Difference between revisions of "Pathway Tools"
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of an organism from its genome, and for creating Pathway/Genome Databases (PGDBs). A PGDB such as [http://ecocyc.org/ 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. | of an organism from its genome, and for creating Pathway/Genome Databases (PGDBs). A PGDB such as [http://ecocyc.org/ 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 supports extensive functionality including prediction, interactive editing, querying, and visualization of metabolic pathways and related datatypes including reactions, metabolites, and enzymes. It also includes query, visualization, and editing support for genes and proteins, | + | Pathway Tools supports extensive functionality including prediction, interactive editing, querying, and [[visualization]] of metabolic pathways and related datatypes including reactions, metabolites, and enzymes. It also includes query, visualization, and editing support for genes and proteins, |
and for transcriptional regulatory networks. | and for transcriptional regulatory networks. | ||
Revision as of 17:33, 27 May 2009
Attend the SRI
Pathway Tools
Workshop
{{#icon: SRILogo.png|Pathway Tools Workshop|120|http://brg.ai.sri.com/ptools09/}}
Pathway Tools is a bioinformatics software system for predicting the metabolic pathways of an organism from its genome, and for creating 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 supports extensive functionality including prediction, interactive editing, querying, and visualization of metabolic pathways and related datatypes including reactions, metabolites, and enzymes. It also includes query, visualization, and editing support for genes and proteins, and for transcriptional regulatory networks.
PGDBs support 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 transcriptional 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
Sun workstation, Windows2000 or XP, or Linux. A Mac version is coming in early 2008.
Documentation
See the Pathway Tools Information Site for links.
