Cytoscape is a standard desktop application for biological network analysis and visualization, but emerging problems include large network datasets that exceed desktop capabilities, demand for collaborative data sharing, and the need for self-publishing networks without web programming skills. CyNetShare is a first step towards a Cytoscape cyberinfrastructure that allows visualization of public network data files through an interactive web application using Cytoscape.js, sharing of visualizations via URL, and runs on both desktops and tablets.

1. 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
NDEx
Other Web Services
PSICQUIC
Services
External Computing Resources
For Graph Layout / Statistical Analysis / Data Preprocessing
Interactive Analysis Shells
RStudio
NumPy
SciPy
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
Database
TablesData Preparation
CSV
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/O
Network
Analysis
JSON I/O
Module
CyNetShare
express
Web Browser
Cytoscape.js AngularJS