Difference between revisions of "Pathway Tools"
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regulatory network. Pathway Tools also computes several variations of | regulatory network. Pathway Tools also computes several variations of | ||
enrichment analysis. | enrichment analysis. | ||
| + | |||
| + | Pathway Tools performs metabolic network analyses including finding | ||
| + | choke points (potential drug targets) in metabolic networks, dead-end metabolite | ||
| + | analysis, and reachability analysis. | ||
Pathway Tools has its own genome browser, which has a microbial orientation. In addition, | Pathway Tools has its own genome browser, which has a microbial orientation. In addition, | ||
Pathway Tools | Pathway Tools | ||
| − | can be coupled with other genome browsers to add support for pathways to an existing MOD. | + | can be coupled with other genome browsers to add support for pathways to an existing MOD, |
| + | such as was done for SGD and DictyBase. | ||
Pathway Tools was developed by [http://www.ai.sri.com/pkarp/ Peter D. Karp] and coworkers at the [http://bioinformatics.ai.sri.com/ Bioinformatics Research Group] at SRI International. | Pathway Tools was developed by [http://www.ai.sri.com/pkarp/ Peter D. Karp] and coworkers at the [http://bioinformatics.ai.sri.com/ Bioinformatics Research Group] at SRI International. | ||
Revision as of 01:27, 4 November 2010
- 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.
Pathway Tools functionality includes:
- Prediction, editing, querying, and visualization of metabolic pathways.
- Querying, editing, and visualization of metabolic reactions and metabolites.
- Generation of metabolic map diagram and of metabolic map poster (example).
- Editing and visualization of signaling pathways.
- Editing, querying, and visualization of regulatory interactions and regulatory networks.
- Genome browser; comparative genome browser; generation of genome poster (example).
Pathway Tools supports analysis of omics datasets (e.g., gene expression and metabolomics) by painting omics data onto a diagram of the full metabolic map of the organism, or onto a diagram of the full regulatory network. Pathway Tools also computes several variations of enrichment analysis.
Pathway Tools performs metabolic network analyses including finding choke points (potential drug targets) in metabolic networks, dead-end metabolite analysis, and reachability analysis.
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, such as was done for SGD and DictyBase.
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.
Publication: Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
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 |
