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 |
