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cyREST: Cytoscape as a Service

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Presentation slides for cyREST project (RECOMB/Cytoscape Workshop 2014 in San Diego).

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cyREST: Cytoscape as a Service

  1. 1. cyREST Cytoscape as a Service REST Keiichiro Ono University of California, San Diego Cytoscape Core Developer Team Trey Ideker Lab
  2. 2. Problem
  3. 3. Systems Biology Biologists Computer Scientists Statisticians → Different Levels of Computing Skills
  4. 4. One Common Aspects They are busy!
  5. 5. They like All-in-One Solution / Tools
  6. 6. This MANIFESTO counters current trends in bioinformatics where institutes and companies are creating monolithic software solutions aimed mostly at end-users.
  7. 7. All-in-one, monolithic solution is great if and only if such tool exists for your workflows
  8. 8. cat genes.txt | uniq | wc -l
  9. 9. fetch | process | visualize
  10. 10. Open Source 200+ Apps De-facto Standard for Network Biology
  11. 11. Universe of Tools for Bioinformatics !
  12. 12. All tools for data analysis must work nicely together with other popular tools
  13. 13. REST
  14. 14. REST Goal - Cytoscape as a Service - Provide platform / language independent access to Cytoscape data models and functions
  15. 15. In-House Databases External Computing Resources Interactive Data Analysis Environments - Graph Layout - Statistical Analysis - Data Pre-processing RStudio - NumPy - SciPy - Pandas - NetworkX IPython Notebook Public Data Repository File / Code Hosting Services EBI RDF Platform PSICQUIC Services Other Bioinformatics Web Applications / Services - igraph - rCurl Command Line Tools > sed > awk > grep > curl Web Browsers Data Repository & Collaboration Service Data Bus (Internet) Your Workstation Cytoscape App Store Apps REST Core Cytoscape Desktop
  16. 16. Demo: Cytoscape Controlled from IPython Notebook REST http://nbviewer.ipython.org/gist/keiono/bd6ee462b5d5c152eb02
  17. 17. We are Hiring! Cytoscape Core Developers @UCSD
  18. 18. http://apps.cytoscape.org/apps/cyrest 2014 Keiichiro Ono kono@ucsd.edu

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