I have an Occulus Rift DK2 that I wrote some software to convert ChIP-Seq peak/tracks to Minecraft maps, and then walk around it in 3D (which was already possible). I learnt a few things:

1) 3D on the occulus is really bad. If anyone tells you otherwise, they are just too proud to admit they paid a lot of money for a phone screen without the phone. Maybe the newer versions are better, but certainly the DK2 was awful. You can see the black lines between the pixels (the screen door effect), and the depth of the Z axis is about half of anything you might see in a 3D movie. It's a new experience, but not a particularly good one. Also it will make you throw up so much you'll think you're 21 again - particularly if you develop software on it.

2) These days it only really plays nice on Windows. Last time i checked they dropped driver support for everything else.

3) Interacting with 3D objects with a mouse and keyboard is about as much fun as interacting with a regular computer with just a scroll wheel and keyboard. Until 3D inputs like the the STEM Sixense can actually be bought (http://sixense.com), interacting with anything in 3D is like having to thread cotton through the eye of a needle, whilst the needle is constantly rotating because it inexplicably hates you.

4) There is absolutely no benefit to looking at ChIP-Seq data in Minecraft. There might be something in using biological data to create maps in games, but 2D data should stay in 2D. Even if you have 2 variables of data and a third time variable, you are better off keeping it as 2D movie than a 3D landscape. In applications like Hi-C I think there's a lot of potential, particularly if you then layer on other signals like RNA/Chip intensity as colour or volumes, but on the whole biological data does not fit 3D all that well, unfortunately. I could give a whole lecture on why, but it boils down to two things: 1) Humans don't see in 3D, they see in double-2D, and and you have to actively distort data to make it render correctly in the human brain. 2) The brain doesn't care much about the third dimension. It cares far more about colour, shape, and speed. If you want to 'see' the sense in the data, you are better off exploiting these features first.
Only in inherently 3D data is 3D really worth the time.

Also try to stay away from the terms like "augmented reality" and other such buzz words. There's a lot of undeserved hype over 3D, and really terms like augmented reality only make sense if you are a PhD student who spends so much time looking at data that you can justifiably redefine your definition of reality ;)

You've clearly never seen one of these sitting abandoned, at great expense, littering a university campus: https://en.wikipedia.org/wiki/Cave_automatic_virtual_environment

I saw protein docking simulations running on that about 10 years go. Although it mostly got used for playing Quake3.

I would say 3D protein structure investigations would be a very interesting application.

Take a 3D structure, walk around it, grab it, push and pull on it, try to unfold it, then let go, see how it folds back,

I always have a hard time with 3D visualizers in that it is difficult to grab exactly what you want and move it where you want it to be.

We're building an interactive 3D+time atlas of a dividing human cell (see a screencast of our HTML5/webGL prototype here (QuickTime movie), note that this is NOT a simulation but is based on real data). At some point someone may be interested in making this a real 3D interactive environment. However, I think people are generally not ready for real 3D yet. For one thing, there are no clear conventions on how to represent things and interact with them in virtual 3D. Then there's the fact that there's actually not so much real 3D data being produced in biology (unless one counts all the multidimensional -omics data). As mentioned before, 3D visualization of protein structures has been tried before (see here for example) but I don't think it's become the norm, maybe because it's still too cumbersome to use or that there's no real benefit to it or it is not good enough. This should not deter you from trying though but choosing a compelling use-case would be key to success.

I am mildly surprised not to see mentions of the 3D virtual worm work: http://blog.openhelix.eu/?p=13872

And just the other day I was watching this video that i thought was fascinating;

Like the cell division stuff, I think there's neat things to be tackled at the cell + developmental front.

Another area that I think is closer is 3D tissue structure stuff, like this printed artery. http://advances.sciencemag.org/content/1/9/e1500758

I can imagine looking at how mutations, or different amounts of structural proteins, or different substrates, impact any of these things and being neat to watch in new ways.

Hi, I'm not sure whether this answers your question exactly, but I had a similar thought in mind a few weeks ago. There's actually an app called Augmented Reality that lets you put any 3D model into the world, viewable by phone or tablet as long as you have an appropriate surface to track it onto.

I wrote a blog post about my attempts with it using R and data from the 1000 genomes project.