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cyREST Cytoscape as a Service
REST
Keiichiro OnoUniversity of California, San DiegoCytoscape Core Developer Team
Trey Ideker Lab
Problem
Biologists Computer Scientists
Statisticians → Different Levels of Computing Skills
Systems Biology
One Common Aspects
They are busy!
They like All-in-One Solution / Tools
This MANIFESTO counters current trends in bioinformatics where institutes and companies are creating monolithic software solutions aimed mostly at end-users.
All-in-one, monolithic solution is great if and only if such tool exists for your workflows
cat genes.txt | uniq | wc -l
fetch | process | visualize
Open Source 200+ Apps
De-facto Standard for Network Biology
Universe of Tools for Bioinformatics
!
All tools for data analysis must work nicely together with other popular tools
REST
- Cytoscape as a Service - Provide platform / language independent access
to Cytoscape data models and functions
GoalREST
Interactive Data Analysis Environments
In-House Databases External Computing Resources
- Graph Layout- Statistical Analysis- Data Pre-processing
RStudio
- NumPy- SciPy- Pandas- NetworkX
IPython Notebook
File / Code Hosting ServicesPublic Data Repository
PSICQUIC Services
EBI RDF Platform
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
Cytoscape Desktop
Apps
Core
REST
Demo: Cytoscape Controlled
from IPython NotebookREST
http://nbviewer.ipython.org/gist/keiono/bd6ee462b5d5c152eb02
We are Hiring! Cytoscape Core Developers @UCSD
2014 Keiichiro Ono kono@ucsd.edu
http://apps.cytoscape.org/apps/cyrest
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