Ellis, L.B., Hershberger, C.D., and Wackett, L.P.. "The University of Minnesota Biocatalysis/Biodegradation database: microorganisms, genomics and prediction." Nucleic Acids Res. 28
(1).
2000.
pp. 377-9.
[ .pdf ] [ PubMed ]
The University of Minnesota Biocatalysis/Biodegradation Database (http://www.labmed.umn.edu/umbbd/ ) begins its fifth year having met its initial goals. It contains approximately 100 pathways for microbial catabolic metabolism of primarily xenobiotic organic compounds, including information on approximately 650 reactions, 600 compounds and 400 enzymes, and containing approximately 250 microorganism entries. It includes information on most known microbial catabolic reaction types and the organic functional groups they transform. Having reached its first goals, it is ready to move beyond them. It is poised to grow in many different ways, including mirror sites; fold prediction for its sequenced enzymes; closer ties to genome and microbial strain databases; and the prediction of biodegradation pathways for compounds it does not contain.
Keywords: Biodegradation ; Catalysis ; *Databases Factual ; *Genome ; *Microbiology
Kanehisa, M. and Goto, S.. "KEGG: kyoto encyclopedia of genes and genomes." Nucleic Acids Res. 28
(1).
2000.
pp. 27-30.
[ .pdf ] [ PubMed ]
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information. The genomic information is stored in the GENES database, which is a collection of gene catalogs for all the completely sequenced genomes and some partial genomes with up-to-date annotation of gene functions. The higher order functional information is stored in the PATHWAY database, which contains graphical representations of cellular processes, such as metabolism, membrane transport, signal transduction and cell cycle. The PATHWAY database is supplemented by a set of ortholog group tables for the information about conserved subpathways (pathway motifs), which are often encoded by positionally coupled genes on the chromosome and which are especially useful in predicting gene functions. A third database in KEGG is LIGAND for the information about chemical compounds, enzyme molecules and enzymatic reactions. KEGG provides Java graphics tools for browsing genome maps, comparing two genome maps and manipulating expression maps, as well as computational tools for sequence comparison, graph comparison and path computation. The KEGG databases are daily updated and made freely available (http://www. genome.ad.jp/kegg/).
Keywords: *Databases Factual ; Gene Expression ; *Genome ; Human ; Information Storage and Retrieval ; Proteins_genetics ; Proteins_metabolism
Kawashima, T., Kawashima, S., Kanehisa, M., Nishida, H., and Makabe, K.W.. "MAGEST: MAboya gene expression patterns and sequence tags." Nucleic Acids Res. 28
(1).
2000.
pp. 133-5.
[ .pdf ] [ PubMed ]
MAGEST is a database for newly identified maternal cDNAs of the ascidian, Halocynthia roretzi, which aims to examine the population of the mRNAs. We have collected 3' and 5' tag sequences of mRNAs and their expression data from whole-mount in situ hybridi-zation in early embryos. To date, we have determined more than 2000 tag-sequences of H.roretzi cDNAs and input them into public databases. The tag sequences and the expression data as well as additional information can be obtained through MAGEST via the WWW at http://www.genome.ad.jp/magest/
Keywords: DNA Complementary ; *Databases Factual ; *Expressed Sequence Tags ; *Gene Expression ; Information Storage and Retrieval ; Urochordata_*genetics
Karp, P.D., Riley, M., Saier, M., Paulsen, I.T., Paley, S.M., and Pellegrini-Toole, A.. "The EcoCyc and MetaCyc databases." Nucleic Acids Res. 28
(1).
2000.
pp. 56-9.
[ .pdf ] [ PubMed ]
EcoCyc is an organism-specific Pathway/Genome Database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, and-a new addition-its transport proteins. MetaCyc is a new metabolic-pathway database that describes pathways and enzymes of many different organisms, with a microbial focus. Both databases are queried using the Pathway Tools graphical user interface, which provides a wide variety of query operations and visualization tools. EcoCyc and MetaCyc are available at http://ecocyc.PangeaSystems.com/ecocyc/
Keywords: Database Management Systems ; *Databases Factual ; Escherichia coli_genetics ; Genome ; Bacterial
Kuffner, R., Zimmer, R., and Lengauer, T.. "Pathway analysis in metabolic databases via differential metabolic display (DMD)." Bioinformatics. 16
(9).
2000.
pp. 825-36.
[ .pdf ] [ PubMed ] [ WebSite ]
MOTIVATION: A number of metabolic databases are available electronically, some with features for querying and visualizing metabolic pathways and regulatory networks. We present a unifying, systematic approach based on PETRI nets for storing, displaying, comparing, searching and simulating such nets from a number of different sources. RESULTS: Information from each data source is extracted and compiled into a PETRI net. Such PETRI nets then allow to investigate the (differential) content in metabolic databases, to map and integrate genomic information and functional annotations, to compare sequence and metabolic databases with respect to their functional annotations, and to define, generate and search paths and pathways in nets. We present an algorithm to systematically generate all pathways satisfying additional constraints in such PETRI nets. Finally, based on the set of valid pathways, so-called differential metabolic displays (DMDs) are introduced to exhibit specific differences between biological systems, i.e. different developmental states, disease states, or different organisms, on the level of paths and pathways. DMDs will be useful for target finding and function prediction, especially in the context of the interpretation of expression data.
Keywords: *Algorithms ; Catalysis ; Computational Biology_*methods ; Computer Simulation ; *Data Display ; *Databases Factual ; Enzymes_genetics ; Enzymes_metabolism ; Glycolysis ; Metabolism_*physiology ; Mycoplasma_metabolism ; Yeasts_metabolism
Matsuno, H., Doi, A., Nagasaki, M., and Miyano, S.. "Hybrid Petri net representation of gene regulatory network." Pac Symp Biocomput. 2000.
pp. 341-52.
[ .pdf ] [ PubMed ]
It is important to provide a representation method of gene regulatory networks which realizes the intuitions of biologists while keeping the universality in its computational ability. In this paper, we propose a method to exploit hybrid Petri net (HPN) for representing gene regulatory networks. The HPN is an extension of Petri nets which have been used to represent many kinds of systems including stochastic ones in the field of computer sciences and engineerings. Since the HPN has continuous and discrete elements, it can easily handle biological factors such as protein and mRNA concentrations. We demonstrate that, by using HPNs, it is possible to translate biological facts into HPNs in a natural manner. It should be also emphasized that a hierarchical approach is taken for our construction of the genetic switch mechanism of lambda phage which is realized by using HPNs. This hierarchical approach with HPNs makes easier the arrangement of the components in the gene regulatory network based on the biological facts and provides us a prospective view of the network. We also show some computational results of the protein dynamics of the lambda phage mechanism that is simulated and observed by implementing the HPN on a currently available tool.
Keywords: Bacteriophage lambda_genetics ; Bacteriophage lambda_growth and development ; Computer Simulation ; Gene Expression Regulation ; Gene Expression Regulation Viral ; Genes Viral ; *Models Genetic ; Operon ; Repressor Proteins_genetics ; Stochastic Processes ; Viral Proteins_genetics
Rana, O.F.. "Automating parallel implementation of neural learning algorithms." Int J Neural Syst. 10
(3).
2000.
pp. 227-41.
[ PubMed ]
Neural learning algorithms generally involve a number of identical processing units, which are fully or partially connected, and involve an update function, such as a ramp, a sigmoid or a Gaussian function for instance. Some variations also exist, where units can be heterogeneous, or where an alternative update technique is employed, such as a pulse stream generator. Associated with connections are numerical values that must be adjusted using a learning rule, and and dictated by parameters that are learning rule specific, such as momentum, a learning rate, a temperature, amongst others. Usually, neural learning algorithms involve local updates, and a global interaction between units is often discouraged, except in instances where units are fully connected, or involve synchronous updates. In all of these instances, concurrency within a neural algorithm cannot be fully exploited without a suitable implementation strategy. A design scheme is described for translating a neural learning algorithm from inception to implementation on a parallel machine using PVM or MPI libraries, or onto programmable logic such as FPGAs. A designer must first describe the algorithm using a specialised Neural Language, from which a Petri net (PN) model is constructed automatically for verification, and building a performance model. The PN model can be used to study issues such as synchronisation points, resource sharing and concurrency within a learning rule. Specialised constructs are provided to enable a designer to express various aspects of a learning rule, such as the number and connectivity of neural nodes, the interconnection strategies, and information flows required by the learning algorithm. A scheduling and mapping strategy is then used to translate this PN model onto a multiprocessor template. We demonstrate our technique using a Kohonen and backpropagation learning rules, implemented on a loosely coupled workstation cluster, and a dedicated parallel machine, with PVM libraries.
Keywords: *Algorithms ; Artificial Intelligence ; Computers ; Models Neurological ; *Neural Networks (Computer) ; Programming Languages
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