SRI Pathway Tools

Category Cross-Omics>Pathway Analysis/Tools

Abstract SRI Pathway Tools is a comprehensive symbolic 'systems biology' software system that supports several ‘use cases’ in bioinformatics and systems biology:

1) Development of organism-specific databases (also called model- organism databases) that integrate many bioinformatics data-types, from genomes to pathways [Pathway/Genome Databases (PGDBs)].

2) Scientific Visualization, web publishing, and dissemination of those organism-specific databases, including:

3) Visual analysis of omics datasets, such as painting omics data onto diagrams of the full metabolic network, full regulatory network, and full genome.

4) Computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers, and prediction of operons, that can be used for genome analysis.

5) Comparative analyses of organism-specific databases.

6) Analysis of biological networks:

Pathway Tools has three (3) software components:

1) PathoLogic (see G6G Abstract Number 20235) -- Can create a new Pathway/Genome Database (PGDB) containing the predicted metabolic pathways of an organism, given a GenBank entry as input.

2) Pathway/Genome Navigator -- Supports query, visualization, and analysis of PGDBs.

The Navigator powers the BioCyc (see G6G Abstract Number 20230) web site.

3) Pathway/Genome Editors -- Provide interactive editing capabilities for PGDBs.

Reasons for Creating a PGDB --

1) The PGDB can aid in the analysis of gene expression, protein expression, and metabolomics experiments through the use of the 'Pathway Tools Omics Viewer' (see G6G Abstract Number 20237), which allows omics datasets to be graphically painted onto three (3) system- level diagrams:

This software can produce animated displays of a series of omics measurements. It can also depict data from multiple omics data-types simultaneously, such as mixing gene-expression and metabolomics data on one diagram.

2) The PGDB can serve as a central resource for capturing, integrating, and disseminating new scientific findings about the organism.

It can serve as 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.

3) The existence of an up-to-date genome annotation for an organism is a prerequisite for performing 'functional genomics' studies of an organism because:

Pathway Tools also 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 make DB updating a snap. INSERT: Enzyme editor snapshot.

System Requirements

See G6G Abstract Number 20230 or BioCyc

Manufacturer

Manufacturer Web Site SRI Pathway Tools

Price Free for academic institutions. Fee required for commercial use. Licence required.

G6G Abstract Number 20236

G6G Manufacturer Number 102506