Bibliography of Year: 1996

  1. 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


  2. Karp, P.D. and Paley, S.M.. "Integrated access to metabolic and genomic data." J Comput Biol. 3 (1). 1996. pp. 191-212.
    [ .pdf ] [ .ps ] [ PubMed ]

    The EcoCyc system consists of a knowledge base (KB) that describes the genes and intermediary metabolism of Escherichia coli, and a graphical user interface (GUI) for accessing that knowledge. This paper addresses two problems: How can we create a GUI that provides integrated access to metabolic and genomic data? We describe the design and implementation of visual presentations that closely mimic those found in the biology literature, and that offer hypertext navigation among related entities, and multiple views of the same entity. We employ a frame knowledge representation system (FRS) called HyperTHEO to manage the EcoCyc knowledge base. Among the advantages of FRSs are an expressive data model for capturing the complexities of biological information, and schema-evolution capabilities that facilitate the constant schema changes that biological databases tend to undergo. HyperTHEO also includes rule-based inference facilities that are the foundation of expert systems, a constraint language for maintaining data integrity, and a declarative query language. A graphic KB editor and browser allow the EcoCyc developers to interactively inspect and modify this evolving KB.

    Keywords: *Artificial Intelligence ; Computer Communication Networks ; Computer Graphics ; Computers ; *Database Management Systems ; Escherichia coli_*genetics ; Escherichia coli_*metabolism ; *Genome ; Bacterial ; Programming Languages ; Systems Integration ; User-Computer Interface


  3. 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


  4. 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