Towards the Cytoscape Cyberinfrastructure

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Ongoing projects and future plan for the Cytoscape Cyberinfrastructure project

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Towards the Cytoscape Cyberinfrastructure

  1. 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. 2. Outline Ongoing Projects: ! ! • Interactive graph visualization sharing web application • RESTful API for Cytoscape
  3. 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. 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. 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. 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. 7. Web Browser
  8. 8. Alpha Version Web Site: http://idekerlab.github.io/cy-net-share/
  9. 9. 2014 Keiichiro Ono kono@ucsd.edu

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