Hofestadt, R. and Meineke, F.. "Interactive modelling and simulation of biochemical networks." Comput Biol Med. 25
(3).
1995.
pp. 321-34.
[ PubMed ]
The analysis of biochemical processes can be supported using methods of modelling and simulation. New methods of computer science are discussed in this field of research. This paper presents a new method which allows the modelling and analysis of complex metabolic networks. Moreover, our simulation shell is based on this formalization and represents the first tool for the interactive simulation of metabolic processes.
Keywords: *Biochemistry ; Cell Communication_physiology ; Databases Factual ; Enzymes_physiology ; Gene Expression_physiology ; Genes Regulator_physiology ; Genetic Diseases Inborn_enzymology ; Genetic Diseases Inborn_genetics ; Genetic Diseases Inborn_metabolism ; *Metabolism ; *Models Chemical ; *Models Genetic ; Probability ; *Software
Reddy, V.N., Liebman, M.N., and Mavrovouniotis, M.L.. "Qualitative analysis of biochemical reaction systems." Comput Biol Med. 26
(1).
1996.
pp. 9-24.
[ PubMed ]
The qualitative analysis of biochemical reaction systems is presented. A discrete event systems approach is used to represent and analyze bioreaction pathways. The approach is based on Petri nets, which are particularly suited to modeling stoichiometric transformations, i.e. the inter-conversion of metabolites in fixed proportions. The properties and methods for the analysis of Petri nets, along with their interpretation for biochemical systems, are presented. As an example, the combined glycolytic and pentose phosphate pathway of the erythrocyte cell is presented to illustrate the concepts of the methodology.
Keywords: Biochemistry ; *Computer Simulation ; Erythrocytes_*physiology ; Glycolysis_*physiology ; Human ; Models Theoretical ; Pentosephosphate Pathway_*physiology