Difference between revisions of "Pathway Tools"
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− | + | {{ :Pathway_Tools/tool_data | template = Template:ToolDisplay }} | |
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− | Pathway Tools | + | {{Tool data |
− | and | + | |name=Pathway Tools |
+ | |full name= | ||
+ | |status=mature | ||
+ | |dev=active | ||
+ | |support=active | ||
+ | |type=Community Annotation, Comparative Genome Visualization , Database schema, Database tools, Gene Expression Visualization, Genome Visualization & Editing, Molecular Pathway Visualization, Ontology Visualization | ||
+ | |platform=web, linux, os x, windows | ||
+ | |about=Pathway Tools is a comprehensive symbolic systems biology software system that supports several use cases in bioinformatics and systems biology: | ||
+ | *Development of organism-specific databases called Pathway/Genome Databases (PGDBs) that integrate many bioinformatics datatypes, from genomes to pathways to regulatory networks. | ||
+ | *Development of metabolic-flux models using flux-balance analysis | ||
+ | *Scientific visualization, web publishing, and dissemination of those organism-specific databases, including: | ||
+ | **Automatic display of metabolic pathways and full metabolic networks; generation of metabolic map diagram and of metabolic map poster ([http://bioinformatics.ai.sri.com/posters/ecoli-metab.pdf example]). | ||
+ | **Genome browser; comparative genome browser; generation of genome poster ([http://bioinformatics.ai.sri.com/posters/ecoli-genome.pdf example]). | ||
+ | **Display of operons, regulons, and full transcriptional regulatory networks | ||
+ | *Analysis of omics datasets, including painting omics data on to diagrams of the full metabolic network, enrichment analysis. | ||
+ | *Computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers, prediction of operons | ||
+ | *Comparative analyses of model-organism databases. | ||
+ | *Analysis of biological networks: | ||
+ | **Interactively tracing metabolites through the metabolic network | ||
+ | **Finding dead-end metabolites in metabolic networks | ||
+ | **Identifying choke points (potential drug targets) in metabolic networks | ||
− | + | Pathway Tools has four components: | |
− | + | *PathoLogic: Creates a new PGDB containing the predicted metabolic pathways of an organism, given a Genbank entry as input. | |
− | + | *Pathway/Genome Navigator: Supports query, visualization, and analysis of PGDBs. The Navigator powers the BioCyc web site at BioCyc.org. | |
− | + | *MetaFlux: Supports development of metabolic flux models from Pathway/Genome Databases. | |
+ | *Pathway/Genome Editors: Provide interactive editing capabilities for PGDBs. | ||
+ | |release date=1999 | ||
+ | |open source=Caveats apply | ||
+ | |licence= | ||
+ | |language= | ||
+ | |input=Genbank format, GFF | ||
+ | |output=Genbank format, SBML, BioPAX | ||
+ | |audience= | ||
+ | |logo=PathwayTools.png | ||
+ | |screenshot= | ||
+ | |survey link=Pathway_Tools | ||
+ | |mail={{MailingListsFor|Pathway Tools}} | ||
+ | |contact email=[mailto:pkarp@ai.sri.com Peter Karp] | ||
+ | |integration= | ||
+ | |papers=*Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. <ref name="PMID:19955237" /> | ||
+ | *An advanced web query interface for biological databases. <ref name="PMID:20624715" /> | ||
+ | *The pathway tools pathway prediction algorithm. <ref name="PMID:22675592" /> | ||
+ | *Regulatory network operations in the Pathway Tools software. <ref name="PMID:22998532" /> | ||
+ | |presentations= | ||
+ | |tutorials=;[http://bioinformatics.ai.sri.com/ptools/ Pathway Tools slides] | ||
+ | :General information about Pathway Tools, including slides from tutorials and user guides | ||
+ | ;[http://bioinformatics.ai.sri.com/ptools/tutorial/ Upcoming Events] | ||
+ | :Pathway Tools tutorials and workshops | ||
+ | |getting started preamble=Start with an annotated genome in the form of a Genbank file; Pathway Tools will do the rest. | ||
+ | |req= | ||
+ | |install= | ||
+ | |config= | ||
+ | |doc=Documentation is available within the software distribution. For an overview of the tool, see [http://www.ncbi.nlm.nih.gov/pubmed/19955237 Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology] <ref name="PMID:19955237" /> | ||
+ | |dev ppl=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. | ||
+ | |dev status=The [http://pathwaytools.blogspot.com/ Pathway Tools Developers' Corner] has updates and information on current and proposed Pathway Tools developments. | ||
+ | |dl tracking= | ||
+ | |logo info= | ||
+ | |see also=See the [http://biocyc.org/samples.shtml samples section] of the BioCyc website for details of the types of data that are stored in a PGDB. | ||
+ | |extra= | ||
+ | }} | ||
− | + | {{SemanticLink | |
− | + | |linkurl=http://biocyc.org/download.shtml | |
− | + | |linktype=download | |
+ | }} | ||
+ | {{SemanticLink | ||
+ | |linkurl=http://bioinformatics.ai.sri.com/ptools/ | ||
+ | |linktype=website | ||
+ | }} | ||
+ | {{SemanticLink | ||
+ | |linkurl=http://biocyc.org/ | ||
+ | |linktype=public server | ||
+ | }} | ||
− | + | {{SemanticLink | |
− | + | |linkurl=http://biocyc.org/ECOLI/ | |
− | = | + | |linktitle=''E. coli PGDB'' |
− | + | |linktype=wild URL | |
− | + | }} | |
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+ | {{SemanticLink | ||
+ | |linkurl=http://biocyc.org/otherpgdbs.shtml | ||
+ | |linktype=wild URL | ||
+ | |linktitle=Other PGDBs | ||
+ | |linkdesc=list of PGDBs hosted elsewhere | ||
+ | }} | ||
[[Category:GMOD Components]] | [[Category:GMOD Components]] | ||
[[Category:Pathway Tools]] | [[Category:Pathway Tools]] |
Latest revision as of 00:07, 16 October 2013
Contents
About Pathway Tools
Pathway Tools is a comprehensive symbolic systems biology software system that supports several use cases in bioinformatics and systems biology:
- Development of organism-specific databases called Pathway/Genome Databases (PGDBs) that integrate many bioinformatics datatypes, from genomes to pathways to regulatory networks.
- Development of metabolic-flux models using flux-balance analysis
- Scientific visualization, web publishing, and dissemination of those organism-specific databases, including:
- Automatic display of metabolic pathways and full metabolic networks; generation of metabolic map diagram and of metabolic map poster (example).
- Genome browser; comparative genome browser; generation of genome poster (example).
- Display of operons, regulons, and full transcriptional regulatory networks
- Analysis of omics datasets, including painting omics data on to diagrams of the full metabolic network, enrichment analysis.
- Computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers, prediction of operons
- Comparative analyses of model-organism databases.
- Analysis of biological networks:
- Interactively tracing metabolites through the metabolic network
- Finding dead-end metabolites in metabolic networks
- Identifying choke points (potential drug targets) in metabolic networks
Pathway Tools has four components:
- PathoLogic: Creates a new PGDB containing the predicted metabolic pathways of an organism, given a Genbank entry as input.
- Pathway/Genome Navigator: Supports query, visualization, and analysis of PGDBs. The Navigator powers the BioCyc web site at BioCyc.org.
- MetaFlux: Supports development of metabolic flux models from Pathway/Genome Databases.
- Pathway/Genome Editors: Provide interactive editing capabilities for PGDBs.
Visit the Pathway Tools website.
Downloads
- Download Pathway Tools: http://biocyc.org/download.shtml
- Source code is available on execution of software license.
Using Pathway Tools
Start with an annotated genome in the form of a Genbank file; Pathway Tools will do the rest.
Documentation
Documentation is available within the software distribution. For an overview of the tool, see Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology [1]
Publications, Tutorials, and Presentations
Publications on or mentioning Pathway Tools
- Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. [1]
- An advanced web query interface for biological databases. [2]
- The pathway tools pathway prediction algorithm. [3]
- Regulatory network operations in the Pathway Tools software. [4]
Tutorials
- Pathway Tools slides
- General information about Pathway Tools, including slides from tutorials and user guides
- Upcoming Events
- Pathway Tools tutorials and workshops
Contacts and Mailing Lists
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 |
Pathway Tools in the wild
Public installations of Pathway Tools: There are a large number of PGDBs available via the BioCyc website, e.g. the E. coli PGDB, as well as a list of PGDBs hosted elsewhere.
Pathway Tools Development
Development team
Pathway Tools was developed by Peter D. Karp and coworkers at the Bioinformatics Research Group at SRI International.
Current status
The Pathway Tools Developers' Corner has updates and information on current and proposed Pathway Tools developments.
See also
See the samples section of the BioCyc website for details of the types of data that are stored in a PGDB.
More on Pathway Tools
- ↑ Cite error: Invalid
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tag; no text was provided for refs namedPMID:19955237
- ↑ Cite error: Invalid
<ref>
tag; no text was provided for refs namedPMID:20624715
- ↑ Cite error: Invalid
<ref>
tag; no text was provided for refs namedPMID:22675592
- ↑ Cite error: Invalid
<ref>
tag; no text was provided for refs namedPMID:22998532
Raw tool data at Pathway Tools/tool data
Available on platform | web +, linux +, os x + and windows + |
Has URL | http://biocyc.org/download.shtml +, http://bioinformatics.ai.sri.com/ptools/ +, http://biocyc.org/ +, http://biocyc.org/ECOLI/ + and http://biocyc.org/otherpgdbs.shtml + |
Has description | Pathway Tools is a comprehensive symbolic … Pathway Tools is a comprehensive symbolic systems biology software system that supports several use cases in bioinformatics and systems biology:
Pathway Tools has four components:
|
Has development status | active + |
Has download URL | http://biocyc.org/download.shtml + |
Has input format | Genbank format + and GFF + |
Has logo | PathwayTools.png + |
Has output format | Genbank format +, SBML + and BioPAX + |
Has software maturity status | mature + |
Has support status | active + |
Has title | E. coli PGDB + and Other PGDBs + |
Has topic | Pathway Tools + |
Has website | http://bioinformatics.ai.sri.com/ptools/ + |
Is open source | Caveats apply + |
Link type | download +, website +, public server + and wild URL + |
Release date | 1999 + |
Tool functionality or classification | Community Annotation +, Comparative Genome Visualization +, Database schema +, Database tools +, Gene Expression Visualization +, Genome Visualization & Editing +, Molecular Pathway Visualization + and Ontology Visualization + |
Has subobjectThis property is a special property in this wiki. | Pathway Tools#http://biocyc.org/download.shtml +, Pathway Tools#http://bioinformatics.ai.sri.com/ptools/ +, Pathway Tools#http://biocyc.org/ +, Pathway Tools#http://biocyc.org/ECOLI/ + and Pathway Tools#http://biocyc.org/otherpgdbs.shtml + |