RuleHub : An environment for developing and sharing rule-based models

Rule-based modeling (RBM) is a molecule centric representation of biological systems that enables a direct translation of knowledge about protein-protein interactions, posttranslational modifications, and enzyme catalysis into executable models. Many models have been developed using this paradigm, but presently there is no centralized database or standard annotation system that allows modelers to exchange model information. In this paper we present RuleHub, a repository that allows for annotation, visualization, simulation, and sharing of RBMs. Encoding of models using rules facilitates model querying and comparison.