cyREST: Cytoscape as a Service
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Transcript of cyREST: Cytoscape as a Service
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cyREST Cytoscape as a Service
REST
Keiichiro OnoUniversity of California, San DiegoCytoscape Core Developer Team
Trey Ideker Lab
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Problem
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Biologists Computer Scientists
Statisticians → Different Levels of Computing Skills
Systems Biology
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One Common Aspects
They are busy!
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They like All-in-One Solution / Tools
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This MANIFESTO counters current trends in bioinformatics where institutes and companies are creating monolithic software solutions aimed mostly at end-users.
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All-in-one, monolithic solution is great if and only if such tool exists for your workflows
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cat genes.txt | uniq | wc -l
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fetch | process | visualize
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Open Source 200+ Apps
De-facto Standard for Network Biology
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Universe of Tools for Bioinformatics
!
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All tools for data analysis must work nicely together with other popular tools
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REST
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- Cytoscape as a Service - Provide platform / language independent access
to Cytoscape data models and functions
GoalREST
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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
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Demo: Cytoscape Controlled
from IPython NotebookREST
http://nbviewer.ipython.org/gist/keiono/bd6ee462b5d5c152eb02
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We are Hiring! Cytoscape Core Developers @UCSD