From the WebApollo development team:
We also have a public demo available so that you can try the software for yourself.
You might want to read the user guide before playing around with the software: WebApollo User Guide (PDF)
We'll be phasing out support for the old desktop Apollo in the next few months. This is the time to try out WebApollo and (hopefully) consider migrating to it.
Please post any questions or issues you may have to the Apollo/WebApollo mailing list.
Lastly, we'd like to give a huge thanks to Rob Buels from the JBrowse team for his invaluable contribution (and countless hours) in helping migrate WebApollo to the current version of JBrowse. Thanks!!!