Keiichiro Ono and Barry Demchak
The Cytoscape Consortium
University of California, San Diego Department of Medicine
Cytosc...
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Cytoscape Untangles the Web: a first step towards Cytoscape Cyberinfrastructure (ISMB 2014 NetBio SIG Poster)

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Introduction to Cytoscape Cyberinfrastructure and a simple web application for network sharing called CyNetShare

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Cytoscape Untangles the Web: a first step towards Cytoscape Cyberinfrastructure (ISMB 2014 NetBio SIG Poster)

  1. 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

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