CCMI - Presentation

UC San Diego NDEx Workshop

Registration will begin in 2019.

The Network Data Exchange (NDEx) Project provides an open-source framework where scientists and organizations can share, store, manipulate and publish biological network knowledge. The NDEx Project maintains a free, public website. Users can also run local copies of the NDEx Server software in cases where the stored networks must be kept in a secure environment (such as for HIPAA compliance) or where high application loads are incompatible with a shared public resource. 

In this workshop, we will first cover essential topics such as: 

  • How create account and group pages
  • How to load their networks to NDEx in several different ways, such as: notebooks, Cytoscape, Other NDEx-enabled loaders
  • How to control network privacy and the degree of indexing for searches

In the second part, we will focus on topics related to disseminating networks:

  • Learn how to beautify networks by: Adding annotations, Adding a style and a layout using Cytoscape, Collecting them in Sets
  • Learn how to use shareable URLs
  • Learn how/when to Showcase networks and network sets
  • Learn how to request a DOI

Finally, we will go through the full workflow showing users how to use NDEx in a peer-reviewed publication.


  • General knowledge of molecular biology and genomics
  • Laptop with a web browser. 


  • Dexter Pratt (, Project Director
  • Rudi Pillich (, Application Manager

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