Figure 2
Algorithm for transforming algebraic rules to assignment rules. The first step is to decide whether the model is overdetermined by creating a matching between the equations and the variables of a model. For this purpose, an initial greedy matching is computed based on a bipartite constructed according to the SBML specifications. To obtain a maximal matching, augmenting paths are determined and the current matching is extended. If there are no augmenting paths available anymore, the computed matching is maximal. Having an unconnected equation vertex results in an overdetermined model. If the matching is not overdetermined, for each algebraic rule an assignment rule is generated. The left-hand side of each rule corresponds to the variable the respective algebraic rule has been matched to.