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 <[email protected]> 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 [email protected]. 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" <[email protected]> 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 >> >> >> >> --------------------------------------------------------------------- >> To unsubscribe, e-mail: [email protected] >> For additional commands, e-mail: [email protected] >> > > > --------------------------------------------------------------------- > To unsubscribe, e-mail: [email protected] > For additional commands, e-mail: [email protected] > > --------------------------------------------------------------------- To unsubscribe, e-mail: [email protected] For additional commands, e-mail: [email protected]
