cyREST provides platform-independent access to Cytoscape's data models and functions via REST. This allows different tools like RStudio, IPython notebooks, command line utilities, and web apps to interact with Cytoscape. The goal is for all bioinformatics tools to work seamlessly together. cyREST demonstrates controlling Cytoscape from an IPython notebook to enable interactive data analysis across environments and computing resources.

1. cyREST
Cytoscape as a Service
REST
Keiichiro Ono
University of California, San Diego
Cytoscape Core Developer Team
Trey Ideker Lab

2. Problem

3. Systems Biology
Biologists
Computer Scientists
Statisticians
→ Different Levels of Computing Skills

4. One Common Aspects
They are busy!

5. They like All-in-One
Solution / Tools

7. This MANIFESTO counters
current trends in
bioinformatics where
institutes and companies
are creating monolithic
software solutions aimed
mostly at end-users.

8. All-in-one, monolithic solution is
great if and only if such tool
exists for your workflows

9. cat genes.txt | uniq | wc -l

10. fetch | process | visualize

12. Open Source
200+ Apps
De-facto Standard
for Network Biology

13. Universe of Tools for Bioinformatics
!

14. All tools for data analysis
must work nicely together
with other popular tools

15. REST

16. REST Goal
- Cytoscape as a Service
- Provide platform / language independent access
to Cytoscape data models and functions

17. In-House Databases External Computing Resources
Interactive Data Analysis
Environments
- Graph Layout
- Statistical Analysis
- Data Pre-processing
RStudio
- NumPy
- SciPy
- Pandas
- NetworkX
IPython Notebook
Public Data Repository File / Code Hosting Services
EBI RDF Platform
PSICQUIC Services
Other Bioinformatics Web Applications / Services
- igraph
- rCurl
Command Line Tools
> sed
> awk
> grep
> curl
Web Browsers
Data Repository & Collaboration Service
Data Bus (Internet)
Your Workstation
Cytoscape App Store
Apps
REST
Core
Cytoscape Desktop

18. Demo:
Cytoscape Controlled
from IPython Notebook
REST
http://nbviewer.ipython.org/gist/keiono/bd6ee462b5d5c152eb02

19. We are Hiring!
Cytoscape Core Developers @UCSD

20. http://apps.cytoscape.org/apps/cyrest
2014 Keiichiro Ono
kono@ucsd.edu