I like the concept of this, this could be used as a way to teach computer modelling. However, for some reason I am unable to add transitions between two states. I've tried on Firefox, Chrome and Edge but it doesn't seem to work for some reason. Hope it gets resolved soon, best of luck with your thesis :)

Edit: I'm using Windows 10
Edit 2: One thing I found that helps mitigate the issue is making sure that the nodes are very close to each other and moving the mouse very quickly. The issue is also present on your website
Edit 3: The newest update fixes the issue I was having, but introduces a new one which crashes the frame due to trying to draw a node which does not exist. The line that crashes is line 48 in canvas.js. For me, deleting that line circumvents the crash and allows for transitions to be made properly. Here's a link for what the crash looks like: https://www.newgrounds.com/dump/item/bc2dec00039ad28d790357259a1dbc73