CellDesigner.org

Utilities

Here is the list of utilites which can use with CellDesignerTM.

CellDesigner Related Utilities

 

File converter: CellDesigner -> Cytoscapse -> BioPAX v.2.0
BiNoM (Cytoscape Plugin)
Version: 1.0
Release Date: 2007
Description: 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.
Url: http://bioinfo-out.curie.fr/projects/binom/
Developed by: Zinovyev A., Viara E., Calzone L., Barillot E.
Reference: Zinovyev A., Viara E., Calzone L., Barillot E. BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. 2007. Bioinformatics doi: 10.1093/bioinformatics/btm553 pdf
Work for CellDesigner 3.5x
CellDesigner File viewer / publisher
BioPP
Version: 1.0
Release Date: 2007
Description: 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.
Url: http://tsb.mssm.edu/pathwayPublisher/broadcast/
Developed by: Viswanathan GA., Nudelman G., Patil S., Sealfon SC
Reference: Viswanathan GA., Nudelman G., Patil S., Sealfon SC., BioPP: a tool for web-publication of biological networks, BMC Bioinformatics. 2007 May 22;8:168.
Work for CellDesigner 4.0
Payao new
Version: 1.0
Release Date: 2010
Description: 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.
Url: http://www.payaologue.org
Developed by: The Systems Biology Institute, Japan
Reference: Matsuoka Y., Ghosh S., Kikuchi N., Kitano H., Payao : A Community Platform for SBML Pathway Model Curation. Bioinformatics 2010
Work for CellDesigner 4.0 and above
CellPublisher new
Version: 1.0
Release Date: 2010
Description: CellPublisher is a free and open web server to share CellDesigner diagrams with a wide audience. The CellDesigner file is converted into a user-friendly interactive map that lives inside a browser. You can then share it with your collaborators using a URL, or download it to your computer to navigate the interactive diagram locally.
Url: http://cellpublisher.gobics.de/
Developed by: Lope Florez, Christoph Lammers, and Jörg Stülke of the University of Göttingen, Germany.
Reference:  
Work for CellDesigner 3.5x

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