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From Grant Ingersoll <gsing...@apache.org>
Subject Re: Anyone using ASF software in bio-informatics?
Date Wed, 10 Mar 2010 16:51:41 GMT
For starters:

Lucene:

http://gmod.org/wiki/Lucegene/

I also know of several big Pharma companies using it, but can't say names.  You can likely
guess, as they are instantly recognizable global brands.

TREC Genomics focused on info retrieval on genome data.  Lucene is used by NIST to setup the
relevance pool, etc.

I know many people that use it to search PubMed and the like and then correlate it with outputs
from internal documents/experiments/etc.  

Hadoop

One I saw: http://www.slideshare.net/cloudera/hw09-hadoop-for-bioinfomatics

I'm sure others in the Hadoop community can name some more.  I recall seeing some others go
by my radar, but don't see URLs.  These days, when your talking TBs of data for a single sequencing
run (or others), you need large scale data crunching capabilities

Mahout

I'd ask on mahout-user@lucene.a.o.  Nothing comes to mind, but we have a lot of lurkers there,
so it might hit home.  Mahout is a very likely candidate for this kind of work.

Some basic searching for "Lucene genetics", etc. will lead you to a good deal of results.

HTH,
Grant


On Mar 10, 2010, at 10:35 AM, Mattmann, Chris A (388J) wrote:

> Hey Grant,
> 
> Here here on that. Some of the same systems we use OODT on use Lucene as well, I'd be
happy to provide some feedback, let me know.
> 
> Cheers,
> Chris
> 
> 
> 
> On 3/10/10 7:18 AM, "Grant Ingersoll" <gsingers@apache.org> wrote:
> 
> Lucene is used in a number of places for bio-informatics.  Hadoop as well and I've heard
rumors of Mahout as well.  I can send pointers here or offline and also have some contacts
if you'd like.
> 
> -Grant
> 
> On Mar 10, 2010, at 4:55 AM, Ross Gardler wrote:
> 
>> I've been invited to keynote at the Open bio-informatics conference in July, wearing
my ASF hat. their invite said:
>> 
>> Is anyone here using ASF software in this space?
>> 
>> Ross
> 
> 
> 
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