic systems biology seeks to understand how the pathways of cell biology can be modeled with the same tools used to model computer circuits.
"Many of the tools we are offering -- and will offer -- to researchers are publicly available and open source," Lincoln notes. "They can already immediately pick up these tools. What we have done it to integrate the tools together were there are not proprietary issues preventing that, and to provide plug-ins that will help link proprietary applications in as well."
That's the concrete aspect of the center's work. At an abstract level, he says, the goal of the center is to have computational biology work on a more symbolic level so that instead of representing data as a "flat sequence of DNA or protein" researchers can view biological systems at a higher level and see how various drug and disease pathways interact and understand the context of those pathways better.
Another way the center plans to help make the business of drug discovery more efficient and productive is to reduce language barriers.
"By bringing people together from such diverse fields as sociology, epidemiology, mathematics and computer science, we can get them talking in a common language," he says. "People get so deep into their own fields that sometimes they start speaking their own language essentially. We want to find the common ground."
The center is funded in part by SRI International's own funds, but also by grants from such agencies as the National Institutes of Health and the National Science Foundation. The center also has received funding for specific contracted projects, such as the Biological Simulation Program for Intra-Cellular Evaluation (BioSPICE) for the Defense Advanced Research Projects Agency, which is the central research and development organization for the U.S. Department of Defense.
Other ongoing projects include Pathway Logic, SRI''s software for modeling biological entities; BioCyc, a collection of pathway/genome databases; Pathway Tools, a bioinformatics software system for pathway analysis of genomes and for creating pathway/genome databases; the HumanCyc bioinformatics database; and Hybrid Qualitative/Quantitative Modeling, SRI's approach for analyzing complex biological systems by modeling continuous and discrete behaviors of the system simultaneously in the HybridSAL language.