Methods, Knowledge Support, and Experimental Tools for Modeling

摘要

Our goal was to provide software and experimental abilities to support quantitative modeling of eukaryotic systems and thus to help enable new kinds of molecular logic. The most significant accomplishments were the development of two programs. One was a collaborative annotation, MONOD. MONOD embodied a number of genuinely novel ideas, particularly in the data structure, which constituted a middle ground between the highly structured relations of objects in a relational database and the unstructured representation of human text-based discourse and notes. The second, Moleculizer, addressed an important problem in simulating chemical reaction networks, the proliferation of closely related species of molecular complexes. This rule-based approach has since been widely adopted. Since the project period, the two programs have had different fates. Despite the notional advantages of MONOD, for the main purpose of knowledge support, we and others have opted for the free form text embodiment in a wiki (at www.openwetware.org). By contrast, work on Moleculizer continues at MSI with money from the Japanese E-cell project, and we have worked with a number of groups to port the basic concepts to other simulation software.