This working group focuses on tools to support the construction, simulation and analysis of computational models of plant function at various scales of resolution and fidelity. Interoperability of disparate modeling tools, and the integration of such tools with the products of other iPG2P working groups (especially those supporting data integration, visualization, and inference), are key points of emphasis. Priorities for analytical tools and modules include support for: parameter estimation; sensitivity analysis; confidence region estimation; integration of statistical and mechanistic models at both cellular and ecophysiological scales; and model verification and validation testing. Over the near-to-intermediate term, components of ecophysiological models will increasingly employ the results of gene-based network studies, thus enhancing their application in breeding and other contexts. This evolution will entail statistical testing of highly nonlinear model elements for genetic associations and/or the use of such models to further improve the phenotype prediction capabilities of existing, whole-genome regression approaches.