You also don't need to file the patent before you publish in the US. You have one year from the day that you publish (or otherwise make it publicly known) to file the patent. After that, you lose the right to seek a patent. In other countries, you must file the patent before you publish.

I use software called SportTracks (http://www.zonefivesoftware.com/SportTracks/) that downloads data my Garmin GPS watch (and other devices too). The software is not open source but it is free and it is fantastic software -- much better than the software that comes with the watch. You can also write plugins for it. I haven't tried, but I'm pretty sure you could get any data you wanted out of the program.

PS. I have no affiliation with the company that makes the software. I'm just a very happy user of the software. I don't donate for free software very often but I did for this one.

The original post says that Red Hat is getting the patent for "defensive" use. What this means is that if someone sues Red Hat for patent infringement, Red Hat could potentially countersue for infringement of its own patent. Having such defensive patents helps discourage other companies (e.g., Microsoft) from suing you. Unfortunately, it doesn't help against patent trolls because trolls don't actually do anything so you can't sue them for patent infringement.

If Red Hat only published its invention, it would prevent people from getting patents on that subject matter but it would not help Red Hat against patent infringement suits on different technology

A patent doesn't give you the right to do anything. A patent only gives you the right to prevent other people from doing something. So getting a patent on this won't prevent other people for suing you for patent infringement. The patent could be useful from a defensive perspective. If you get sued by a competitor for patent infringement, then you could potentially countersue for infringement of your own patent. If you are sued by a troll, however, that won't help because trolls don't do anything and thus can't be sued for patent infringement.

Just publishing something makes it available as prior art and allows it to be used to prevent someone else from obtaining a patent. The prior art rules in the US are slightly different for publications and patents (look up 35 USC 102) but if there is any significant difference it probably wouldn't be worth the expense of obtaining the patent.

I don't think that is correct characterization of the Bayh-Dole Act (BDA). Before the BDA, the US govt could claim ownership of IP rights that were developed at universities with govt funds. After the BDA, the university gets to own the IP even if it was funded by the govt.

This has nothing to do with whether a student or a university owns the ideas created by a student. I imagine that universities make incoming students sign some kind of document that give the university over student inventions created using university resources.