Ongoing projects and future plan for the Cytoscape Cyberinfrastructure project

1. Towards the Cytoscape Cyberinfrastructure
Keiichiro Ono
Cytoscape Core Developer Team
UC, San Diego Trey Ideker Lab / National Resource for Network Biology
!
7/7/2014 Lab Meeting

2. Outline
Ongoing Projects:
!
!
• Interactive graph visualization
sharing web application
• RESTful API for Cytoscape

3. Cytoscape Cyberinfrastructure
• Integrate Cytoscape eco-
system into larger workflows
• Data and computing
resources will be shared
over the network
• Utilizes standard tools, such
as RStudio / IPython
Notebook, as the primary
workbench for advanced
users
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

4. 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

5. CyNetShare:
A simple web application to
share network visualization
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
CyGraphShare
express
Web Browser
Cytoscape.js AngularJS

6. 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
CyGraphShare
express
Cytoscape.js AngularJS

7. Web Browser

8. Alpha Version Web Site:
http://idekerlab.github.io/cy-net-share/

9. 2014 Keiichiro Ono
kono@ucsd.edu