Keiichiro Ono and Barry Demchak

The Cytoscape Consortium

University of California, San Diego Department of Medicine

Cytoscape Untangles the Web

@cytoscape

Background

Data Bus (Internet)

Raw Data Files

Annotations

Experimental Data

Networks

Internal Databases Web Application using Cytoscape.js

Web Browsers

Public Data Services

NDExOther Web Services

PSICQUIC Services

External Computing Resources

For Graph Layout / Statistical Analysis / Data Preprocessing

Interactive Analysis Shells

RStudio

NumPySciPy

NetworkXIPython Notebook

File Hosting Services

Cytoscape Desktop

RESTful API Module for Cytoscape

Cytoscape Apps

For Data Sharing / Visualization

Solution: CyNetShare

Cytoscape Desktop

Input

Networks

XGMML

SIF

Data Preparation

CSV

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Database

TablesData Preparation

CSV

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Database

Output

Image Files Publication

Session Files Supplemental Data

Apps

Try it now!

- Large Network Data Sets - Demand for computational power and storage beyond desktop

- Collaborative Data Sharing - Web-based data sharing and interactive visualization

- Self Data Publishing - Need a way to publish network data without web programming

A First Step Towards the Cytoscape Cyberinfrastructure

Emerging Problems:

github.com/idekerlab/cy-net-share

CyNetShare: a first step towards Cyto-

scape Cyberinfrastructure, an integrated

environment for large-scale network data

analysis, visualization, and sharing.

Features:CyNetShare is a simple graph data visual-

ization sharing system generated with Cy-

toscape.

- Visualize any public network data files

- Visualizations are interactive

- Selectable Custom Visual Styles

- Runs on both desktops and tablets

- Visualizations are sharable via URL

- Open source

idekerlab.github.io/cy-net-share

Cytoscape is a de-facto

standard desktop appli-

cation for biological net-

work analysis and visual-

ization.

Cytoscape Cyberinfrastructure

Data Files

Annotations

Experimental Data

Networks Style JSON Network / Table JSON

Public Files

Cytoscape Desktop

Cytoscape Apps

Layout Data I/ONetwork Analysis

JSON I/O Module

CyNetShare

express

Web Browser

Cytoscape.js AngularJS