A random walk down the genomes: DNA evolution in Valis

The authors propose a new software system that incorporates biological data and domain-specific knowledge and show how biologists can use it to model, analyze, and experiment with genomic evolutionary processes. A better understanding of biology will come through information-theoretic studies of genomes that provide insights into DNA's role in governing metabolic and regulatory pathways. Understanding the evolutionary processes that act on these "codes of life" requires the ability to analyze vast amounts of continually generated genomic data. Researchers in the emerging bioinformatics discipline require more complex mechanisms to investigate the full ensemble of available biological facts. To meet this challenge, New York University's Bioinformatics Group is creating a computational environment called Valis, the vast active living intelligent system. Valis is designed to solve the immediate genomic and proteomic problems that the biological community currently faces, while remaining flexible enough to adapt to the maturing bioinformatics field.