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PathwayAccess: CellDesigner plugins for pathway databases
Summary: 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 us...
Autores principales: | , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935416/ https://www.ncbi.nlm.nih.gov/pubmed/20647521 http://dx.doi.org/10.1093/bioinformatics/btq423 |
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author | Van Hemert, John L. Dickerson, Julie A. |
author_facet | Van Hemert, John L. Dickerson, Julie A. |
author_sort | Van Hemert, John L. |
collection | PubMed |
description | Summary: 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. Availability: 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 Contact: julied@iastate.edu Supplementary information: Supplementary data are available at Bioinformatics online. |
format | Text |
id | pubmed-2935416 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-29354162010-09-08 PathwayAccess: CellDesigner plugins for pathway databases Van Hemert, John L. Dickerson, Julie A. Bioinformatics Applications Note Summary: 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. Availability: 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 Contact: julied@iastate.edu Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2010-09-15 2010-07-20 /pmc/articles/PMC2935416/ /pubmed/20647521 http://dx.doi.org/10.1093/bioinformatics/btq423 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Note Van Hemert, John L. Dickerson, Julie A. PathwayAccess: CellDesigner plugins for pathway databases |
title | PathwayAccess: CellDesigner plugins for pathway databases |
title_full | PathwayAccess: CellDesigner plugins for pathway databases |
title_fullStr | PathwayAccess: CellDesigner plugins for pathway databases |
title_full_unstemmed | PathwayAccess: CellDesigner plugins for pathway databases |
title_short | PathwayAccess: CellDesigner plugins for pathway databases |
title_sort | pathwayaccess: celldesigner plugins for pathway databases |
topic | Applications Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935416/ https://www.ncbi.nlm.nih.gov/pubmed/20647521 http://dx.doi.org/10.1093/bioinformatics/btq423 |
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