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
Karp, P.D., Riley, M., Paley, S.M., and Pellegrini-Toole, A.. "EcoCyc: an encyclopedia of Escherichia coli genes and metabolism." Nucleic Acids Res. 24
(1).
1996.
pp. 32-9.
[ .pdf ] [ PubMed ]
The encyclopedia of Escherichia coli genes and metabolism (EcoCyc) is a database that combines information about the genome and the intermediary metabolism of E.coli. It describes 2034 genes, 306 enzymes encoded by these genes, 580 metabolic reactions that occur in E.coli and the organization of these reactions into 100 metabolic pathways. The EcoCyc graphical user interface allows query and exploration of the EcoCyc database using visualization tools such as genomic map browsers and automatic layouts of metabolic pathways. EcoCyc spans the space from sequence to function to allow investigation of an unusually broad range of questions. EcoCyc can be thought of as both an electronic review article, because of its copious references to the primary literature, and as an in silico model of E.coli that can be probed and analyzed through computational means.
Keywords: Computer Communication Networks ; *Databases Factual ; Enzymes_metabolism ; Escherichia coli_enzymology ; Escherichia coli_*genetics ; Escherichia coli_*metabolism ; *Genome ; Bacterial ; Information Storage and Retrieval ; Software ; User-Computer Interface
Karp, P.D.. "Pathway databases: a case study in computational symbolic theories." Science. 293
(5537).
2001.
pp. 2040-4.
[ .pdf ] [ PubMed ]
A pathway database (DB) is a DB that describes biochemical pathways, reactions, and enzymes. The EcoCyc pathway DB (see http://ecocyc.org) describes the metabolic, transport, and genetic-regulatory networks of Escherichia coli. EcoCyc is an example of a computational symbolic theory, which is a DB that structures a scientific theory within a formal ontology so that it is available for computational analysis. It is argued that by encoding scientific theories in symbolic form, we open new realms of analysis and understanding for theories that would otherwise be too large and complex for scientists to reason with effectively.
Keywords: Artificial Intelligence ; *Computational Biology ; Culture Media ; *Databases Factual ; Escherichia coli_enzymology ; Escherichia coli_*genetics ; Escherichia coli_growth and development ; Escherichia coli_*metabolism ; *Genome Bacterial ; Internet ; Software
Stevens, R., Baker, P.G., Bechhofer, S., Ng, G., Jacoby, A., Paton, N.W., Goble, C.A., and Brass, A.. "TAMBIS: transparent access to multiple bioinformatics information sources." Bioinformatics. 16
(2).
2000.
pp. 184-5.
[ PubMed ] [ WebSite ]
SUMMARY: TAMBIS (Transparent Access to Multiple Bioinformatics Information Sources) is an application that allows biologists to ask rich and complex questions over a range of bioinformatics resources. It is based on a model of the knowledge of the concepts and their relationships in molecular biology and bioinformatics. AVAILABILITY: TAMBIS is available as an applet from http://img.cs.man.ac.uk/tambis SUPPLEMENTARY: A full manual tutorial and videos can be found at http://img.cs.man.ac.uk/tambis. CONTACT: tambis
Keywords: Computational Biology ; *Information Storage and Retrieval ; *Software
Schuster, S., Pfeiffer, T., Moldenhauer, F., Koch, I., and Dandekar, T.. "Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae." Bioinformatics. 18
(2).
2002.
pp. 351-61.
[ PubMed ] [ WebSite ]
MOTIVATION: Reconstructing and analyzing the metabolic map of microorganisms is an important challenge in bioinformatics. Pathway analysis of large metabolic networks meets with the problem of combinatorial explosion of pathways. Therefore, appropriate algorithms for an automated decomposition of these networks into smaller subsystems are needed. RESULTS: A decomposition algorithm for metabolic networks based on the local connectivity of metabolites is presented. Interrelations of this algorithm with alternative methods proposed in the literature and the theory of small world networks are discussed. The applicability of our method is illustrated by an analysis of the metabolism of Mycoplasma pneumoniae, which is an organism of considerable medical interest. The decomposition gives rise to 19 subnetworks. Three of these are here discussed in biochemical terms: arginine degradation, the tetrahydrofolate system, and nucleotide metabolism. The interrelations of pathway analysis of biochemical networks with Petri net theory are outlined.
Keywords: Algorithms ; Arginine_metabolism ; Computational Biology ; *Metabolism ; Models Biological ; Mycoplasma pneumoniae_*metabolism ; Nucleotides_metabolism ; *Software