Presentation slides for cyREST project (RECOMB/Cytoscape Workshop 2014 in San Diego).

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