A critical review on modelling formalisms and simulation tools in computational biosystems
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Tidor_A critical review.pdf
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Author(s)
Machado, Daniel
Costa, Rafael S.
Rocha, Miguel
Rocha, Isabel
Tidor, Bruce
Ferreira, Eugenio C.
Date Issued
June 2009
Journal
Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living
Publisher
Springer Berlin / Heidelberg
Citation
Machado, Daniel et al. “A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems.” Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living. Ed. Sigeru Omatu et al. LNCS Vol. 5518. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. 1063–1070.
Version
Author's final manuscript
Abstract
Integration of different kinds of biological processes is an ultimate goal for whole-cell modelling. We briefly review modelling formalisms that have been used in Systems Biology and identify the criteria that must be addressed by an integrating framework capable of modelling, analysing and simulating different biological networks. Aware that no formalism can fit all purposes we realize Petri nets as a suitable model for Metabolic Engineering and take a deeper perspective on the role of this formalism as an integrating framework for regulatory and metabolic networks.
Description
10th International Work-Conference on Artificial Neural Networks, IWANN 2009 Workshops, Salamanca, Spain, June 10-12, 2009. Proceedings, Part II
MIT Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Massachusetts Institute of Technology. Department of Biological Engineering
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Creative Commons Attribution-Noncommercial-Share Alike 3.0
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DOI of Published Version
https://doi.org/10.1007/978-3-642-02481-8_161
