A Random Walk Down the Genomes: DNA

W hile chemistry and physics are thesubstrate of biology, researchers nowbelieve that a better understanding ofbiology will come through informa-tion-theoretic studies of genomes, providing new insights into DNA’s role in govern-ing metabolic and regulatory pathways. Conse-quently, the mathematical approaches derived from systems sciences—dynamical systems, control the-ory, game theory, information and decision theory, and mathematical logic—are playing increasingly important roles in biological research. Understanding the evolutionary processes that act on these “codes of life”—including point muta-tion, recombination, gene conversion, replication slippage, DNA repair, translocation, imprinting, and horizontal transfer—requires the ability to analyze vast amounts of continually generated genomic data. The challenges, intrigues, and excite-ment that these genomic sequences have come to symbolize have catapulted the embryonic field of bioinformatics to the forefront of scientific research. Bioinformatics currently consists of a set of tools to “contig ” genomic sequences and organize, anno-tate, and search sequence databases and generate computationally or statistically intriguing problems. However, researchers in this emerging discipline require more complex mechanisms to investigate the full ensemble of available biological facts. VALIS To meet this challenge, New York University’s Bioinformatics Group is creating a computational environment—the vast active living intelligent system (Valis)—designed to solve the immediate genomic and proteomic problems that the biologi-cal community currently faces but flexible enough to adapt to the maturing bioinformatics fiel