Cytoscape

Cytoscape is an open-source software platform for visualizing and analyzing complex networks, with particular emphasis on biomolecular interaction networks. It enables users to integrate networks with various state data such as gene expression, phenotypes, and annotations, to interpret biological systems.

History: It was developed in the early 2000s at the Institute for Systems Biology and has grown into a platform maintained by the Cytoscape Consortium and a broad developer community. It is written in Java and runs on Windows, macOS, and Linux.

Key features: Core visualization and analytics environment, multiple layout algorithms (force-directed, circle, grid, hierarchical), attribute mapping on nodes/edges, and support for extensibility via apps (plugins). Notable apps include MCODE for cluster detection, BiNGO for GO term enrichment, cytoHubba for network hub analysis, and stringApp for retrieving data from the STRING database. The platform also supports programmatic access via REST and scripting interfaces.

Data formats and interoperability: Cytoscape can import networks from standard formats such as SIF and XGMML, as well as tab-delimited or CSV data for node attributes. It can integrate data from external resources and other tools through apps, enabling pathway or functional analyses.

Impact and usage: Cytoscape is widely used in systems biology, pharmacology, and biomedical research to visualize protein-protein interaction networks, signaling pathways, and gene regulatory networks, and to interpret omics data. It supports a modular architecture that allows researchers to tailor workflows to their data.