Overview of The Pathway Tools Software
Bioinformatics Research Group
SRI International, AE206
333 Ravenswood Ave
Menlo Park, CA 94025
What is a Pathway/Genome Database and What is Pathway Tools?A PGDB is a bioinformatics DB that integrates genomic data with detailed functional annotations of the genome, such as descriptions of metabolic and signalling pathways, and of the regulatory network. The EcoCyc and HumanCyc DBs are PGDBs (see EcoCyc.org and HumanCyc.org).
A PGDB serves as a central resource for capturing, integrating, and disseminating new scientific findings about the organism. It is a vehicle for tracking the evolving annotation of the genome, metabolic network, and genetic network of the organism, and for communicating that evolving knowledge through the Web. All genome annotations produced to date are incomplete, and contain significant numbers of errors. For organisms with active experimental communities, ongoing efforts are required to update those annotations to reflect new computational inferences, and new gene identifications and pathways reported in the experimental literature.
The existence of an up-to-date genome annotation for an organism is a prerequisite for performing functional genomics studies of an organism because (a) one aim of functional genomics is to determine the functions of genes whose function is not already known, therefore, functional genomics efforts require access to the most accurate genome annotation possible; (b) the extensive new knowledge about gene function and gene regulation that will be gleaned from functional genomics studies must be integrated and disseminated to the scientific community, such as through a PGDB.
Pathway Tools supports creation, editing, querying, visualization, and analysis of PGDBs. The software also allows users to publish a PGDB on the Web for access by the scientific community.
For a comprehensive summary of the Pathway Tools capabilities click here.
Pathway/Genome Navigator: Querying and Visualization of PGDBsThe Bioinformatics datatypes supported by the Pathway/Genome Navigator component of Pathway Tools are listed below. For each of the datatypes , Pathway Tools provides querying capabilities, visualization tools (such as for drawing pathways and genome maps), and interactive editing tools to allow users to update data (such as modifying a metabolic pathway or defining a new DNA binding site for a transcription factor). The visualization and querying capabilities allow PGDBs to be published on the Web, or to be accessed as a desktop application on the PC, Mac, and Linux platforms. The desktop and Web capabilities of the software overlap substantially, with some differences [details].
Pathway/Genome Navigator: Analysis of Large-Scale Datasets
Pathway Tools can aid analyses of gene expression, protein expression, and metabolomics experiments through the Pathway Tools Omics Viewers, which allow omics datasets to be graphically painted onto three system-level diagrams: a diagram of the full metabolic network of the organism, a diagram of the full regulatory network of the organism, and a diagram of the full genome of the organism. The software can produce animated displays of a series of omics measurements. It can also depict data from multiple omics datatypes simultaneously, such as mixing gene-expression and metabolomics data on one diagram.
Other Pathway Tools capabilities for analysis of large-scale datasets include:
Other Pathway/Genome Navigator Operations
MetaFlux: Flux-Balance AnalysisThe MetaFlux component of Pathway Tools supports development and execution of steady-state metabolic flux models using flux-balance analysis. Its gap filler module accelerates model development by suggesting improvements to a model such as addition of missing reactions. Reaction fluxes computed by MetaFlux can be painted onto the metabolic map diagram to speed understanding of modeling results. MetaFlux can simulate gene knock outs for selected genes, or for all genes in the organism.
Pathway/Genome Editors: Curation ToolsPathway Tools includes a suite of interactive editing tools for adding new information to a PGDB, and for updating existing information. Tools such as a pathway editor, gene editor, and enzyme editor speed database development.
Other Aspects of Pathway ToolsPathway Tools has a large user community, who have already successfully used the software to create database for many organisms.
Extensive user documentation is available, as is an online information site at bioinformatics.ai.sri.com/.
The software is freely available to academic and government users. Users own and therefore control the PGDBs that they create.
How to Learn More
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