We demonstrate an approach to automatically generating kinetic models of metabolic networks. In a first step, the metabolic network is characterised by its stoichiometric structure. Then to each reaction a kinetic equation is associated describing the metabolic flux. For the kinetics we use a formula that is universally applicable to reactions with arbitrary numbers of substrates and products. ...

A biological cell forms an extremely complex system with a complicated metabolic reaction network. The functionality of the cell is controlled by the genome consisting of thousands of individual genes. Novel measurement technologies provide us with huge amounts of biological data in a quantitative form, but the suitable modeling methods to deal with the high dimensionality and large systems are...

The complex process of genome-scale metabolic network reconstruction involves semi-automatic reaction inference, analysis, and refinement through curation by human experts. Unfortunately, decisions by experts are hampered by the complexity of the network, which can mask errors in the inferred network. In order to aid an expert in making sense out of the thousands of reactions in the organism's ...

Correlated reaction sets (Co-Sets) are mathematically defined modules in biochemical reaction networks which facilitate the study of biological processes by decomposing complex reaction networks into conceptually simple units. According to the degree of association, Co-Sets can be classified into three types: perfect, partial and directional. Five approaches have been developed to calculate Co-...

The process modeling tool ProMoT [6, 5] has been developed for the object-oriented and equation-based modeling of chemical processes. This contribution presents the application of ProMoT to a novel application field: the design and implementation of a knowledge base for modeling metabolic networks in living cells. This knowledge base contains predefined modeling entities for the hierarchical ag...

The products of five structural genes and two regulatory genes of the qa gene cluster of Neurospora crassa control the metabolism of quinic acid (QA) as a carbon source. A detailed genetic network model of this metabolic process has been reported. This investigation is designed to expand the current model of the QA reaction network. The ensemble method of network identification was used to mode...

Streptomyces are filamentous soil bacteria that produce more than half of the known microbial antibiotics. We present the first genome-scale metabolic model of a representative of this group--Streptomyces coelicolor A3(2). The metabolism reconstruction was based on annotated genes, physiological and biochemical information. The stoichiometric model includes 819 biochemical conversions and 152 t...

The availability of large-scale datasets has led to more effort being made to understand characteristics of metabolic reaction networks. However, because the large-scale data are semi-quantitative, and may contain biological variations and/or analytical errors, it remains a challenge to construct a mathematical model with precise parameters using only these data. The present work proposes a sim...