Research article
Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies
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* Corresponding authors: Andreas Dräger andreas.draeger@uni-tuebingen.de - Marcel Kronfeld marcel.kronfeld@uni-tuebingen.de - Michael J Ziller michael.ziller@student.uni-tuebingen.de
1 Center for Bioinformatics Tübingen (ZBIT), Wilhelm-Schickard-Institut für Informatik, Sand 1, 72076 Tübingen, Germany
2 NNE Pharmaplan, Siemensstraße 21, 61352 Bad Homburg, Germany
3 Forschungszentrum Jülich, Institut für Biotechnologie 2, 52425 Jülich, Germany
BMC Systems Biology 2009, 3:5 doi:10.1186/1752-0509-3-5
Published: 14 January 2009Additional files
Additional file 1:
Nature-inspired heuristics for optimization. This document provides a detailed introduction to the basic concepts of all evolutionary and swarm intelligence algorithms that are used in this study.
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Additional file 2:
Modeling the valine and leucine metabolism in Corynebacterium glutamicum. This document gives a comprehensive introduction to mathematical modeling of biochemical systems and all four kinds of rate laws that are used in this study. Additionally, the method to introduce inhibition effects to the generalized mass action rate law is derived in this document. Histograms are presented showing the distribution of the parameters. For the best-performing optimization algorithms, the fitness is plotted depending on the evaluations of the objective function.
Format: PDF Size: 1.8MB Download file
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