Diff for "Cytoscape_User_Manual/Introduction"

Differences between revisions 23 and 24

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 theCytoscape_User_Manual/Acknowledgements below.

What’s New in @version@

Cytoscape version @version@ contains several new features, plus improvements to the performance and usability of the software.

Node Custom Graphics

Internally, Cytoscape has Custom Graphics API for developers since 2.3. From this version, end-users can access this feature from standard VizMap GUI. You can add up to nine Custom Graphics objects per node. Each Custom Graphics object has position Visual Property and you can adjust its position from intuitive GUI.

==== Attribute Function ==== (Please add description)

Other New Features and Bug Fixes

Plugin search: you can search plugins by keywords
Many, many bug fixes!

-  ← Revision 23 as of 2009-02-12 01:03:49 →
  Size: 3072
  Editor: localhost
  Comment: converted to 1.6 markup
+  ← Revision 24 as of 2010-07-28 02:49:11 →
  Size: 2740
  Editor: KeiichiroOno
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 16:
-Cytoscape version @version@ contains several new features, plus improvements to the performance and usability of the software. These include:
+Cytoscape version @version@ contains several new features, plus improvements to the performance and usability of the software.
 Line 18:
- * Web Service Client Manager framework to integrate web service clients into Cytoscape.

 * Web Service client plugins for downloading networks from [[http://www.pathwaycommons.org/pc/|PathwayCommons]], [[http://www.ebi.ac.uk/intact/site/index.jsf|IntAct]], and [[http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene|NCBI Entrez Gene]]. 

 * Annotation import web service plugin for [[http://www.biomart.org/|BioMart]].  This is mainly for ID translation/synonym mapping. 

 * Cytoscape themes.

 * Dynamic filters.

 * Network Manager supports multiple network selection.

 * Label Positioning has been improved.

 * Session saving occurs in memory.

 * XGMML Improvements.

 * Network loading improvements.

 * Linkout integrated with attribute browser.

 * Extra sample Visual Styles using new visual properties introduced in 2.5.
+==== Node Custom Graphics ====



Internally, Cytoscape has Custom Graphics API for developers since 2.3.  From this version, end-users can access this feature from standard VizMap GUI.  You can add up to nine Custom Graphics objects per node.  Each Custom Graphics object has position Visual Property and you can adjust its position from intuitive GUI.



==== Attribute Function ==== 

(Please add description)

 

==== Other New Features and Bug Fixes ====

 * Plugin search: you can search plugins by keywords