A critical review on modelling formalisms and simulation tools in computational biosystems

Author(s)
Machado, Daniel; Costa, Rafael S.; Rocha, Miguel; Rocha, Isabel; Tidor, Bruce; ... Show more
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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
Date issued
2009-06
URI
http://hdl.handle.net/1721.1/73902
Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory; Massachusetts Institute of Technology. Department of Biological Engineering
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
ISBN
978-3-642-02480-1
ISSN
0302-9743
1611-3349
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