A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems

Authors:
Daniel Machado;Rafael S. Costa;Miguel Rocha;Isabel Rocha;Bruce Tidor;Eugénio C. Ferreira
Affiliations:
IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Braga, Portugal 4710-057;IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Braga, Portugal 4710-057;Department of Informatics/CCTC, University of Minho, Braga, Portugal 4710-057;IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Braga, Portugal 4710-057;Department of Biological Engineering/Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, USA MA 02139;IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Braga, Portugal 4710-057
Venue:
IWANN '09 Proceedings of the 10th International Work-Conference on Artificial Neural Networks: Part II: Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living
Year:
2009

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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.