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Technical data of the pathwaytools.com

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HTTP Header Analysis

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DNS

HtmlToText

information pathway tools overview academic download publications release note history contributions pathway tools blog technical datasheet contact us technical specs web services pathway tools apis installation guide ontologies operations file formats support submitting bug reports tutorials user forum / faq user group meetings webinars pathway tools tutorial at sri, june 4-8, 2007 -- pathway tools is a comprehensive symbolic systems biology software system that is associated with the biocyc database collection. the software has been licensed by more than 8,000 groups and powers a number of websites for biological databases. a pathway tools supports several use cases in bioinformatics and systems biology: development of organism-specific databases (also called model-organism databases) that integrate many bioinformatics datatypes, from genomes to pathways. metabolic reconstruction and modeling. scientific visualization, web publishing, and dissemination of those organism-specific databases, including: automatic display of metabolic pathways and full metabolic networks a genome browser display of operons, regulons, and full transcriptional regulatory networks visual analysis of gene-expression and metabolomics datasets, such as painting omics data onto diagrams of the full metabolic network, full regulatory network, and full genome. computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers, and prediction of operons, that can be used for genome analysis. comparative genome and pathway analyses analysis of biological networks: search for routes between specified metabolites find dead-end metabolites identify choke points (potential drug targets) in metabolic networks pathway tools has four components pathologic: creates a new pathway/genome database (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. pathway/genome editors: provide interactive editing capabilities for pgdbs. please see the pathway tools overview document for more details on the capabilities of the software. pathway tools was developed by peter d. karp and coworkers at the bioinformatics research group at sri international. pathway tools availability pathway tools is freely available to academics for research purposes , and is available for a pathway tools publications see the biocyc and pathway tools publications page contributions to pathway tools we solicit contributions of new functionality to pathway tools. this is by no means an exclusive list, but rather a set of ideas for what might be contributed. contributions can be integrated directly into the pathway tools build at sri, or can be distributed separately by their authors for loading into pathway tools. pathway tools source code is available. interested? contact . interface bioinformatics prediction algorithms to pathway tools so that predictions made by these tools can be integrated into a pgdb. example predictors could include predictors of protein cellular location, or of regulatory elements. contribute new comparative capabilities to pathway tools. contribute metabolic engineering capabilities to pathway tools. past contributors we gratefully acknowledge the following contributions: development of the perlcyc perl api to pathway tools by lukas mueller of boyce thompson institute development of the javacyc java api to pathway tools by the tair project development of the rcyc api for the r project by tomer altman of stanford university development of the sbml output module by jeremy zucker of the broad institute pathway tools user group meetings 2005 meeting in geneva 2006 meeting at sri international 2009 meeting at sri international 2010 meeting at sri international 2013 meeting at sri international 2018 meeting at sri international additional pathway tools information license pathway tools for download and installation faq for pathway tools users pathway tools blog desktop vs web mode release note history -- describes new features in past releases of pathway tools pathway tools installation guide (includes solaris,linux and windows system requirements) curator's guide for pathway/genome databases submit a bug report for pathway tools write queries to pathway/genome dbs: using the python, java, perl, and lisp apis by querying flatfile dabases installing patches for the pathway tools ontologies used within pathway tools evidence ontology html form of the evidence ontology paper describing the evidence ontology: "an evidence ontology for use in pathway/genome databases," pacific symposium on biocomputing 9:190-201 2004. cell component ontology html form of the cell component ontology protein features ontology html form of the protein-features ontology file formats input format: sample pathologic format file input format: sample pathologic genetic-elements.dat file input format: sample .fba files output format: flatfile format for pathway/genome dbs operations how to copy a pgdb between computers how to import a flat-file pgdb into pathway tools instructions for creating an oracle database for use with the pathway tools how to logout after starting the web interface of pathway tools reference for gkb-editor , the pathway tools frame and class hierarchy editor tutorial slides tutorial slides by topic overview navigator metabolic overview and omics viewer the pathway tools schema editors pathologic writing queries in lisp, perl, and java administration contact us to report software bugs or for other questions, please contact us at . subscribe to the pathway tools mailing list : mailing list members receive periodic news and updates about pathway tools, such as announcements regarding new releases of the software and databases. the mail volume tends to be less than 1 announcement per month. to subscribe to the pathway tools mailing list, send an email to with the word subscribe in the subject. to unsubscribe, send an email to with the word unsubscribe in the subject. funding sources the development of pathway tools is funded by grants gm077678, gm080746, and gm75742 from the national institutes of health. privacy policy ©2017 sri international, 333 ravenswood avenue, menlo park, ca 94025-3493 sri international is an independent, nonprofit corporation. privacy policy disclaimer

URL analysis for pathwaytools.com

http://www.pathwaytools.com/ptools-overview.html
http://www.pathwaytools.com/copy-patho-db.html
http://www.pathwaytools.com/fba-examples/
http://www.pathwaytools.com/protein-features-ontology.html
http://www.pathwaytools.com/release-notes.html
http://www.pathwaytools.com/input-file-format.shtml
http://www.pathwaytools.com/web-logout.html
http://www.pathwaytools.com/ontologies.shtml
http://www.pathwaytools.com/contributors.html
http://www.pathwaytools.com/bug.html
http://www.pathwaytools.com/flatfile-format.html
http://www.pathwaytools.com/tpal.pf
http://www.pathwaytools.com/ptools-resources.shtml
http://www.pathwaytools.com/user-grp-mtgs.html
http://www.pathwaytools.com/ptools-resources.html#flatfile

Whois Information

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Domain Name: PATHWAYTOOLS.COM
Registry Domain ID: 1697494547_DOMAIN_COM-VRSN
Registrar WHOIS Server: whois.1and1.com
Registrar URL: http://registrar.1and1.info
Updated Date: 2018-03-17T14:53:04Z
Creation Date: 2012-01-17T23:02:14Z
Registry Expiry Date: 2019-01-17T23:02:14Z
Registrar: 1&1 Internet SE
Registrar IANA ID: 83
Registrar Abuse Contact Email: [email protected]
Registrar Abuse Contact Phone: +1.6105601459
Domain Status: clientTransferProhibited https://icann.org/epp#clientTransferProhibited
Name Server: NS1072.UI-DNS.BIZ
Name Server: NS1072.UI-DNS.COM
Name Server: NS1072.UI-DNS.DE
Name Server: NS1072.UI-DNS.ORG
DNSSEC: unsigned
URL of the ICANN Whois Inaccuracy Complaint Form: https://www.icann.org/wicf/
>>> Last update of whois database: 2018-07-28T01:10:10Z <<<

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The Registry database contains ONLY .COM, .NET, .EDU domains and
Registrars.

  REGISTRAR 1&1 Internet SE

SERVERS

  SERVER com.whois-servers.net

  ARGS domain =pathwaytools.com

  PORT 43

  TYPE domain

DOMAIN

  NAME pathwaytools.com

  CHANGED 2018-03-17

  CREATED 2012-01-17

STATUS
clientTransferProhibited https://icann.org/epp#clientTransferProhibited

NSERVER

  NS1072.UI-DNS.BIZ 217.160.81.72

  NS1072.UI-DNS.COM 217.160.82.72

  NS1072.UI-DNS.DE 217.160.80.72

  NS1072.UI-DNS.ORG 217.160.83.72

  REGISTERED yes

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