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| === What’s New in 2.4 === | === What’s New in 2.5 === |
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| Cytoscape version 2.4 contains several new features, plus improvements to the performance and usability of the software. These include: | Cytoscape version 2.5 contains several new features, plus improvements to the performance and usability of the software. These include: |
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* Publication quality image generation. This includes: * Node label position adjustment. * Automatic Visual Legend generator. * Node position fine-tuning by arrow keys. * The ability to override selected !VizMap settings. |
* New VizMapper user interface (UI) * More Intuitive UI. * Continuous mapping editors. * Visual editor for default view. * Visual Mapping Mapping Browser. * Improved visual legend generator. * Utilities to generate discrete values. |
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| * Full integration of the Quick Find plugin. | * New Filter UI. |
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| * New Cytoscape icons for a cleaner user interface. | * Layout Manager/Broker |
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* Consolidated network import capabilities. * Import network from remote data sources (through http or ftp). * Default support for the following file formats: * [http://sbml.org/index.psp Systems Biology Markup Language (SBML)] * [http://www.biopax.org/ BioPAX Level 1 and 2] * [http://psidev.sourceforge.net/mi/xml/doc/user/ PSI-MI (Level 1 and 2.5)] * Delimited text table (TAB delimited text file, CSV, etc.) * Excel (.xls) format file. |
* Plugin Manager and new plugin website |
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* New Ontology Server. This will eventually replace the !BioDataServer. New Ontology Server features include: * Native support for OBO format ontology files. Users can import many different ontologies in the OBO format. * Ability to visualize the ontology tree as a network (DAG). * Full support for Gene Association files. |
* Undo Manager * * Group API for plugin developers. * Node stacking |
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| * Support for Java SE 5. | * Tested on both Java SE 5 and 6. |
Cytoscape is a project dedicated to building open-source network visualization and analysis software. A software "Core" provides basic functionality to layout and query the network and to visually integrate the network with state data. The Core is extensible through a plug-in architecture, allowing rapid development of additional computational analyses and features.
Cytoscape's roots are in Systems Biology, where it is used for integrating biomolecular interaction networks with high-throughput expression data and other molecular state information. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape allows the visual integration of the network with expression profiles, phenotypes, and other molecular state information, and links the network to databases of functional annotations.
The central organizing metaphor of Cytoscape is a network (graph), with genes, proteins, and molecules represented as nodes and interactions represented as links, i.e. edges, between nodes.
Development
Cytoscape is a collaborative project between the Institute for Systems Biology (Leroy Hood lab), the University of California San Diego (Trey Ideker lab), Memorial Sloan-Kettering Cancer Center (Chris Sander lab), the Institut Pasteur (Benno Schwikowski lab), Agilent Technologies (Annette Adler lab) and the University of California, San Francisco (Bruce Conklin lab).
Visit http://www.cytoscape.org for more information.
License
Cytoscape is protected under the GNU LGPL (Lesser General Public License). The License is included as an appendix to this manual, but can also be found online: http://www.gnu.org/copyleft/lesser.txt. Cytoscape also includes a number of other open source libraries, which are detailed in the[:Cytoscape_User_Manual/Acknowledgements:Acknowledgements] below.
What’s New in 2.5
Cytoscape version 2.5 contains several new features, plus improvements to the performance and usability of the software. These include:
New VizMapper user interface (UI)
- More Intuitive UI.
- Continuous mapping editors.
- Visual editor for default view.
- Visual Mapping Mapping Browser.
- Improved visual legend generator.
- Utilities to generate discrete values.
- New Filter UI.
- Layout Manager/Broker
- Plugin Manager and new plugin website
- Undo Manager
- Group API for plugin developers.
- Node stacking
- Tested on both Java SE 5 and 6.
- Many, many bug fixes!