Section: Research Program

Modeling by successive refinement

Describing the links between diversity in traits and diversity in function will require comprehensive models, assembled from and refining existing models. A recurring difficulty in building comprehensive models of biological systems is that accurate models for subsystems are built using different formalisms and simulation techniques, and hand-tuned models tend to be so focused in scope that it is difficult to repurpose them [14]. Our belief is that a sustainable effort in building efficient behavioral models must proceed incrementally, rather than by modeling individual processes de novo. Hierarchical modeling [11] is one way of combining specific models into networks. Effective use of hierarchical models requires both formal definition of the semantics of such composition, and efficient simulation tools for exploring the large space of complex behaviors. We have previously shown that this approach can be effective for certains kinds of systems in biotechnology [2], [15] and medicine [13]. Our challenge is to adapt incremental, hierarchical refinement to modeling organisms and communities in metagenomic and comparative genomic applications.