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CellDesignerTM Plugins allow developers to extend the function of CellDesigner. CellDesignerTM 4.0 onwards support Plugin functions.
If you are interested in building your own CellDesigner Plugin, please check the following documents:
| Plugins | |
| BioPax Export | Export Model data to BioPAX Level3 format |
| Import Notes | Import Notes data from CSV file |
| iPathwaysPlus Register | Upload, Register Model to iPathways+, web-based pathway repository |
| Mapping Array Mass | Mapping experimental array data to the model |
| Merge Models | Merge CellDesigner's models |
| PathwayAccess | a suite of CellDesigner plugins directly interact with pathway datasources to download and integrate one or more pathways to a CellDesigner model, and upload (or commit) a CellDesigner model to a datasource. |
| Payao Uploader | Upload CellDesigner model to Payao system |
| Relayout Model | Resize Model keeping the layout, straighten the reactions |
| SBML2SMW | A CellDesigner plugin and a semantic translation server to bidirectional read/write from/in Semantic Media Wiki. |
| SBMLsqueezer | A CellDesigner plugin to generate kinetic rate equations for biochemical networks |
| SBSI CellDesigner plugin | A CellDesigner plugin to bridge the functionalities of CellDesigner and SBSI |
| CellDesginer related utilities: | |
| BiNoM (Cytoscape Plugin) | Export CellDesigner maps to other formats, with partial support of CellDesigner semantics. Our Cytoscape plugin BiNoM can convert CellDesigner files to Cytoscape, and to BioPAX v.2.0 formats. |
| BioPP | BioPP suite is a web-based application that allows pathway knowledgebases stored in CellDesigner-SBML to be web published with an easily navigated user interface. |
| Payao | Payao is a community-based, collaborative web service platform for gene-regulatory and biochemical pathway model curation. Payao reads the models in SBML format, displays them with CellDesigner, and provides an interface for model enrichment (adding tags and comments to the models) for the access-controlled community members. |
| CellPublisher | CellPublisher is a free and open web server to share CellDesigner diagrams with a wide audience. |
| Relayout Model | |
| Version: | 1.0 |
| Release Date: | April 2014 |
| Description: | A CellDesigner plugin to relayout models |
| Url: | http://celldesigner.org/plugin/relayoutModel.jar |
| Reference: | |
| Work in | CellDesigner 4.3, 4.4 |
| iPathwaysPlus Register | |
| Version: | 1.0 |
| Release Date: | Jan. 2014 |
| Description: | This plugin is to register, manage Models to iPathways+, a web-based pathway repository. |
| Url: | http://celldesigner.org/plugin/iPathwaysPlusRegister.zip |
| Reference: | User Manual |
| Work in | CellDesigner 4.3 |
| BioPAX export | |
| Version: | 1.0 |
| Release Date: | Oct. 2011 |
| Description: | This plugin is to export the CellDesigner pathway model into BioPAX Level 3 format. |
| Url: | ftp://ftp.pantherdb.org/CellDesigner/plugins/BioPAX/ |
| Reference: | Mi H, Muruganujan A, Demir E, Matsuoka Y, Funahashi A, Kitano H, Thomas PD, BioPAX Support in CellDesigner. Bioinformatics (2011) |
| Work in | CellDesigner 4.1 |
| SBSI CellDesigner Plugin | |
| Version: | 1.0b |
| Release Date: | Jan. 2011 |
| Description: | The purpose of this plugin is to bridge the functionalities of CellDesigner and SBSI. This way a user will have the ability to design his models in CellDesigner and then optimize them using SBSI without the need to switch between programs (http://www.sbsi.ed.ac.uk/). |
| Url: | http://sourceforge.net/ |
| Reference: | |
| Work in | CellDesigner 4.1 |
| Merge Models | |
| Version: | 1.03 |
| Release Date: | Nov 16. 2010 |
| Description: | A CellDesigner plugin to merge models |
| Url: | http://celldesigner.org/plugin/plugin_mergemodel.jar |
| Reference: | User Manual (pdf) |
| Work in | CellDesigner 4.1 |
| Payao Uploader | |
| Version: | 1.0 |
| Release Date: | Oct. 10, 2010 |
| Description: | A CellDesigner plugin to upload a model to Payao (http://www.payaologue.org) - a web-based cummunity pathway curation platform. |
| Url: | http://celldesigner.org/plugin/plugin_payao.jar |
| Reference: | User Manual (pdf) |
| Work in | CellDesigner 4.1 |
| SBML2SMW | |
| Version: | 1.0 |
| Release Date: | July 29. 2010 |
| Description: | A CellDesigner plugin and a semantic translation server to bidirectional read/write from/in Semantic Media Wiki. |
| Url: | http://code.google.com/p/sbml2smw/ |
| Reference: |
SBML2SMW: bridging System Biology with semantic web technologies for biomedical knowledge acquisition and hypothesis elicitation. Tobias Mathäß, Peter Haase, Hiroaki Kitano, Luca Toldo. Accepted at the 2nd Workshop of Ontologies in Biomedicine and Life Sciences, OBML2010, Mannheim, Germany, https://wiki.imise.uni-leipzig.de/Gruppen/OBML/Workshops/2010en http://www.onto-med.de/obml/ws2010/obml2010report.pdf; http://fluidops.net/wp-content/uploads/downloads/2010/08/Publications/obml2010.pdf |
| Work in | CellDesigner 4.1beta and above |
| License | LGPL |
| PathwayAccess | |
| Version: | 1.0 |
| Release Date: | July 20. 2010 |
| Description: | a suite of CellDesigner plugins directly interact with pathway datasources to - download and integrate one or more pathways to a CellDesigner model - upload (or commit) a CellDesigner model to a datasource. |
| Url: | http://vrac.iastate.edu/~jlv/pathwayaccess/ |
| Reference: |
PathwayAccess: CellDesigner Plugins for Pathway Databases John L. Van Hemert; Julie A. Dickerson Bioinformatics 2010; doi: 10.1093/bioinformatics/btq423 PMID: 20647521 |
| Work in | CellDesigner 4.0.1 and above |
| SBMLsqueezer | |
| Version: | 1.3 |
| Release Date: | April 4. 2010 |
| Description: | A CellDesigner plugin to generate kinetic rate equations for biochemical networks |
| Url: | http://www.ra.cs.uni-tuebingen.de/software/SBMLsqueezer |
| Reference: | Andreas Draeger , Nadine Hassis , Jochen Supper , Adrian Schroeder and Andreas Zell, SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks, BMC Systems Biology 2008, 2:39doi:10.1186/1752-0509-2-39, http://www.biomedcentral.com/1752-0509/2/39/abstract. |
| Work in | CellDesigner 4.0alpha and above |
| Import Notes | |
| Version: | 1.1 |
| Release Date: | Aug 4, 2008 |
| Description: | Import Notes data from CSV file |
| Download: | Jar File, Readme |
| Reference: | |
| Work in | CellDesigner 4.0 |
| Mapping Array Mass | |
| Version: | 2.0 |
| Release Date: | Aug 28, 2009 |
| Description: | Mapping Array Data to the model for CellDesigner 4.1beta. Set color to the Species according to the data value. |
| Download: | Jar File (installed with CellDesigner), Readme & Sample Data |
| Reference: | |
| Work in | CellDesigner 4.1beta (as sample plugin) |
PlugIn License Policy:
Plugins are separate works which use CellDesigner as a Java code library. Plugins are therefore governed by independent software licenses distributed with and specific to each plugin.
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