Diff for "Cytoscape_User_Manual/Introduction"

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"] 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 Features for Visual Style
  • Transparency (opacity) support.
  • Continuous edge width.
  • Color visual property is separated from Arrow and Edge.
• New Filter UI
  • Use intuitive UI widgets for basic filters
  • Suggest search values with indexing
  • Have options to save in session or globally
• Layout Manager/Broker
• Plugin Manager and new plugin website
  • Install/Update/Delete plugins from within Cytoscape.
  • Search for version compatible plugins from any host site.
  • Display list of installed plugins.
• Undo Manager
• Group API for plugin developers.
• Node stacking
• Tested on both Java SE 5 and 6.
• Many, many bug fixes!