Lisp at Use of Lisp for research in biology

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A new website, www.biolisp.org, supports a growing community of researchers who are using Lisp to better analyze and manipulate biological data.

Recent advances in bioinformatics, dramatically punctuated by the completion of the human genome sequence, have generated an overwhelming amount of data. While the last century might be thought of as the century of biological data, this century is certain to be considered the age of biological knowledge. Clearly, understanding what to do with these massive amounts of data -- and how to do it - will provide the opportunities of the future.

Lisp, the second oldest programming language in common use, remains the principal language of knowledge representation, knowledge-based programming, and automated reasoning. Unlike Perl, the current language of choice among many bioinformaticians, Lisp is one of the few programming languages robust and powerful enough to manage the complex systems modeling, knowledge-based annotation, and automated scientific reasoning needed to take bioinformatics to the next level.

Larry Hunter, Director of the Center for Computational Pharmacology and a member of www.biolisp.org's Steering Committee, says that although there are many competing programming environments for bioinformaticians, Lisp provides some powerful advantages. "The basic philosophy of Lisp programming is to create high-level functions that are easily composed. 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," says Hunter.

"EcoCyc(TM), 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. It was recently ported from Sun Unix to Windows 2000 in a little over a week," says Peter Karp, Director of the Bioinformatics Research Group at SRI International. "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."

"BioLisp.org was organized to promote and support Lisp-based applications in bioinformatics," says Jeff Shrager of the Carnegie Institute of Washington and the website's editor. "This industry is evolving rapidly towards knowledge-based methods rather than simple data crunching. We wanted to provide a resource for the community to share methods and information."

Other members of www.biolisp.org's Steering Committee include Russ Altman, Stanford Biomedical Informatics, Stanford University; and Imran Shah, University of Colorado School of Medicine.

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Last update : 19/02/2001