I've spent a bit more time cleaning up my LaTeX template to make for fully automated web display. You can find it over on GitHub. This is currently set up for the canalization paper, but it should make a good basis for any sort of scientific manuscript. I've provided style sheets and a ruby script to cleanup output from TeX4ht into a presentable web version. This web version is hosted automatically through GitHub pages. Thus, by running a single script, the LaTeX source is compiled to HTML and with a GitHub push you can update the public web version of the manuscript. I hope this sort of approach will prove useful for collaborative writing.

It was easy to run this on my previous manuscripts written in LaTeX. I now have web versions of the tree topology and the global migration dynamics papers up.