Please use this identifier to cite or link to this item: https://hdl.handle.net/1822/22495

TitleModeling formalisms in systems biology
Author(s)Machado, C. D.
Costa, Rafael S.
Rocha, Miguel
Ferreira, Eugénio C.
Tidor, Bruce
Rocha, I.
KeywordsSystems biology
Modeling formalisms
Biological networks
Issue date2011
PublisherSpringer
JournalAmb Express
Abstract(s)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.
TypeArticle
URIhttps://hdl.handle.net/1822/22495
DOI10.1186/2191-0855-1-45
ISSN2191-0855
Peer-Reviewedyes
AccessOpen access
Appears in Collections:CEB - Publicações em Revistas/Séries Internacionais / Publications in International Journals/Series

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