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.
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"/>
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
Re-release your webapp and you should see the interaction displayer
on gene report pages.
The network visualisation can be exported as:
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
A short list of Java files found on the Intermine side:
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
The web page to display the network