Automata
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Add help/shortcuts button
You should add a help button which shows the available keyboard shortcuts (or add them as buttons on the toolbar).
At the moment it's practically impossible for a new user to find out how to mark a state as initial (i) or accepting, which he will be needing if he's using the website.
Agreed. Need to come up with a good way to put those in the UI. Other helpful shortcuts are the arrow keys for the runner which should also be mentioned.
Gives me an idea. http://4.bp.blogspot.com/-VQxu0jhRbqU/TcSf-REO-BI/AAAAAAAAAA0/gC4JkR2v-6A/s1600/paperclip.jpg