Author: Suzanne Paley
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Groups: Knowledge Spreadsheets for Symbolic Biocomputing
‘Groups’ is an implementation of Knowledge Spreadsheets (KSs) within the Pathway Tools system.
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Groups: Knowledge Spreadsheets for symbolic biocomputing
Groups allows Pathway Tools users to define a group of objects (e.g. groups of genes or metabolites) from a Pathway/Genome Database.
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Data Mining in the Metacyc Family of Pathway Databases
The MetaCyc family of pathway databases consists of thousands of databases that were derived through computational inference of metabolic pathways from the MetaCyc pathway/genome database (PGDB).
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Regulatory Network Operations in the Pathway Tools Software
Pathway Tools provides a comprehensive environment for manipulating molecular regulatory interactions that integrates regulatory data with an organism’s genome and metabolic network.
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Browsing Metabolic and Regulatory Networks with BioCyc
The BioCyc database collection at BioCyc.org integrates genome and cellular network information for more than 1,100 organisms.
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Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB).
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The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
New developments include atom mappings in reactions, a new representation of glycan degradation pathways, improved compound structure display, better coverage of enzyme kinetic data, enhancements of the Web Groups functionality…
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Multidimensional annotation of the Escherichia coli K-12 genome
The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annotations.
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The Pathway Tools Cellular Overview Diagram and Omics Viewer
Pathway Tools supports interrogation and exploration of cellular biochemical networks through the overview diagram and a software component called the Omics Viewer.
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Creating Fungal Pathway/Genome Databases Using Pathway Tools
The Pathway Tools software allows a group of scientists to create, update, and publish on the Web an evolving knowledge resource describing the genome and biochemical networks of the organism.
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MetaCyc: a multiorganism database of metabolic pathways and enzymes
MetaCyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and review-level comments.
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MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Research
In conjunction with the Pathway Tools software, MetaCyc can be used to computationally predict the metabolic pathway complement of an annotated genome.