CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED

Summary: CytoSEED is a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created using the Model SEED. The CytoSEED plugin enables users of the Model SEED to create informative visualizations of the reaction networks generated for their organisms of interest. These visualizat...

Descripción completa

Detalles Bibliográficos
Autores principales: DeJongh, Matthew, Bockstege, Benjamin, Frybarger, Paul, Hazekamp, Nicholas, Kammeraad, Joshua, McGeehan, Travis
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3307106/
https://www.ncbi.nlm.nih.gov/pubmed/22210867
http://dx.doi.org/10.1093/bioinformatics/btr719
_version_ 1782227290380304384
author DeJongh, Matthew
Bockstege, Benjamin
Frybarger, Paul
Hazekamp, Nicholas
Kammeraad, Joshua
McGeehan, Travis
author_facet DeJongh, Matthew
Bockstege, Benjamin
Frybarger, Paul
Hazekamp, Nicholas
Kammeraad, Joshua
McGeehan, Travis
author_sort DeJongh, Matthew
collection PubMed
description Summary: CytoSEED is a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created using the Model SEED. The CytoSEED plugin enables users of the Model SEED to create informative visualizations of the reaction networks generated for their organisms of interest. These visualizations are useful for understanding organism-specific biochemistry and for highlighting the results of flux variability analysis experiments. Availability and Implementation: Freely available for download on the web at http://sourceforge.net/projects/cytoseed/. Implemented in Java SE 6 and supported on all platforms that support Cytoscape. Contact: dejongh@hope.edu Supplementary information: Installation instructions, a tutorial, and full-size figures are available at http://www.cs.hope.edu/cytoseed/.
format Online
Article
Text
id pubmed-3307106
institution National Center for Biotechnology Information
language English
publishDate 2012
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-33071062012-03-19 CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED DeJongh, Matthew Bockstege, Benjamin Frybarger, Paul Hazekamp, Nicholas Kammeraad, Joshua McGeehan, Travis Bioinformatics Applications Note Summary: CytoSEED is a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created using the Model SEED. The CytoSEED plugin enables users of the Model SEED to create informative visualizations of the reaction networks generated for their organisms of interest. These visualizations are useful for understanding organism-specific biochemistry and for highlighting the results of flux variability analysis experiments. Availability and Implementation: Freely available for download on the web at http://sourceforge.net/projects/cytoseed/. Implemented in Java SE 6 and supported on all platforms that support Cytoscape. Contact: dejongh@hope.edu Supplementary information: Installation instructions, a tutorial, and full-size figures are available at http://www.cs.hope.edu/cytoseed/. Oxford University Press 2012-03-15 2011-12-30 /pmc/articles/PMC3307106/ /pubmed/22210867 http://dx.doi.org/10.1093/bioinformatics/btr719 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
DeJongh, Matthew
Bockstege, Benjamin
Frybarger, Paul
Hazekamp, Nicholas
Kammeraad, Joshua
McGeehan, Travis
CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED
title CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED
title_full CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED
title_fullStr CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED
title_full_unstemmed CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED
title_short CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED
title_sort cytoseed: a cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the model seed
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3307106/
https://www.ncbi.nlm.nih.gov/pubmed/22210867
http://dx.doi.org/10.1093/bioinformatics/btr719
work_keys_str_mv AT dejonghmatthew cytoseedacytoscapepluginforviewingmanipulatingandanalyzingmetabolicmodelscreatedbythemodelseed
AT bockstegebenjamin cytoseedacytoscapepluginforviewingmanipulatingandanalyzingmetabolicmodelscreatedbythemodelseed
AT frybargerpaul cytoseedacytoscapepluginforviewingmanipulatingandanalyzingmetabolicmodelscreatedbythemodelseed
AT hazekampnicholas cytoseedacytoscapepluginforviewingmanipulatingandanalyzingmetabolicmodelscreatedbythemodelseed
AT kammeraadjoshua cytoseedacytoscapepluginforviewingmanipulatingandanalyzingmetabolicmodelscreatedbythemodelseed
AT mcgeehantravis cytoseedacytoscapepluginforviewingmanipulatingandanalyzingmetabolicmodelscreatedbythemodelseed

Ejemplares similares