Cytoscape
Cytoscape 3.1.0
Developed by:
License: GPL / GNU General Public License
Web page : Tool homepage
Tool type : Application software
The last edition of this page was on: 2014/03/04
The Completion level of this page is : Low
The last edition of this page was on: 2014/03/04 The Completion level of this page is : Low
SHORT DESCRIPTION
[[has description::Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization.
Additional features are available as Apps (formerly called Plugins). Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases. They may be developed by anyone using the Cytoscape open API based on Java™ technology and App community development is encouraged. Most of the Apps are freely available from Cytoscape App Store.
See Cytoscape App store]]
TOOL CHARACTERISTICS
Usability
Tool orientation
Data mining type
Manipulation type
IMPORT FORMAT :
EXPORT FORMAT :
| Tool objective(s) in the field of Learning Sciences | |
|
☑ Analysis & Visualisation of data |
☑ Providing feedback for supporting instructors: |
Tool can perform:
- Data extraction of type:
- Transformation of type:
- Data analysis of type:
- Data visualisation of type: (These visualisations can be interactive and updated in "real time")
ABOUT USERS
Tool is suitable for:
Required skills:
STATISTICS: N/A
PROGRAMMING: N/A
SYSTEM ADMINISTRATION: N/A
DATA MINING MODELS: N/A
FREE TEXT
| Tool version : Cytoscape 3.1.0 (blank line) Developed by : |
|
Contents
SHORT DESCRIPTION
Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization.
Additional features are available as Apps (formerly called Plugins). Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases. They may be developed by anyone using the Cytoscape open API based on Java™ technology and App community development is encouraged. Most of the Apps are freely available from Cytoscape App Store.
TOOL CHARACTERISTICS
| Tool orientation | Data mining type | Usability |
|---|---|---|
| This tool is designed for general purpose analysis. | This tool is designed for Structured data mining. | Authors of this page consider that this tool is . |
| Data import format | Data export format |
|---|---|
| . | . |
| Tool objective(s) in the field of Learning Sciences | |
|
☑ Analysis & Visualisation of data |
☑ Providing feedback for supporting instructors: |
Can perform data extraction of type:
Can perform data transformation of type:
Can perform data analysis of type:
Can perform data visualisation of type:
(These visualisations can be interactive and updated in "real time")
ABOUT USER
| Tool is suitable for: | ||||
| Students/Learners/Consumers:☑ | Teachers/Tutors/Managers:☑ | Researchers:☑ | Organisations/Institutions/Firms:☑ | Others:☑ |
| Required skills: | |||
| Statistics: | Programming: | System administration: | Data mining models: |
OTHER TOOL INFORMATION
|
|
| Cytoscape screenshot.jpg |
| Cytoscape logo.jpg |
| Cytoscape |
| GPL / GNU General Public License |
| Free&Open source |
| 3.1.0 |
| http://www.cytoscape.org/ |
| [[has description::Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization.
Additional features are available as Apps (formerly called Plugins). Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases. They may be developed by anyone using the Cytoscape open API based on Java™ technology and App community development is encouraged. Most of the Apps are freely available from Cytoscape App Store. See Cytoscape App store]] |
| General analysis |
| N/A |
| N/A |
| N/A |
| N/A |
| Application software |
| Structured data mining |
| Data analysis, Data visualisation |
| Low |
Features ( from Wikipedia):
Input
- Input and construct molecular interaction networks from raw interaction files (SIF format) containing lists of protein-protein and/or protein-DNA interaction pairs. For yeast and other model organisms, large sources of pairwise interactions are available through the BIND and TRANSFAC databases. User-defined interaction types are also supported.
- Load and save previously-constructed interaction networks in GML format (Graph Modelling Language).
- Load and save networks and node/edge attributes in an XML document format called XGMML (eXtensible Graph Markup and Modeling Language).
- Input mRNA expression profiles from tab- or space-delimited text files.
- Load and save arbitrary attributes on nodes and edges. For example, input a set of custom annotation terms for your proteins, create a set of confidence values for your protein-protein interactions.
- Import gene functional annotations from the Gene Ontology (GO) and KEGG databases.
- Directly import GO Terms and annotations from OBO and Gene Association files.
- Load and save state of the Cytoscape session in a Cytoscape Session (.cys) file. Cytoscape Session file includes networks, attributes (for node/edge/network), Desktop states (selected/hidden nodes and edges, window sizes), Properties, and Visual Styles.
Visualization
- Customize network data display using powerful visual styles.
- View a superposition of gene expression ratios and p-values on the network. Expression data can be mapped to node color, label, border thickness, or border color, etc. according to user-configurable colors and visualization schemes.
- Layout networks in two dimensions. A variety of layout algorithms are available, including cyclic and spring-embedded layouts.
- Zoom in/out and pan for browsing the network.
- Use the network manager to easily organize multiple networks. And this structure can be saved in a session file.
- Use the bird's eye view to easily navigate large networks.
- Easily navigate large networks (100,000+ nodes and edges) by efficient rendering engine.
Analysis
- Plugins available for network and molecular profile analysis. For example:
- Filter the network to select subsets of nodes and/or interactions based on the current data. For instance, users may select nodes involved in a threshold number of interactions, nodes that share a particular GO annotation, or nodes whose gene expression levels change significantly in one or more conditions according to p-values loaded with the gene expression data.
- Find active subnetworks/pathway modules. The network is screened against gene expression data to identify connected sets of interactions, i.e. interaction subnetworks, whose genes show particularly high levels of differential expression. The interactions contained in each subnetwork provide hypotheses for the regulatory and signaling interactions in control of the observed expression changes.
- Find clusters (highly interconnected regions) in any network loaded into Cytoscape. Depending on the type of network, clusters may mean different things. For instance, clusters in a protein-protein interaction network have been shown to be protein complexes and parts of pathways. Clusters in a protein similarity network represent protein families.