title: Modeling formalisms in Systems Biology.
abstract: Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their interconnection demands a whole-cell modeling framework for a complete understanding of cellular systems. We describe the features required by an integrated framework for modeling, analyzing and simulating biological processes, and review several modeling formalisms that have been used in Systems Biology including Boolean networks, Bayesian networks, Petri nets, process algebras, constraint-based models, differential equations, rule-based models, interacting state machines, cellular automata, and agent-based models. We compare the features provided by different formalisms, and discuss recent approaches in the integration of these formalisms, as well as possible directions for the future.
authors.affiliation: IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal. dmachado@deb.uminho.pt.
authors.forename: Daniel
authors.initials: D
authors.lastname: Machado
authors.forename: Rafael S
authors.initials: RS
authors.lastname: Costa
authors.forename: Miguel
authors.initials: M
authors.lastname: Rocha
authors.forename: Eugénio C
authors.initials: EC
authors.lastname: Ferreira
authors.forename: Bruce
authors.initials: B
authors.lastname: Tidor
authors.forename: Isabel
authors.initials: I
authors.lastname: Rocha