Cytoscape
Cytoscape
About this Gateway
Cytoscape
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. Cytoscape Apps are software applications written in Java that customize and extend the functionality of Cytoscape for network data integration, analysis and visualization. Cytoscape 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. There is a steady stream of Cytoscape Apps being produced by developers around the world and deposited at the Cytoscape App Store.
Scope of the Cytoscape Gateway
The Cytoscape gateway is designed to feature several different facts of the wider Cytoscape community – namely, to publish software tools articles highlighting both Apps with clear use cases for network researchers and relevant implementation tips for other App developers, as well as technical extensions which have been written using either R or Python. Additionally, we encourage the submission of both protocols and method articles involving the wider Cytoscape ecosystem.
The author guidelines were customized for this gateway to encourage relevant use cases and useful implementation details in a short article format. Researchers will find Apps that connect to KEGG, Reactome and WikiPathways, perform identifier mapping, interface with R, GenomeSpace and GeneMANIA, perform network alignment and topological analysis, add pie charts to nodes, and export networks to the Web. App developers will find descriptions of Cytoscape API usage, including TaskIterator, CyNetworkReader, VisualMappingManager and CyCustomGraphics, as well as command interfaces exposed by other Apps and links to their code.
Every Cytoscape App and technical extension that is published in this gateway is freely available and open source, as are the featured methodology and protocol articles.
If you have any questions regarding the Cytoscape Gateway, please reach out to info@f1000.com.
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. Cytoscape Apps are software applications written in Java that customize and extend the functionality of Cytoscape for network data integration, analysis and visualization. Cytoscape 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. There is a steady stream of Cytoscape Apps being produced by developers around the world and deposited at the Cytoscape App Store.
Scope of the Cytoscape Gateway
The Cytoscape gateway is designed to feature several different facts of the wider Cytoscape community – namely, to publish software tools articles highlighting both Apps with clear use cases for network researchers and relevant implementation tips for other App developers, as well as technical extensions which have been written using either R or Python. Additionally, we encourage the submission of both protocols and method articles involving the wider Cytoscape ecosystem.
The author guidelines were customized for this gateway to encourage relevant use cases and useful implementation details in a short article format. Researchers will find Apps that connect to KEGG, Reactome and WikiPathways, perform identifier mapping, interface with R, GenomeSpace and GeneMANIA, perform network alignment and topological analysis, add pie charts to nodes, and export networks to the Web. App developers will find descriptions of Cytoscape API usage, including TaskIterator, CyNetworkReader, VisualMappingManager and CyCustomGraphics, as well as command interfaces exposed by other Apps and links to their code.
Every Cytoscape App and technical extension that is published in this gateway is freely available and open source, as are the featured methodology and protocol articles.
If you have any questions regarding the Cytoscape Gateway, please reach out to info@f1000.com.
Gateway Areas
Cytoscape Automation enables scripting languages (e.g., Python, R or Javascript) to call Cytoscape functions. These papers describe new callable functionality exposed in a number of highly used Cytoscape apps.
Gateway Advisors
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Alexander Pico
Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA -
Barry Demchak
UC San Diego School of Medicine, USA