In Systems Biology, insights are often driven by a virtuous combination of collaboration, rich data sets, and robust computational and visualization algorithms. The application of Internet technologies in each of these areas has empowered researchers to discover and leverage prior work more quickly and effectively than ever before. At the same time, counterproductive technological and cultural silos have arisen, where resources are spent integrating incompatible data sources and reprising existing computations and visualizations. In this abstract, we describe how the Cytoscape Cyberinfrastructure (CI) can improve research productivity by enabling the integration of siloed collaboration, data, and computational systems while also providing a path to scalability and evolvability. Systems Biology researchers increasingly create network analysis and visualization workflows using modern programming systems such as R, MATLAB, and iPython. These systems provide reusable components, common data formats, collaboration features, and user communities. However, by nature they also discourage collaboration between communities and component reuse across systems, thus creating silos. Web-based data sets create their own silos by delivering data in their own formats, different from all others. The CI is a framework organized as a Service Oriented Architecture (SOA) where workflows and algorithms are each written in the language that best suits their function. Algorithms are packaged as Microservices that exchange network data in the common and extensible CX format, and which can execute on servers distributed across the Internet. For example, the NDEx service allows network data to be stored, retrieved, and shared between users and groups of users. Other services include an ID mapper (e.g., Gene Symbol to Entrez ID), heat dissipation, network layout, and Network Based Stratification, with others on the way. We present a prototype of a CI-enabled web application that demonstrates how services can be organized into a workflow that fetches a network from an NDEx database, merges it with experiment data, visualizes it, and then writes it back to NDEx. The application is organized as a collection of user interface elements (called widgets) that call the CI services and are themselves reusable for building new Systems Biology applications. By enabling the use of bioinformatic services regardless of the language in which they are written, CI applications encourage the creation and reuse of best-of-breed functionality while enabling the integration of siloed communities into a larger, more productive community. It incentivizes the constant sharing and iteration of information, thereby enabling more fluid, agile, reproducible, and opportunistic bioinformatic research.

1. No More Silos!
Cytoscape CI Enables Interoperability
Barry Demchak (bdemchak@ucsd.edu), Keichiro Ono, Dexter Pratt & Trey Ideker
National Resource for Network Biology - University of California, San Diego
This material is based upon work supported by the National Institutes of Health
under Grants P41 RR031228 and GM103504
Context
Network Apps Authorship
• Workflows need custom code
• Value in both browser
presentation & complex
algorithms
• Apps are purpose-built and not
componentized
Solution
Cytoscape
Cyberinfrastructure†1,2
• Enables communications
between applications and
Network Biology services
• Services can be diverse &
complex workflows
CyWidgets
• Enables GUI building blocks
based on common technology
• Based on Facebook’s React
Results
Status
• NDEx Valet in progress
• Deep integration of Internet-
shared networks (via NDEx)
• Delivery in web apps &
Cytoscape
• Current availability
• Simple network viewer
• NDEx network repository
• Enrichment, ID Translate &
other services
• Services in Java, Python,
Matlab, Javascript, etc
Future Work
• Add interfaces to cBioPortal,
GeneMANIA, et al
• More CyServices & CyWidgets
• Filtering & styles
• Table view & update
• Network analysis
• Graph & network
f
†Cyberinfrastructures (CI) f
References
An Internet-based research computing environment that supports data acquisition, data storage, data
management, data integration, data mining, data visualization, and other computing and information
processing services. Different stakeholders produce, consume, manage, and govern a CI, and their
requirements must be simultaneously met or else the integrity of the CI degrades.
1. Atkins D, Droegemier K, Feldman S, Garcia-Molina H, Klein M, Messerschmitt D, et al. Revolutionizing Science
and Engineering Through Cyberinfrastructure. Washington, CD: National Science Foundation. 2003.
2. National Science Foundation. Cyberinfrastructure Vision for 21st Century Discovery. Retrieved June 3, 2011 from
http://www.nsf.gov/pubs/2007/nsf0728/nsf0728.pdf. March 2007.
3. M. Arrott, B. Demchak, V. Ermagan, C. Farcas, E. Farcas, I. H. Krüger, and M. Menarini. Rich Services: The
Integration Piece of the SOA Puzzle. In Proceedings of the IEEE International Conference on Web Services
(ICWS), Salt Lake City, Utah, USA. IEEE, Jul. 2007, pp. 176-183.
4. Kiczales G, Lamping J, Mendhekar A, Maeda C, Lopes C, Loingtier J, et al. Aspect-Oriented Programming.
Proceedings of the Eur Conf on OOP. Helsinki, Finland: Springer-Verlag LNCS 1241.
5. Gamma E, Helm R, Johnson R and Vlissides J. Design Patterns: Elements of Reusable Object-Oriented Software.
Addison-Wesley Professional. 1995..
Techniques
Service Oriented
Architecture3-based
execution & deployment
• High reusability, availability,
reliability, scalability,
distributability, & testability
• CX interchange format as
aspect-oriented4 data structure
• Leverage standard patterns5:
strategy, messaging, routing, &
composite pattern
• Leverage role-based
interaction & choreography
techniques
Problem
Network Biology apps costly
to construct and reuse
Insight
Reusable components
enable rapid releases
• Browser-based apps leverage
library of powerful and evolving
widgets
• Service model enables
economical algorithm
publication & use
• Common interchange
simplifies reuse
Message Bus (Internet) – CX interchange formatMessage Bus (Internet) – CX interchange format
AnalyticsAnalyticsAnalyticsAnalytics
Application ServiceLegend:
NDEx
(Store/
Retrieve)
ID
Translate
Enrichment
Cytoscape
Desktop
Journal
Publishing
R/Python/
Matlab
Cytoscape
.js App
AnalyticsAnalyticsAnalyticsLayout
Cytoscape Cyberinfrastructure
Reusable cyWidgets
Reusable CyServices
backed by
CXCXCX