The Virtual Biology Laboratory

Hiroaki Kitano, Sony Computer Science Laboratory, Tokyo, Japan

The Virtual Biology Laboratory is a project aimed at the construction of a detailed computer simulation model of major biological system, such as Saccharomyces cerevisiae, C. elegans, Drosophila, and Homo Sapiens. The ultimate goal of the project is the establishment of a methodology which enables highly accurate predictions of genes involved in the system and possible interactions among them. By combining the simulation system, a large scale parameter identifier, and a hypotheses generator, we intend to make systematic predictions of genetic interaction concerning the developmental process. Just like theoretical particle physicists predict the existence and characteristics of elementary particles, confirmed later by experimental physicists, we intend to offer a set of predictions to be hopefully confirmed by experimental biologists.

As the project is in its infancy, we are concentrating on simulating of rather simple and well-understood phenomena involved in the developmental process, such as axis formation, ommatidia formation, and the leg formation of Drosophila as well as embryogensis of C. elegans. The difficulty in creating simulation model is that only partial information is available from molecular biologists, and genetic interaction believed to present are often wrong. Thus, our challenges are (1) to efficiently find a set of parameters which reproduces spatio-temporal dynamics of gene expression patterns, and (2) to identify possible candidates of correct and complete genetic regulation networks and their associated metabolic pathways.

In this talk, I will describe our initial attempt to accomplish the above goals and will demonstrate some simple simulation systems, primarily about Drosophila embryogenesis.