Logic modeling with CellNOptR in Cytoscape

A few months ago, I started work as a post-doc at the Systems Biomedicine group of the EBI. Our group makes heavy use of logical modelling as a means to understand how pathways work. For me, the most interesting thing about logical modelling is that it shows a very dynamic picture of how a pathway changes over time. By comparison, the pictures that you get from WikiPathways are very static.

We have our own logical modelling software called CellNetOptimizer (a.k.a CellNOptR). One of my current projects is to make the CellNOptR software more interoperable with popular tools such as Cytoscape. To this end, Emanuel Gonçalves, a master student in our group, has implemented a plug-in that makes CellNOptR available from Cytoscape. Work on the plug-in is progressing nicely. Below you see the video that he made, to show off some of the features of this new plug-in.


In the video, you see how you can:

  • open a network
  • Start the CellNOptR wizard
  • Import and view experimental data
  • Train the network against the data
  • View the optimized network in Cytoscape

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