PathwayAccess: CellDesigner plugins for pathway databases.

Bioinformatics
John L Van Hemert, Julie A Dickerson

Abstract

CellDesigner provides a user-friendly interface for graphical biochemical pathway description. Many pathway databases are not directly exportable to CellDesigner models. PathwayAccess is an extensible suite of CellDesigner plugins, which connect CellDesigner directly to pathway databases using respective Java application programming interfaces. The process is streamlined for creating new PathwayAccess plugins for specific pathway databases. Three PathwayAccess plugins, MetNetAccess, BioCycAccess and ReactomeAccess, directly connect CellDesigner to the pathway databases MetNetDB, BioCyc and Reactome. PathwayAccess plugins enable CellDesigner users to expose pathway data to analytical CellDesigner functions, curate their pathway databases and visually integrate pathway data from different databases using standard Systems Biology Markup Language and Systems Biology Graphical Notation. Implemented in Java, PathwayAccess plugins run with CellDesigner version 4.0.1 and were tested on Ubuntu Linux, Windows XP and 7, and MacOSX. Source code, binaries, documentation and video walkthroughs are freely available at http://vrac.iastate.edu/~jlv.

References

Jun 18, 2005·Bioinformatics·Markus KrummenackerPeter D Karp
Jul 13, 2005·Plant Physiology·Lukas A MuellerSteven D Tanksley
Oct 26, 2005·Nucleic Acids Research·Peter D KarpNúria López-Bigas
Nov 5, 2008·Nucleic Acids Research·Lisa MatthewsPeter D'Eustachio

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Citations

Sep 29, 2011·Briefings in Bioinformatics·Yves Sucaet, Taru Deva
Nov 15, 2011·Nucleic Acids Research·Preeti BaisJulie A Dickerson
Oct 17, 2012·BMC Bioinformatics·Yves SucaetEve Syrkin Wurtele

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Software Mentioned

JavaCyc
Systems Graphical Notation ( SBGN
MetNetDB
JavaCycO
SQL
Reactome
MetNet
CellDesigner
PathwayAccess
ReactomeAccess

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