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