New Web site promotes use of Lisp for bioinformatics
Advances in bioinformatics, coupled with the completion of the human genome sequence, have resulted in an increased amount of data. Lisp, the second oldest programming language in use, can be used to manage complex systems modeling, knowledge-based annotation and automated scientific reasoning.
"The basic philosophy of Lisp programming is to create high-level functions that are easily composed," said Larry Hunter, Director of the Center for Computational Pharmacology and a member of BioLisp.org's Steering Committee. "This approach encourages code reuse, integration of multiple data sources and algorithms, and easy experimentation. Modern implementations provide state-of-the-art programming environments, integrated persistent databases and Web servers, and full CORBA connectivity."
According to Jeff Shrager of the Carnegie Institute of Washington and editor of the Web site, BioLisp.org was organized to promote and support Lisp-based applications in bioinformatics. "This industry is evolving rapidly towards knowledge-based methods rather than simple data crunching," he said. "We wanted to provide a resource for the community to share methods and information."
"EcoCyc, a comprehensive database and software system for manipulating the genome and the metabolic pathways of E.coli that was co-developed by SRI International, contains more than 160,000 lines of Lisp code," said Peter Karp, Director of the Bioinformatics Research Group at SRI International. "It was recently ported from Sun Unix to Windows 2000 in a little over a week. Lisp gives us a powerful software development environment that lets our group efficiently maintain a large code base, so we can focus our main efforts on our research."