Collado-Vides, J., Hofestadt, R., Mavrovouniotis, M.L., and Michal, G.. "Modeling and simulation of gene regulation and metabolic pathways." Biosystems. 49
(1).
1999.
pp. 79-82.
[ .pdf ] [ PubMed ]
Keywords: *Gene Expression Regulation ; *Metabolism ; *Models Genetic
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
Hofestadt, R., Mavrovouniotis, M.L., Collado-Vides, J., and Loffler, M.. "Modeling and simulation of metabolic pathways, gene regulation and cell differentiation. October 22-27, 1995. International Conference and Research Center for Computer Science, Schloss Dagstuhl, Saarland, Germany." Bioessays. 18
(4).
1996.
pp. 333-5.
[ PubMed ]
Keywords: Cell Differentiation ; *Computer Simulation ; Gene Expression Regulation ; Information Systems ; Metabolism ; *Models Biological
Hofestadt, R. and Thelen, S.. "Quantitative modeling of biochemical networks." In Silico Biol. 1
(1).
1998.
pp. 39-53.
[ PubMed ] [ WebSite ]
Today different database systems for molecular structures (genes and proteins) and metabolic pathways are available. All these systems are characterized by the static data representation. For progress in biotechnology the dynamic representation of this data is important. The metabolism can be characterized as a complex biochemical network. Different models for the quantitative simulation of biochemical networks are discussed, but no useful formalization is available. This paper shows that the theory of Petrinets is useful for the quantitative modeling of biochemical networks.
Keywords: *Biochemistry ; Biotechnology ; Catalysis ; Computational Biology ; *Computer Simulation ; Databases Factual ; Glycolysis ; Models Biological ; Protein Engineering
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