cytoscape untangles the web: a first step towards cytoscape cyberinfrastructure (ismb 2014 netbio...
DESCRIPTION
Introduction to Cytoscape Cyberinfrastructure and a simple web application for network sharing called CyNetShareTRANSCRIPT
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