Pathway Tools
- Mature release
- Active development
- Active support
Pathway Tools is a comprehensive software environment that supports construction of organism-specific databases
called Pathway/Genome Databases (PGDBs). A PGDB such as EcoCyc
is a bioinformatics DB that integrates genomic data with detailed functional annotations
of the genome, such as descriptions of metabolic and signaling pathways. A PGDB is a
type of model-organism DB.
Components of Pathway Tools include:
- Prediction, editing, querying, and visualization of metabolic pathways.
- Querying, editing, and visualization of metabolic reactions and metabolites.
- Generation of metabolic map diagram.
- Editing and visualization of signaling pathways.
- Editing, querying, and visualization of regulatory interactions and regulatory networks.
- Genome browser.
- Analysis of omics datasets by painting omics data onto a diagram
of the full metabolic map of the organism, or onto a diagram of the full regulatory network. In addition, the software can generate a metabolic map poster for the organism (example).
Pathway Tools has its own genome browser, which has a microbial orientation. In addition, Pathway Tools can be coupled with other genome browsers to add support for pathways to an existing MOD.
Pathway Tools was developed by Peter D. Karp and coworkers at the Bioinformatics Research Group at SRI International.
Demo & Screenshots
See Samples
Requirements
Runs on Linux, Windows, and Macintosh.
Documentation
See the Pathway Tools Information Site for links.
Contact
| Mailing List Link | Description | Archive(s) | |
|---|---|---|---|
| Pathway Tools | ptools-users@ai.sri.com | Pathway Tools users list. To subscribe to this list, send a request to ptools-support@ai.sri.com. | None |
