Short article on the growth of accelerators in life science work

I am quoted in there quite a bit. This is GenomeWeb magazine covering the many aspects of what is called Bio-IT. One of the massive problems around Bio-IT is moving data (go figure), storing data (again …), and processing data. I’ve heard some people provide arguments as to why accelerators won’t play there … and then I hear from people who have a limited time to get their work done, subject to an ever growing mound of data. Their only real hope are accelerators. I suspect we will see more of these going on. BTW: what got me looking at that was seeing people searching Google for GPU-HMMer from NVidia press releases … for our competitors. Its amusing … at some level …

BTW, I should point out that, due to a trademark just granted Sean Eddy at Janelia farms, anyone (including us) who have something that “isn’t HMMer”, will either have to a) rename it to avoid confusing the mark, or b) simply stop distributing it. The rationale behind this is explained in this post. I take issue with the discussion on forking, as from what I understand it, the team tried to submit the changes back to the core team. They were not accepted as I remember. So, it is quite likely that our patches will be resubmitted. Question of whether or not they will be accepted is another story. However, I should point out that in the GPL world, such use of trademark with GPL to control distribution and what gets called the product, usually winds up with something not unlike what has happened to Mozilla. In Debian, Ubuntu, and a myriad of other distributions, which have applied styling, or security patches, bug fixes, etc. you are not legally allowed to call that product Mozilla *. So Icecat has been born. And Icefox. And … You get the idea. Basically, the effort that went into “protecting” the trademark simply pissed off the developers adding value and they forked it. Now there are multiple, partially incompatible versions of mozilla, which aren’t really mozilla for trademark reasons, but are in truth, mozilla. And mozilla corp has … well … not just egg on its face, but lost some of its … mojo … for lack of a better term, in the OSS community due to this. I fear that may be the outcome here. Others have written extensively on this. It is a far more common outcome than you might think. I am wondering if there is a better approach here. Defining the algorithm correctness as a measure of whether or not you may use the trademark. That is, if it doesn’t pass all the tests, you can’t call it the same thing. Because it isn’t. And have the test suite adapt over time. So that the things to test don’t aim just for the test suite. But it’s not my decision to make. I am hoping for a good outcome on this, that lets everyone contribute to HMMer going forward.