Cytoscape

Overview of Cytoscape

Cytoscape is an open source software platform designed for visualizing complex networks and integrating them with various types of attribute data. This powerful tool serves researchers, bioinformaticians, and data scientists working with network analysis across multiple domains including molecular biology, genomics, and social network analysis. The platform handles molecular and genetic interaction datasets in numerous formats while enabling users to project and integrate global datasets with functional annotations.

Available in both desktop and web versions, Cytoscape provides flexible deployment options for different user needs. The desktop application offers private, offline functionality with access to advanced features and workflows, while the web-based version facilitates easy collaboration and sharing among colleagues. Supported by the Collaboration Tool and Mind Mapping Tool categories, Cytoscape has become an essential resource in bioinformatics research and network visualization.

How to Use Cytoscape

Getting started with Cytoscape involves downloading the desktop application from the official website or accessing the web version directly in your browser. Users can load molecular interaction data in multiple formats, establish visual mappings across datasets, and perform advanced analysis using the extensive plugin ecosystem. The platform integrates with NDEx (Network Data Exchange) for gene analysis queries and provides comprehensive tutorials for learning network visualization techniques. For developers, Cytoscape offers app development documentation to create custom plugins and extensions.

Core Features of Cytoscape

1. Network Visualization – Advanced tools for displaying complex networks with customizable layouts and styles
2. Data Integration – Capability to merge multiple data types and formats into unified network views
3. Plugin Ecosystem – Extensive library of plugins for specialized analysis and functionality extensions
4. Multi-Platform Access – Desktop application for offline work and web version for collaboration
5. Bioinformatics Support – Specialized tools for molecular biology, genomics, and proteomics research

Use Cases for Cytoscape

• Molecular and systems biology research projects
• Genomic and proteomic data analysis workflows
• Social network analysis and visualization
• Pathway dataset visualization including Reactome and KEGG
• Bioinformatics education and research training
• Semantic web applications and data integration
• Genetic interaction network mapping and analysis

Support and Contact

For support and inquiries, visit the official Cytoscape website or contact via email at contact@cytoscape.org. The platform is developed as an open source project with community support through documentation and tutorials. Additional contact information can be found on the Cytoscape Consortium website.

Company Info

Cytoscape is developed as an open source project supported by the National Resource for Network Biology and the National Human Genome Research Institute. The project operates under open source licensing and is maintained by the Cytoscape Consortium, which coordinates development and community support for this widely-used bioinformatics platform.

Login and Signup

Cytoscape is available for download and immediate use without registration requirements. Access the desktop application at Download Cytoscape or use the web version directly at Cytoscape Web. No login or signup is needed for basic functionality, making it easily accessible for researchers and students.