Biomedical subjects

S M Paley

Publications and source records attributed to S M Paley.

7 recordsLinked to original sources

PubMed2000

The EcoCyc and MetaCyc databases.

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/

Database Management Systems↗

PubMed1999

Eco Cyc: encyclopedia of Escherichia coli genes and metabolism.

The EcoCyc database describes the genome and gene products of Escherichia coli, its metabolic and signal-transduction pathways, and its tRNAs. The database describes 4391 genes of E.coli, 695 enzymes encoded by a subset of these genes, 904 metabolic reactions that occur in E.coli, and the organization of these reactions into 129 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 has many references to the primary literature, and is a (qualitative) computational model of E. coli metabolism. EcoCyc is available at URL http://ecocyc. PangeaSystems.com/ecocyc/

Classification↗

PubMed1998

EcoCyc: Encyclopedia of Escherichia coli genes and metabolism.

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/

Computer Graphics↗

PubMed1997

EcoCyc: Enyclopedia of Escherichia coli Genes and Metabolism.

The Encyclopedia of Genes and Metabolism (EcoCyc) is a database that combines information about the genome and the intermediary metabolism of Escherichia coli. It describes 2970 genes of E.coli, 547 enzymes encoded by these genes, 702 metabolic reactions that occur in E.coli and the organization of these reactions into 107 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 spans the space from sequence to function to allow scientists to investigate 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 silicio model of E.coli metabolism that can be probed and analyzed through computational means.

Amino Acid Sequence↗

PubMed1996

Adapting EcoCyc for use on the World Wide Web.

The World Wide Web (WWW) offers the potential to deliver specialized information to an audience of unprecedented size. Along with this exciting new opportunity comes a challenge for software developers: instead of rewriting our software applications to operate over the WWW, how can we maximize software reuse by retrofitting existing applications? We have developed a Web server tool, written in Common Lisp, that allows existing graphical user interface applications written using the Common Lisp Interface Manager (CLIM) to hook easily into the WWW. This tool-CWEST (CLIM-WEb Server Tool, pronounced "quest")-was developed to operate with EcoCyc, an electronic encyclopedia of the genes and metabolism of the bacterium E. coli. EcoCyc consists of a database of objects relevant to E. coli biochemistry and a user interface, implemented in CLIM, that runs on the X-window system and generates graphical displays appropriate to biological objects. Each query to the EcoCyc WWW server is treated as a command to the EcoCyc program, which dynamically generates an appropriate CLIM drawing. CWEST translates that drawing, which can be a mixture of text and graphics, into the HyperText Markup Language (HTML) and/or the Graphics Interchange Format (GIF), which are returned to the client. Sensitive regions embedded in the CLIM drawing are converted to hyperlinks with Universal Resource Locators (URLs) that generate further EcoCyc queries. This tight coupling of CLIM output with Web output makes CLIM a powerful high-level programming tool for Web applications. The flexibility of Common Lisp and CLIM made implementation of the server tool surprisingly easy, requiring few changes to the existing EcoCyc program. The results can be seen at URL http: @www.ai.sri.com/ecocyc/browser.html. We have made CWEST available to the CLIM community at large, with the hope that it will spur other software developers to make their CLIM applications available over the WWW.

Computer Communication Networks↗

PubMed1996

EcoCyc: an encyclopedia of Escherichia coli genes and metabolism.

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.

Computer Communication Networks↗

PubMed1994

Representations of metabolic knowledge: pathways.

The automatic generation of drawings of metabolic pathways is a challenging problem that depends intimately on exactly what information has been recorded for each pathway, and on how that information is encoded. The chief contributions of the paper are a minimized representation for biochemical pathways called the predecessor list, and inference procedures for converting the predecessor list into a pathway-graph representation that can serve as input to a pathway-drawing algorithm. The predecessor list has several advantages over the pathway graph, including its compactness and its lack of redundancy. The conversion between the two representations can be formulated as both a constraint-satisfaction problem and a logical inference problem, whose goal is to assign directions to reactions, and to determine which are the main chemical compounds in the reaction. We describe a set of production rules that solves this inference problem. We also present heuristics for inferring whether the exterior compounds that are substrates of reactions at the periphery of a pathway are side or main compounds. These techniques were evaluated on 18 metabolic pathways from the EcoCyc knowledge base.

Animals↗