High performance computing and medical research.

ioinformatics, the use of computer technology to solve biological and medical problems, is a relatively new discipline. 1 Toronto's Hospital for Sick Children established a centre for bioinformatics (see www .bioinformatics-canada.org/) in 1998. The motivation to invest in this infrastructure was to provide researchers with a competitive advantage in coping with massive amounts of scientific data. The Bioinformatics Supercomputing Centre is the 455th-most powerful computing centre in the world and the largest centre devoted solely to biomedical research. Its computing power is equivalent to 1700 personal computers. The need for this level of computing resource is driven both by the amount and complexity of biological data; more biological data will be generated in the year 2000 than the total of all data collected up to that point. The medical researcher is, therefore, burdened with the prospect of sifting through this information to cull the data that is relevant to a particular query. Although the ability to quickly sort biological data is aided by supercomputers that are configured to maximize efficiency at data retrieval or complex analysis, for scientists to use the biomedical software effectively, they must also must be trained in how to conduct different types of analyses properly. The Bioinfor-matics Supercomputing Centre provides researchers with training on the principles and tools of basic bioinformatics analyses (e.g., DNA sequence-homology searching, 2 protein folding, 3 gene-finding algorithms 4), as well as help using the software. However, the researcher with a DNA sequence of interest can literally spend weeks performing complex data analysis, even on the fastest supercomputers. The implementation of a successful data acquisition, cura-tion and dissemination system 5 and the modelling of biological data are key components of many scientific endeavors , the most relevant of which is the human genome project. The Origin 2000 serves as the workhorse for the Bioin-formatics Supercomputing Centre. The computational power of the Origin 2000 is supplemented by an IBM RS/6000 SP3 system, a group of 5 nodes that are accessed independently and optimized for database use. In addition to providing a suite of programming languages, the centre hosts several bioinformatics applications. The most widely used application, BLAST (Basic Local Alignment and Search Tool), is accessible through a Web interface developed at the centre (http://blast.bioinfo.sickkids.on.ca /index.html); this application is designed to compare protein and nucleic acid sequences against a selection of genetic databases to calculate percent homology. The system also supports the Genome Database …