REPRESENTATION LANGUAGES AND SIMULATION SYSTEMS

Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology) -- by James M. Bower and Hamid Bolouri (Eds) explores various modeling approaches and their application to different biological networks.

The e-cell project, a modeling and simulation environment for biochemical and genetic processes

CellML is an XML-based markup language for storage and exchange of computer-based biological models. It includes information about model structure, mathematics and metadata.

The Caltech ERATO Kitano project aims to provide software infrastructure that will enable sharing of models and resources between simulation and analysis tools for systems biology. The groups develops the Systems Biology Markup Language (SBML), a common exchange language which is tailored towards representing biochemical network models, and the Systems Biology Workbench (SBW) a software infrastructure for sharing of computational resources.

Petri nets are graphical formalisms of concurrency, primarily used for modeling metabolic pathways

Bio-calculus, a unified knowledge description language for biological systems. Includes a simulation system.

Glossa, a language that defines the semantics of biological ideas as executable code, was developed for distributed computations among independent databases, by Toni Kazic’s group.

The Alchemy project, by Walter Fontana and Leo Buss, builds a theory of biological organization based on the lambda calculus