A hybrid modeling technique is proposed to make models during the development phase of a fed-batch bioprocess. A limited amount of data is available and experimental data are therefore combined with a priori information about the mass balances and the chemical reaction network inside the cell (the metabolic network). This information highly constraints the model, and only a few degrees of freed...

The metabolism of individual organisms and biological communities can be viewed as a network of metabolites connected to each other through chemical reactions. In metabolic networks, chemical reactions transform reactants into products, thereby transferring elements between these metabolites. Knowledge of how elements are transferred through reactant/product pairs allows for the identification ...

MOTIVATION Misannotation in sequence databases is an important obstacle for automated tools for gene function annotation, which rely extensively on comparison with sequences with known function. To improve current annotations and prevent future propagation of errors, sequence-independent tools are, therefore, needed to assist in the identification of misannotated gene products. In the case of e...

The microbial community present in the human mouth is engaged in a complex network of diverse metabolic activities. In addition to serving as energy and building-block sources, metabolites are key players in interspecies and host-pathogen interactions. Metabolites are also implicated in triggering the local inflammatory response, which can affect systemic conditions such as atherosclerosis, obe...

Recently there has not been a systematic, objective assessment of the metabolic capabilities of the human platelet. A manually curated, functionally tested, and validated biochemical reaction network of platelet metabolism, iAT-PLT-636, was reconstructed using 33 proteomic datasets and 354 literature references. The network contains enzymes mapping to 403 diseases and 231 FDA approved drugs, al...

Metabolic networks are complex systems of interconnected biochemical reactions. Mathematically, such a complex network can be conveniently represented by a set of ordinary differential equations. Mathematical models for metabolism aim to improve the understanding of metabolic regulation by quantifying essential aspects of a metabolic system. Because of the large number of species involved in th...

MOTIVATION Genome-scale metabolic networks can be modeled in a constraint-based fashion. Reaction stoichiometry combined with flux capacity constraints determine the space of allowable reaction rates. This space is often large and a central challenge in metabolic modeling is finding the biologically most relevant flux distributions. A widely used method is flux balance analysis (FBA), which opt...

We model chemical reaction networks as directed hypergraphs that are generated in rule-based manner, using graph grammars as models of given sets of reaction mechanisms. Graphs serve as abstractions of molecules. This provide a level of chemical realism sufficient to ensure conservation of mass, atom type, and charge. Atom maps, for instance, are thus consistently defined within the model. The ...

The analysis of complex reaction networks is of great importance in several chemical and biochemical fields (interstellar chemistry, prebiotic chemistry, reaction mechanism, etc). In this article, we propose to simultaneously refine and extend for general chemical reaction systems the formalism initially introduced for the description of metabolic networks. The classical approaches through the ...