Rename short tags to ?php echo

The new server does not enable short tags by default.
Fix another short tag.
RNA 3D Hub has been published it is not beta

Remove the beta symbol as this has already been published and there is no reason
to mark it as beta anymore.
Add some js scripts

These scripts were loaded from rna.bgsu.edu without looking at the baseurl. This
was probably done so they can be easily shared across different sites, but this
means this site is not self-contained. This means the content is blocked when
running in the new test server. For this reason I'm adding the scripts to this
site.
Use short tags and load using baseurl

This way we don't point at outside resources making our site more self
contained.
Merge branch 'dev' of github.com:BGSU-RNA/RNA-3D-Hub into dev