Microbial cells operate under governing constraints that limit their range of possible
functions. With the availability of annotated genome sequences, it has become possible to …

Novel techniques for acquiring metabolomics data continue to emerge. Such data require
proper storage in suitably configured databases, which then permit one to establish the size …

Network reconstructions are a common denominator in systems biology. Bottom–up
metabolic network reconstructions have been developed over the last 10 years. These …

Motivation: Simulation and modeling is becoming a standard approach to understand
complex biochemical processes. Therefore, there is a big need for software tools that allow …

The manner in which microorganisms utilize their metabolic processes can be predicted
using constraint-based analysis of genome-scale metabolic networks. Herein, we present …

The relationship between structure, function and regulation in complex cellular networks is a
still largely open question,,. Systems biology aims to explain this relationship by combining …

The rate of production of methane in many environments depends upon mutualistic
interactions between sulfate‐reducing bacteria and methanogens. To enhance our …

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 …

Interactions between microbial species are sometimes mediated by the exchange of small
molecules, secreted by one species and metabolized by another. Both one-way …

Background Over the last few years a number of methods have been proposed for the
phenotype simulation of microorganisms under different environmental and genetic …