Background Mathematical modelling of cellular networks is an integral part of Systems
Biology and requires appropriate software tools. An important class of methods in Systems …

Mathematical models of the cellular metabolism have become an essential tool for the
optimization of biotechnological processes. They help to obtain a systemic understanding of …

Background Structural analysis of cellular interaction networks contributes to a deeper
understanding of network-wide interdependencies, causal relationships, and basic …

Motivation: The analysis of structure, pathways and flux distributions in metabolic networks
has become an important approach for understanding the functionality of metabolic systems …

Biophysical models have been used in biology for decades, but they have been limited in
scope and size. In this book, Bernhard Ø. Palsson shows how network reconstructions that …

Background Modeling of metabolic networks includes tasks such as network assembly,
network overview, calculation of metabolic fluxes and testing the robustness of the network …

Background Signal transduction pathways are usually modelled using classical quantitative
methods, which are based on ordinary differential equations (ODEs). However, some …

Signal transduction networks have only been studied at a small scale because large-scale
reconstructions and suitable in silico analysis methods have not been available. Since …

The increasing availability of large network datasets along with the progresses in
experimental high-throughput technologies have prompted the need for tools allowing easy …

Understanding of the logic and dynamics of gene-regulatory and biochemical networks is a
major challenge of systems biology. To facilitate this research topic, we have developed a …