A Software Tool for the Simulation and Optimization of Dynamic Metabolic Models

Authors:
Pedro Evangelista;Isabel Rocha;Eugénio C. Ferreira;Miguel Rocha
Affiliations:
IBB - Institute for Biotechnology and Bioengineering Center of Biological Engineering, University of Minho, and Departament of Informatics / CCTC, University of Minho, Braga, Portugal 4710-057;IBB - Institute for Biotechnology and Bioengineering Center of Biological Engineering, University of Minho,;IBB - Institute for Biotechnology and Bioengineering Center of Biological Engineering, University of Minho,;Departament of Informatics / CCTC, 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

In Systems Biology, there is a growing need for simulation and optimization tools for the prediction of the phenotypical behavior of microorganisms. In this paper, an open-source software platform is proposed to provide support for research in Metabolic Engineering, by implementing tools that enable the simulation and optimization of dynamic metabolic models using ordinary differential equations. Its main functionalities are related with (i) phenotype simulation of both wild type and mutant strains under given environmental conditions and (ii) strain optimization tackling tasks such as gene knockout selection or the definition of the optimal level of enzyme expression, given appropriate objective functions. The central carbon metabolism of E. coli was used as a case study, to illustrate the main features of the software.