Network propagation is an important and widely used algorithm in systems biology, with applications in protein function prediction, disease gene prioritization, and patient stratification. However, up to this point it has required significant expertise to run. Here we extend the popular network analysis program Cytoscape to perform network propagation as an integrated function. Such integration greatly increases the access to network propagation by putting it in the hands of biologists and linking it to the many other types of network analysis and visualization available through Cytoscape. We demonstrate the power and utility of the algorithm by identifying mutations conferring resistance to Vemurafenib.

UNLABELLED: We developed cyNeo4j, a Cytoscape App to link Cytoscape and Neo4j databases to utilize the performance and storage capacities Neo4j offers. We implemented a Neo4j NetworkAnalyzer, ForceAtlas2 layout and Cypher component to demonstrate the possibilities a distributed setup of Cytoscape and Neo4j have. AVAILABILITY AND IMPLEMENTATION: The app is available from the Cytoscape App Store at http://apps.cytoscape.org/apps/cyneo4j, the Neo4j plugins at www.github.com/gsummer/cyneo4j-parent and the community and commercial editions of Neo4j can be found at http://www.neo4j.com. CONTACT: [email protected].

One of the key challenges to successful systems-of-systems integration using Web services technologies is how to address crosscutting architectural concerns such as policy management, governance, and authentication, while still maintaining the lightweight implementation and deployment Jlavor that distinguishes Web services fiom earlier attempts at providing interoperable enterprise systems. To address this challenge, this article introduces the notion of a Rich Service, an extension of the standard service notion, based on an architectural pattern that allows hierarchical decomposition of system architecture according to separate concerns. Rich Services enable the capture of dzfferent system aspects and their interactions. By leveraging emerging Enterprise Service Bus technologies, Rich Services also enable a direct transition from a logical to a deployed service-oriented architecture (SOA). This results in immediate beneJits not only in SOA design, implementation, deployment, and quality assurance, but also in the traceability of architectural requirements to an SOA implementation.