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VPH NoE ToolKit

tool icone cytoscape 

Date added: 17.2.2012  Hot Hits: 82   0 
Version:  v2.8  mature  Submitter:  John Fenner  This e-mail address is being protected from spambots. You need JavaScript enabled to view it  Web Site License:  LGPL v2.1
Supported platform:  Windows Macintosh Linux Target user group: Researchers; Students; Industry Software technology type:  Graphical application
Website Tags: Network analysis Data integration Visualization Categories: Data Conversion Tools | Data Fusion

cytoscape http://www.cytoscape.org/what_is_cytoscape.html

Main Features:  Supports many standards (SIF, GML etc.)
Operates as a web service client
Session file support
Standard file import/export
Image export
VizMapper visualization tool
Target node search/filter
Modules/clusters find
Support for plug-ins

Author(s):  This e-mail address is being protected from spambots. You need JavaScript enabled to view it    This e-mail address is being protected from spambots. You need JavaScript enabled to view it   

Publication(s):  Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks; Shannon et al., Genome Research (2003) 13:2498-2504  Nature. 2011 May 26;473(7348):463-9. A 2020 vision for vaccines against HIV, tuberculosis and malaria. Rappuoli R, Aderem A.  

Requirements:  Java SE 5 or greater

See also:  Cytoscape Wiki  

Installation method:  Several installation methods...
• Automatic installation packages exist for Windows, Mac OS X, and Linux platforms.
• Install Cytoscape from a compressed archive distribution.
• Build Cytoscape from the source code.
• You can check out the latest and greatest software from our Subversion repository.

Data formats supported:  SIF
NNF
GML
XGMML
SBML
BioPAX
PSI-MI
Excel

Supported input formats:  SBML

Supported output formats:  SBML

Documentation: 

http://www.cytoscape.org/community.html#

http://www.cytoscape.org/documentation_developers.html

Users:  http://www.cytoscape.org/who_is_using.html

Users of the technology:  Empty list

Future development plans:  Anticipated release of v3

Testing:  Nature. 2011 May 26;473(7348):463-9. A 2020 vision for vaccines against HIV, tuberculosis and malaria. Rappuoli R, Aderem A.
http://wiki.cytoscape.org/Conferences
http://www.cytoscape.org/documentation_developers.html

Constraints:  Incompatible with Java 1.4.x or less

Support available:  Forum  

Funding status:  Funding for Cytoscape is provided by a federal grant from NIGMS Division of Biomedical Technology, Bioinformatics, and Computational Biology (BBCB) , National Resource for Network Biology (NRNB) RR031228, and the U.S. National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH) under award number GM070743.

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