Cytoscape Cyberinfrastructure: Leveraging Microservices to the Cloud and Beyond (Chapter 1)

Cytoscape is an indispensable tool for network data analysis and visualization. One of Cytoscape’s greatest strengths is that it is powered by a vibrant array of developer-contributed apps. However, as network biologists’ requirements evolve, Cytoscape is challenged not only to keep pace, but to lead new and existing developers to create even greater value. Currently, multiscale and multifaceted networks push the memory limits of a Cytoscape workstation, while complex calculations such as Network Based Stratification and Network Based GWAS strain workstation processors. Increasingly, users demand support for collaborative projects, reproducible workflows, and interoperability with external tool chains. Finally, economic pressures favour solutions that promote code and algorithm reusability and evolvability. In response, we have created the Cytoscape Cyber infrastructure (CI), which is both an Internet-scale distributed system (based on Microservices 1 ) and the network biology community it serves. Its mission is to enable and encourage network biologists to create and deploy high quality, innovative and scalable services focusing on network-based computation, collaboration and visualization. Microservices can be written in any language, and are highly testable and evolvable. They can run on servers ranging from a single thread to a large cloud-based cluster. They can easily be reused in reproducible workflows or can serve as components in larger services. The CI links microservices via a light weight REST-based aspect-oriented interchange protocol (called CX), which enables tailored data streams while supporting service innovation via evolvable standards. CI infrastructure services support user authentication, long duration job execution, and a service repository that enables researchers to publish their services or discover services published by others. This model builds on the successful Cytoscape app community, which is based on similar mechanisms though at the scale of individual workstations. Prominent examples of microservices include NDEx 2 (a repository for biological networks), NodeWalker (which uses heat dispersion to identify the most relevant subnetworks containing a given set of genes), cyNetShare 3 (which visualizes a network in a browser) and Cytoscape itself (which can also call CI services). Interfaces are available for Python, I Python, R and Matlab. Future work includes adding clustering, analysis, layout, publishing and display microservices and interfaces to Galaxy and Taverna workflows. Already though, our researchers are leveraging existing microservices in multiple contexts, thus demonstrating the increased flexibility and productivity available in the CI. 1 http://martinfowler.com/articles/microservices.html 2 http://home.ndexbio.org/about-ndex-2/ 3 http://idekerlab.github.io/cy-net-share/