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From James Carman <ja...@carmanconsulting.com>
Subject Re: Anyone using ASF software in bio-informatics?
Date Wed, 10 Mar 2010 18:25:44 GMT
My client is using a variety of Apache projects in their
bio-informatics work.  We're using Wicket, a lot of the Commons stuff
(VFS is a *big* one), Lucene, HttpClient, Subversion, Velocity, etc.
We looked into using Hadoop, but decided to go with Mallet instead.
Hadoop was a little overly-complicated for our needs.

On Wed, Mar 10, 2010 at 11:51 AM, Grant Ingersoll <gsingers@apache.org> wrote:
> 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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>
>
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