The document describes the CyREST platform for delivering complex and reproducible network biology workflows. CyREST uses a microservices architecture and Kubernetes deployment to provide scalable and repeatable Cytoscape applications and services. Currently available services include diffusion heat propagation, NDEx network repository, and cxMate universal CX adapter. Future work includes more cyberinfrastructure services, boosting network layouts, and availability on high performance infrastructure.

1. The New CyREST:
Economical Delivery of Complex, Reproducible
Network Biology Workflows
Barry Demchak (bdemchak@ucsd.edu), Keiichiro Ono, David Otasek & Eric Sage
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, GM103504 and W911-NF-14-1-0397.
Context
Powerful Cytoscape Apps
• Cytoscape is a defacto
standard network biology
platform
• ~325 Apps in app store, many
highly capable and popular
• Need platform for scalable
and repeatable workflows
• Workflow usage creates
value
Solution
Cytoscape Automation via
CyREST2
• REST-based
communications between
applications and services
• Component of Cytoscape
Cyberinfrastructure†
• Kubernetes for high
availability
Problem
Deliver Cytoscape
functions to scalable,
repeatable, auditable
workflows
Insight
Microservices deliver same
algorithm to all workflows
• Environment-specific
repository-based service
stubs promote:
• Encapsulation
• Discovery
• Ease of use
• Leverage REST frameworks
for high availability
Results
Currently Available
• Diffusion heat propagation
(Python)
• NDEx network repository
(Java)
• SANA (C++) in development
• cxMate universal CX adapter
• Kubernetes1 infrastructure
(Google & Amazon)
w/common logging2 &
metering3
• Stubs in Java, Python,
Javascript, etc
Future Work
• More CI services
• Boost network layouts
• Cytoscape network
layouts
• Enrichments
• Availability on NRNB-funded
high performance/availability
infrastructure
• Support long running
services, variable service
execution times
• Collaborations
Techniques
Service Oriented
Architecture-based
execution & deployment
• High reusability, availability,
reliability, scalability,
distributability, & testability
• CX interchange format as
aspect-oriented4 data
structure
• Leverage role-based
interaction & choreography
techniques
References
1. The Kubernetes Authors. kubernetes. Retrieved March 8, 2017 from http://kubernetes.io.
March 2017.
2. Elasticsearch. Elastic. Retrieved March 8, 2017 from http://www.elastic.co. March 2017.
3. Prometheus. Retrieved March 8, 2017 from http://prometheus.io. March 2017.
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.
†Cyberinfrastructures (CI)
An Internet-based research computing environment that supports data acquisition,
storage, management, integration, mining, 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.
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