Re: [Seqan-dev] seqan-dev Digest, Vol 59, Issue 11

[Theodore Omtzigt <theo@stillwater-sc.com>]

This is fantastic! I am a big fan of Seqan and khmer and we have been
trying to figure out how to hardware accelerate khmer, in particular,
the digital renormalization step. Seqan's meta-programmed API is meant
to abstract away the underlying 'algorithm' and is thus the perfect
interface for hardware accelerated systems. This collaboration would
solve the hardware acceleration dilemma of too many software packages
with too many APIs and with too little structure. Hardware acceleration
for genomics/proteomics has such a phenomenal upside since the core
operators, small alphabets, string operators, string search, Bloom
filters, hash functions, etc. are so poorly supported by general purpose
CPUs and GPUs that custom hardware can easily get to 100x speedups. The
biggest problem is the broad and unstructured software landscape. Seqan
as a common library would go a long way to resolve the software
proliferation problem.

Let me know if there is anything we can help with.

Theo
CEO
Stillwater Supercomputing, Inc.
http://www.stillwater-sc.com/
 
On 11/22/2014 6:00 AM, seqan-dev-request@lists.fu-berlin.de wrote:
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> Today's Topics:
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>    1. Hello from the khmer project! (C. Titus Brown)
>    2. Re: Hello from the khmer project! (C. Titus Brown)
>    3. Re: Hello from the khmer project! (Reinert, Knut)
>    4. Re: Hello from the khmer project! (C. Titus Brown)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 21 Nov 2014 09:38:57 -0500
> From: "C. Titus Brown" <ctb@msu.edu>
> To: seqan-dev@lists.fu-berlin.de
> Cc: "Michael R. Crusoe" <mcrusoe@msu.edu>
> Subject: [Seqan-dev] Hello from the khmer project!
> Message-ID: <170A0CA2-59F1-41A7-A998-317B81059EF0@msu.edu>
> Content-Type: text/plain; charset=windows-1252
>
> Dear SeqAn,
>
> just a brief intro and heads up ? we have a PR for the khmer project,
>
> https://github.com/ged-lab/khmer/pull/642
>
> that switches over to using SeqAn for our sequencing parsing.  It will most likely be merged for the next major release, v1.2
>
> If you?re unfamiliar with khmer, here?s an intro paper: http://files.figshare.com/1194736/wssspe13_ged.pdf
>
> At some point we hope to be chatting with you more closely about issues that include streaming support and threading.  In the meantime please rely on us for any letters of support or collaboration that you can use!
>
> I?m the PI on the main khmer grant, and Michael Crusoe, CCed, is the lead khmer developer and community liaison.
>
> best,
> ?titus
> -----------------------------
>
> Dr. C. Titus Brown, ctbrown@ucdavis.edu
> Visiting Associate Prof., UC Davis
> http://ged.msu.edu/
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 21 Nov 2014 06:45:28 -0800
> From: "C. Titus Brown" <ctb@msu.edu>
> To: seqan-dev@lists.fu-berlin.de
> Cc: "Michael R. Crusoe" <mcrusoe@msu.edu>
> Subject: Re: [Seqan-dev] Hello from the khmer project!
> Message-ID: <20141121144528.GB32133@idyll.org>
> Content-Type: text/plain; charset=us-ascii
>
> And, uhh, p.s. -- thanks for all the work on SeqAn! :)  Sorry, forgot to say
> that!
>
> cheers,
> --titus
>
> On Fri, Nov 21, 2014 at 09:38:57AM -0500, C. Titus Brown wrote:
>> Dear SeqAn,
>>
>> just a brief intro and heads up ? we have a PR for the khmer project,
>>
>> https://github.com/ged-lab/khmer/pull/642
>>
>> that switches over to using SeqAn for our sequencing parsing.  It will most likely be merged for the next major release, v1.2
>>
>> If you?re unfamiliar with khmer, here?s an intro paper: http://files.figshare.com/1194736/wssspe13_ged.pdf
>>
>> At some point we hope to be chatting with you more closely about issues that include streaming support and threading.  In the meantime please rely on us for any letters of support or collaboration that you can use!
>>
>> I?m the PI on the main khmer grant, and Michael Crusoe, CCed, is the lead khmer developer and community liaison.
>>
>> best,
>> ?titus
>> -----------------------------
>>
>> Dr. C. Titus Brown, ctbrown@ucdavis.edu
>> Visiting Associate Prof., UC Davis
>> http://ged.msu.edu/
>> _______________________________________________
>> seqan-dev mailing list
>> seqan-dev@lists.fu-berlin.de
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