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Cytoscape network viewer

This tool takes gene interaction data from Intermine and visualises it using cytoscape.js, a fabulous network visualisation tool. It replaces the flash-based CytoscapeWeb network viewer found in previous versions of the tool.


  1. add the following entry to your ‘’‘webconfig-model.xml’‘’ file:
<reportdisplayer javaClass=""
  1. If you host your own Intermine CDN, make sure to pull the most recent update, as the interaction displayer script is loaded via CDN, under js/intermine/gene-interaction-displayer.
  2. re-release your webapp and you should see the interaction displayer on gene report pages.

Data export format

The network visualisation can be exported as:

  • PNG
  • JPG
  • TSV
  • CSV


This tool accesses the list of gene interactions for the target gene by calling a web service, sorting the data into edges and nodes, and inserting them into an HTML canvas for display. It can also be used externally to the report page as a stand alone application. For external setup instructions, see the Cytoscape Intermine repo, and the standalone app demo page

Dependencies: This tool uses imjs to query the data, and imtables to display table data.

A short list of Java files found on the Intermine side:
the report displayer class, get a set of genes interacting with the report gene, in your case, the genes/proteins on the same pathway as the report gene/protein
the web page to display the network
service class