[Biojava-l] Interested in the "cloudization" of BioJava

[Mic]

I have never tried it out by myself. In the next 3 years some GPUs will
have 20 000 cores.

Looking at this http://jogamp.org/jocl/www/ benchmark it is a huge
difference between GPU and CPU code. In Aparapi

http://blogs.amd.com/developer/2011/09/14/i-dont-always-write-gpu-code-in-java-but-when-i-do-i-like-to-use-aparapi/
you
write everything in Java.


On Fri, Apr 6, 2012 at 3:28 PM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Do you have any experience with that? I don;t have first hand, but
> from what I know GPU programming is very much hardware specific and
> not as nicely platform independent as Java...
>
> Andreas
>
> On Thu, Apr 5, 2012 at 6:37 PM, Mic <mictadlo at gmail.com> wrote:
> > maybe also to include OpenCL in order to able to run it on GPU.
> >
> > On Fri, Apr 6, 2012 at 1:49 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
> >>
> >> Hi Arthur,
> >>
> >> > 1) The first one and the one i find most interesting can be to try to
> >> > introduce the map-reduce framework to help to speed-up the pairwise
> >> > alignment in the creation of the muliple sequence alignment.
> >>
> >> That would be a possible application.
> >>
> >> > 2)If the input files are big enough, it can be interesting to perform
> >> > the
> >> > parsing on this files while using a distributed infrastructure to
> >> > speedup
> >> > the process,
> >>
> >> I am not sure if I have encountered such large files as of yet. Do you
> >> have an example?
> >>
> >> > 3)Another idea can be to try to have a hadoopify version of blast, in
> >> > which
> >> > the input file also can be splitted and then for each sequence in a
> >> > chunk,
> >> > the node would perform a local blast query.
> >>
> >> I agree, another possible application...
> >>
> >> What frameworks did you think about using?
> >>
> >> Andreas
> >> _______________________________________________
> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> >
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------
>