Version: 4.0.0

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.

Configuration#

  1. Add the following entry to your '''webconfig-model.xml''' file:

    <reportdisplayer javaClass="org.intermine.bio.web.displayer.CytoscapeNetworkDisplayer"
    jspName="model/cytoscapeNetworkDisplayer.jsp"
    replacesFields="interactions"
    placement="Interactions"
    types="Gene,Protein"/>

  2. 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.

  3. 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

Implementation#

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:

CytoscapeNetworkDisplayer.java

The report displayer class, gets a set of genes interacting with the report gene, in your case, the genes/proteins on the same pathway as the report gene/protein

CytoscapeNetworkDisplayer.jsp

The web page to display the network

CytoscapeNetworkService.java

Service class

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