Computer models of biochemical networks are able to connect the genotype with the phenotype. In this primer we will give an introduction to biochemical network analysis with a special focus on constraint-based analysis.
We will introduce basic concepts of network reconstruction and constraint-based analysis of biological networks. In particular we will cover the process of building (genome-scale) metabolic models and study the steady state behavior of these networks with flux-balance analysis (FBA), metabolic pathway analysis (MPA) and related methods. Finally we will show that these methods are successfully used in metabolic engineering, where the constraint-based modeling approaches mentioned above are standard approaches for the rationally designing of microbial cell factories.
- Basic mathematical concepts in systems biology and constraint-based analysis
- Reconstruction of biochemical networks
- Stoichiometric networks and their analysis
- Applications in biotechnology
- Hands-on computer tutorials
- COPASI, http://copasi.org/
- OptFlux, http://www.optflux.org/