The Cytoscape Cyberinfrastructure and the NDEx Network Cloud

The Ideker lab is involved in development of several bioinformatic resources for network analysis that are widely used by the biological research community. The most visible of these is a collaborative open-source software project called Cytoscape (http://www.cytoscape.org). Cytoscape is one of the principal tools used by researchers to analyze and visualize molecular interaction networks, with approximately 17,000 downloads per month, and it is also used in almost all of the lab’s research activities. Now in its 16th year, the Cytoscape codebase is curated by four main institutions via funding from the P41 NIGMS National Resource for Network Biology and an NHGRI R01, both of which Dr. Ideker directs. In the past few years the platform has been substantially extended to include a cloud-based storage system for networks, much like Google Drive and DropBox provide for online storage and sharing of other types of documents. This network store, which we call the Network Data Exchange (NDEx), is funded through a separate U24 grant from NCI. 

The core Cytoscape application has been frequently extended through a straightforward plug-in architecture, giving ready access to over 330 plug-ins (Cytoscape ‘Apps’) which are presently available and approximately half of which have been described in their own peer-reviewed publications. Approximately 160 of these Apps have been newly published or significantly updated in the past three-year review period, most of which are by independent groups and do not include me or my team as authors. Popular Apps extend Cytoscape in areas such as network query and download; network integration and filtering; attribute-directed network layout; Gene Ontology enrichment analysis; as well as network motif, functional module, protein complex, or domain interaction detection. Our plan for Cytoscape development for the remainder of 2018 is to release Cytoscape 3.7, which will involve major upgrades to the core architecture and seamless roundtrip connectivity to NDEx.