Our department which currently runs a 1000+ core machine and 2500+ core machine for MD simulations is still waiting on jumping onto the Amazon/Cloud bandwagon mostly because it's still not cheaper than owning a cluster for a few years. Granted, being at a large research university means they're not the only clusters on campus and there's an infrastructure already in place to maintain it.
In terms of speed, I would assume Amazon to be faster than most clusters since they probably offer the latest and greatest computers. Lastly, MD is an embarassingly parallel problem (don't ask me how it is) so latency isn't a major issue.
The main message I got from talking to people involved in systems biology is that we don't even get qualitative agreement between simulation and experiment, nevermind any sort of quantitative data, on extremely well studied systems like the lac operon. It seems like we're at least 25 years away from decent models.
I think the most promising method is DNA nanopore tech (http://en.wikipedia.org/wiki/Nanopore_sequencing). It doesn't require labeling, amplification, and, I suppose, could be done in vitro. Maybe that's what the article is referring to?
I'm not 100% sure on this, but it also may be much more accurate than current methods since it doens't suffer from many of the biases present in current next-gen sequencers.
I'm working on my PhD in computational biophysics and this is truly an exciting time to be doing cutting edge bio-stuff like this. Sometimes I think people will look back on the 2010's and say this was like Silicon Valley in the 70s and 80s... the beginning of something big.
My problem with the Timeline is that I refuse to give Facebook any more information than they already have on my life. I can't stand when people talk about how they went back in time on their Timeline, grooming it with important life events and baby photos. Just another vector to sell us more stuff, I guess.
In terms of speed, I would assume Amazon to be faster than most clusters since they probably offer the latest and greatest computers. Lastly, MD is an embarassingly parallel problem (don't ask me how it is) so latency isn't a major issue.