Cytoscape

Formerly cytoscape

Cytoscape is a software solution developed by the Cytoscape Consortium, designed for network data integration, analysis, and visualization. It caters to businesses of various sizes, from small companies to large research institutions. Professionals in industries such as biology, genetics, bioinformatics, systems biology, proteomics research, and social network analysis rely on Cytoscape for their network analysis needs.

Key Features

Network Data Integration: Cytoscape enables users to integrate and visualize complex networks, including molecular and genetic interaction data sets, in various standard formats. Users can load and project global datasets and functional annotations onto their networks. The software supports the establishment of visual mappings across different types of attribute data.

Analysis and Modeling: Cytoscape provides advanced analysis and modeling capabilities through its Apps. Users can perform various analyses, such as network clustering, pathway enrichment, and network motif detection. The platform supports the creation and execution of custom analysis workflows.

Visualization: Cytoscape offers powerful visualization tools for exploring and analyzing network data. Users can create customizable visualizations of their networks, including options for node and edge colors, shapes, and sizes. The software supports the integration of external data sources to enhance visualizations.

App Ecosystem: Cytoscape has a variety of Apps available for different problem domains, including bioinformatics, social network analysis, and semantic web. Users can extend the functionality of Cytoscape by installing and using these Apps. The platform provides a marketplace for discovering and downloading new Apps.

Data Import and Export: Cytoscape allows users to import and export network and attribute data in various formats, including standard file formats and web services. The software supports the integration of external data sources, such as molecular interaction databases and pathway datasets. Users can easily share their network data with others by exporting it in a compatible format.

Community and Support: Cytoscape has an active and supportive community of users and developers. Users can access tutorials, documentation, and sample visualizations to learn and explore the capabilities of the software. The platform offers support through forums and mailing lists, where users can ask questions and receive assistance from the community.

Automation and Integration: Cytoscape provides automation capabilities through its CyREST API, allowing users to leverage command-line tools, R, and Python libraries. Users can automate their analysis workflows and integrate Cytoscape with other software or data analysis pipelines. The platform supports the development of custom Apps and extensions through its developer documentation and resources.

Network Analysis in Biology: Cytoscape is widely used in molecular and systems biology, genomics, and proteomics research. The software supports the analysis of molecular and genetic interaction data, functional annotations, and curated pathway datasets. Users can visualize and analyze biological networks to gain insights into complex biological processes.

Social Network Analysis: Cytoscape is also used for social network analysis in the field of social sciences. The software provides tools for analyzing and visualizing social networks, including options for community detection and centrality measures. Users can apply network analysis techniques to study social relationships and patterns.

Semantic Web Analysis: Cytoscape supports the analysis of semantic web data and ontologies. Users can import and visualize RDF and OWL data and perform semantic network analysis. The software provides tools for exploring relationships and hierarchies within semantic networks.