You can see an example of the existing pathway browser here. In particular, what we want to replace is the pane showing the actual pathway diagram. The other two panes, showing the hierarchy (on the left) and the text details (at the bottom) are fine and we would be happy to leave them as they are.
This project should address a big issue: how to use the current version of Cytoscape Web to draw our pathway diagrams. The current version of CytoscapeWeb can be used to draw pairwise simple interaction network only. Though we have done some work to use Cytoscape to draw our pathway diagrams, the results actually are far from ideal.
A prototype system was implemented using regular Cytoscape some time ago, you can find out more about this here. This may give you some hints on how to adapt CytoscapeWeb so that it can be used to display reactions and pathways, rather than interactions.