by Faith Short
Stockholm, SWEEDEN — In the spring of 2000, the Knut and Alice Wallenberg Foundation awarded 7.5 million Swedish crowns (MSEK) for bioinformatics development to Gunnar von Heijne and Bjˆrn Engquist. The grant will be awarded over 5 years, at 1.5 MSEK per year, and is part of an 800 MSEK grant for functional genomics.
Professor of biochemistry at Stockholm University, von Heijne is the head of the Stockholm Bioinformatics Center (SBC) – a national facility designed to provide a critical mass of bioinformatics and computer science expertise for high-level research, methods development, and advanced post-graduate training in bioinformatics. Engquist, professor in the department of numerical analysis and computing science, is the director of Parallelldatorcentrum (PDC), Sweden’s major high-performance computing center.
Together, SBC and PDC will build an initial cluster of personal computers; this will incrementally become a supercomputer, made up of 100-200 PCs, for bioinformatics. As they learn more about how to use these machines, they will continue adding to the cluster.
“The initial cluster will be built during the fall of 2000,” according to von Heijne, “and our two groups are now planning the best way to integrate the current computing environments at Stockholm University and PDC.”
Bioinformatics, or biomedical computing, is the application of computer science and technology to problems in the biomolecular sciences. It is one of the key areas in the present data explosion in biology brought about by the genome projects and the new developments in functional genomics and proteomics.
The Human Genome Project, an international project to identify all the genes of the human body, is one of the prime examples of this combination of technology and biology. The existence of the human genetic map will lay the foundation for a revolution in medical diagnosis and treatment.
Bioinformatics research and methods development are currently expanding rapidly in Sweden. Von Heijne describes the area as “the use of computer technology to handle, analyze, and add value to the flood of data coming out of modern genomics and proteomics research.” The field includes such applications as information processing (storage, retrieval, and analysis) and modeling biological and behavioral processes.
Research at SBC is focused in three areas: protein sequence and structure, molecular evolution, and modeling of cellular function.
Researchers can analyze and make predictions about protein structure from the amino acid sequence. These kinds of predictions can aid in areas like drug design for pharmaceutical development. The analysis and comparison of whole-genome data is a very important aspect of such studies.
Molecular evolution looks at how proteins have evolved and how organisms are related to each other. Using the PC cluster, scientists have opportunities for data-mining protein family databases and DNA sequence databases, among others. There are masses of these kinds of data, and this type of research has many implications. “For example,” says von Heijne, “we can begin to make evolutionary deductions about bacteria, which is important in the health field, given the increasing numbers of drug-resistant strains of bacteria.”
Another use of the cluster is to develop models of signaling networks in cells, which can shed light on how genes are turned on and off. “We can study metabolic responses at the cellular level, to gain a comprehensive view of the cell from a theoretical perspective.” For more information, see http://www.sbc.su.se .