Diff for "Cytoscape_User_Manual/Introduction"

Cytoscape is an open-source community software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular state information for visualization and analysis. 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. A software “Core” provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular state information; and to link the network to databases of functional annotations. The Core is extensible through a plug-in architecture, allowing rapid development of additional computational analyses and features. 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 [#acknowledgements Acknowledgements] below.

What’s New in 2.4

Cytoscape version 2.4 contains several new features, plus improvements to the performance and usability of the software. These include:

• Publication quality image generation. This includes:
  • Node label position adjustment.
  • Automatic Visual Legend generator.
  • Node position fine-tuning by arrow keys.

• Quick Find plugin.

• New Cytoscape icons for a cleaner user interface.
• Editor support for hyperedges.
• 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.

• New Ontology Server. This will eventually replace BioDataServer. Ontology Server has the following new features:

  • Native support for OBO format ontology files. Users can import many different ontologies in OBO format.
  • Ability to visualize ontology tree (DAG).
  • Full support for Gene Association files.
• Support for Java SE 5.

Are you an experienced Cytoscape user? If so, you should definitely read the following sections because important parts of Cytoscape have changed and what used to work, may no longer work as you expect!!!

• [#properties Properties (cytoscape.props and vizmap.props) handling.]
• [#renderer Rendering Engine.]
• [#command_line_args Command line arguments.]
• [#menus The menu system.]
• [#navigation Network Panel Navigation.]