It's excellent to see this discussion pop up again. Kudos to Joe (Larry?) for keeping things close to the road. The key thing about FPGAs from my perspective is that FPGA boards are not general purpose compute engines. It's not a one to one substitution from FPGAs to compute nodes. They are a component that can accelerate a particular sort of computation. They no more solve the general purpose computing problem than "faster disk drives" solves data bottlenecks. Therefore, the question is almost never "should I get an FPGA OR a cluster." It's usually "Would a couple of FPGA boards make my cluster more useful?" The core question is "is my cluster spending most of its time crunching on some algorithm for which an accelerator board exists?" If so, FPGA systems may be a decent investment. TimeLogic's marketing material, back when I last saw it, focused on the fact that the rest of your cluster would be free do do other stuff, if only you were able to move all the BLAST, HMM, and Smith Waterman searches off to a special purpose resource. There is an ancillary question: "Am I willing to make my computing system slightly more complex, and possibly dedicate resources to maintaining and exploiting this complexity?" Depending on how much local resource a group is willing to dedicate to their custom systems, lots of interesting tools become quite appealing. My opinion on truly "general purpose" FPGAs is that they're not well suited for *direct* purchase by most life sciences cluster users. This is because *most* of the bio-cluster people aren't all that interested in spending money developing or optimizing custom codes. Most of the folks I work with are not that interested in profiling, re-compiling, optimizing, tuning, etc. Some certainly are, and many of those people read this list. So, there is certainly an opportunity for companies to make optimized / accelerated versions of some standard applications and re- sell them, which brings us back to where the thread began. -Chris Dwan