Baker, P.G., Brass, A., Bechhofer, S., Goble, C.A., Paton, N.W., and Stevens, R.. "TAMBIS--Transparent Access to Multiple Bioinformatics Information Sources." Proc Int Conf Intell Syst Mol Biol.
vol. 6.
1998.
pp. 25-34.
[ .pdf ] [ .ps ] [ PubMed ] [ WebSite ]
The TAMBIS project aims to provide transparent access to disparate biological databases and analysis tools, enabling users to utilize a wide range of resources with the minimum of effort. A prototype system has been developed that includes a knowledge base of biological terminology (the biological Concept Model), a model of the underlying data sources (the Source Model) and a 'knowledge-driven' user interface. Biological concepts are captured in the knowledge base using a description logic called GRAIL. The Concept Model provides the user with the concepts necessary to construct a wide range of multiple-source queries, and the user interface provides a flexible means of constructing and manipulating those queries. The Source Model provides a description of the underlying sources and mappings between terms used in the sources and terms in the biological Concept Model. The Concept Model and Source Model provide a level of indirection that shields the user from source details, providing a high level of source transparency. Source independent, declarative queries formed from terms in the Concept Model are transformed into a set of source dependent, executable procedures. Query formulation, translation and execution is demonstrated using a working example.
Keywords: Artificial Intelligence ; *Computational Biology ; Databases Factual ; User-Computer Interface
Goss, P.J. and Peccoud, J.. "Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets." Proc Natl Acad Sci U S A. 95
(12).
1998.
pp. 6750-5.
[ .pdf ] [ PubMed ]
An integrated understanding of molecular and developmental biology must consider the large number of molecular species involved and the low concentrations of many species in vivo. Quantitative stochastic models of molecular interaction networks can be expressed as stochastic Petri nets (SPNs), a mathematical formalism developed in computer science. Existing software can be used to define molecular interaction networks as SPNs and solve such models for the probability distributions of molecular species. This approach allows biologists to focus on the content of models and their interpretation, rather than their implementation. The standardized format of SPNs also facilitates the replication, extension, and transfer of models between researchers. A simple chemical system is presented to demonstrate the link between stochastic models of molecular interactions and SPNs. The approach is illustrated with examples of models of genetic and biochemical phenomena where the ULTRASAN package is used to present results from numerical analysis and the outcome of simulations.
Keywords: *Computer Simulation ; Human ; *Models Molecular ; *Molecular Biology ; *Stochastic Processes
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
Karp, P.D., Riley, M., Paley, S.M., Pellegrini-Toole, A., and Krummenacker, M.. "EcoCyc: Encyclopedia of Escherichia coli genes and metabolism." Nucleic Acids Res. 26
(1).
1998.
pp. 50-3.
[ .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. The database describes 3030 genes of E.coli , 695 enzymes encoded by a subset of these genes, 595 metabolic reactions that occur in E.coli, and the organization of these reactions into 123 metabolic pathways. The EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways. EcoCyc can be thought of as an electronic review article because of its copious references to the primary literature, and as a (qualitative) computational model of E.coli metabolism. EcoCyc is available at URL http://ecocyc.PangeaSystems.com/ecocyc/
Keywords: Computer Graphics ; *Databases Factual_trends ; Encyclopedias ; Escherichia coli_*genetics ; Escherichia coli_*metabolism ; *Genes Bacterial ; User-Computer Interface