Tuesday, May 19, 2015 12:31:33 PM
Genomic Analysis involves branchy code - it does not lend itself to FP/GPU processing. I don't see how you get big gains with HPC unless you're talking about integer computing and my impression is that HPC is about FLOPs.
The presentation doesn't really provide solutions to the political and software problems. It appears that they provide consulting services on the hardware/storage/network side where they can give you a solution that provides good performance but solving the other issues are related to people and culture and that's a lot harder to change.
The guy in the video has the Bio guys vs IT and he said that the Bio guys win - that's the politics of life sciences right now and I don't think that this is going to change anytime soon.
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There's a industry standard piece of open source code used a lot that tries to find A U B - (A intersection B).
It reads through B and creates an index. Then it reads through A doing key lookups on the B index and writes out records that aren't in B.
It then reads through A and creates an Index. Then it reads through B doing key lookups on the A index and writes out records that aren't in A.
Anyone with an undergraduate CS degree would look at this and ask: 'Are you Kidding?"
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