In previous posts[1,2] I’ve described some of my experiences with Cytoscape including a short wishlist of features. In this latest release I was pleased to discover that a number of those issues have been addressed.
Exporting Networks As JSON
One of the first things on my wishlist was a simple way to export a Cytoscape network as JSON. This was driven in large part by some experimentation with the Cytoscape.js javascript library. I wanted to quickly assess the capabilities of the Cytoscape.js library without spending a lot of time manually building a network in JSON.
With the new functionality, you can now export your network as JSON, and then import it into your web page. This is a nice way to make your network viewable by colleagues and potential collaborators without forcing them to download and install the desktop version of Cytoscape.
To export the network, simply select File/Export/Network… from the menu. The Export Network dialog will then appear. Select the Cytoscape.js export format and enter the name of an output file.
You can also export the styles that you used in the desktop version of Cytoscape, by selecting File/Export/Style… When the Export Style dialog appears, select the Style for cytoscape.js export format and enter the name of the output file.
Exporting the network as HTML
The second thing I asked for was a way to further simplify this process by allowing the user to export the network using a simple HTML template. Rather than making the user create their own HTML page to display the data, you simply export the results as HTML and include the JSON in the content of the web page. This makes it easy for people with limited HTML skills to produce something that can be easily viewed in a browser. If you’re a wiz at HTML and templating, you can modify the template to produce fancier output.
Visualising JSON
Cytoscape supports 2 JSON formats — CytoscapeJS JSON, and CX. These formats bring with them the possibility that developers could use a text mining library to identify protein-protein interactions from literature, and write the results out as JSON so that they can be easily visualised in both the desktop and web versions of Cytoscape.