Hofestadt, R.. "Grammatical formalization of metabolic processes." Proc Int Conf Intell Syst Mol Biol.
vol. 1.
1993.
pp. 181-9.
[ PubMed ]
In the field of biotechnology and medicine it is of interest to model and simulate metabolic processes. The usual methods to model metabolic pathways are chemical descriptions and differential equations. Moreover, the graph theoretical aspect is discussed and the development of expert systems is in process. In this paper we present the formalization of metabolic processes. Our formalization is based on the theory of formal languages. This formalization is called genetic grammar and represents an expansion of the Semi-Thue-System.
Keywords: *Computer Simulation ; *Expert Systems ; Gene Expression ; *Metabolism ; *Models Biological ; Programming Languages
Mavrovouniotis, M.L.. "Identification of localized and distributed bottlenecks in metabolic pathways." Proc Int Conf Intell Syst Mol Biol.
vol. 1.
1993.
pp. 275-83.
[ PubMed ]
The usual thermodynamic evaluation, based solely on the Standard Gibbs Energy of reaction, does not take into account the permissible ranges of concentrations of metabolites, and it faces further difficulties when, instead of isolated reactions, we are examining whole pathways. For pathways, we seek not only to decide whether they are feasible but also to pinpoint the pathway segment that causes any thermodynamic difficulties. We define a set of scaled quantities which reformulate the thermodynamic-feasibility problem for the whole pathway. We present an algorithm which analyzes individual reactions and selective construction of larger subpathways and uncovers localized and distributed thermodynamic bottlenecks of the biotransformation. This type of thermodynamic treatment contributes to the effort to include more physical, chemical, and biological factors in the computer-aided analysis of metabolic pathways.
Keywords: *Algorithms ; *Computer Simulation ; Glycolysis ; *Metabolism ; *Models Biological ; *Thermodynamics
Reddy, V.N., Mavrovouniotis, M.L., and Liebman, M.N.. "Petri net representations in metabolic pathways." Proc Int Conf Intell Syst Mol Biol.
vol. 1.
1993.
pp. 328-36.
[ PubMed ]
The present methods for representing metabolic pathways are limited in their ability to handle complex systems, incorporate new information, and to provide for drawing qualitative conclusions from the structure of pathways. The theory of Petri nets is introduced as a tool for computer-implementable representation of pathways. Petri nets have the potential to overcome the present limitations, and through a multitude of properties, enable the preliminary qualitative analysis of pathways.
Keywords: *Computer Simulation ; Fructose_metabolism ; Liver_metabolism ; *Metabolism ; *Models Biological