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| 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.''' | 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. |
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| __'''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). |
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). |
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| __'''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. |
=== 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. |
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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. |
* 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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| * '''''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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| * Editor support for hyperedges. | * Plugin Manager and new plugin website |
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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. |
* Undo Manager |
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* 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. |
* Group API for plugin developers. |
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| * Support for Java SE 5. |
* Node stacking * Tested on both Java SE 5 and 6. |
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'''''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.] |
* Many, many bug fixes! |
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!