You are viewing a plain text version of this content. The canonical link for it is here.
Posted to general@incubator.apache.org by Ross Gardler <rg...@apache.org> on 2010/03/10 10:55:39 UTC
Anyone using ASF software in bio-informatics?
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: general-unsubscribe@incubator.apache.org
For additional commands, e-mail: general-help@incubator.apache.org
Re: Anyone using ASF software in bio-informatics?
Posted by Sally Khudairi <sk...@apache.org>.
Send the pointers here, please! It helps with my media/analyst outreach -- folks are *always* asking "where is Apache [PROJECTNAME] being used?"
Thanks,
Sally
--- On Wed, 3/10/10, Grant Ingersoll <gs...@apache.org> wrote:
> From: Grant Ingersoll <gs...@apache.org>
> Subject: Re: Anyone using ASF software in bio-informatics?
> To: members@apache.org
> Cc: general@incubator.apache.org
> Date: Wednesday, March 10, 2010, 10:18 AM
> 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: general-unsubscribe@incubator.apache.org
For additional commands, e-mail: general-help@incubator.apache.org
Re: Anyone using ASF software in bio-informatics?
Posted by James Carman <ja...@carmanconsulting.com>.
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 <gs...@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" <gs...@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
>>
>>
>>
>> ---------------------------------------------------------------------
>> To unsubscribe, e-mail: general-unsubscribe@incubator.apache.org
>> For additional commands, e-mail: general-help@incubator.apache.org
>>
>
>
> ---------------------------------------------------------------------
> To unsubscribe, e-mail: general-unsubscribe@incubator.apache.org
> For additional commands, e-mail: general-help@incubator.apache.org
>
>
---------------------------------------------------------------------
To unsubscribe, e-mail: general-unsubscribe@incubator.apache.org
For additional commands, e-mail: general-help@incubator.apache.org
Re: Anyone using ASF software in bio-informatics?
Posted by Grant Ingersoll <gs...@apache.org>.
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" <gs...@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
>
>
>
> ---------------------------------------------------------------------
> To unsubscribe, e-mail: general-unsubscribe@incubator.apache.org
> For additional commands, e-mail: general-help@incubator.apache.org
>
---------------------------------------------------------------------
To unsubscribe, e-mail: general-unsubscribe@incubator.apache.org
For additional commands, e-mail: general-help@incubator.apache.org
Re: Anyone using ASF software in bio-informatics?
Posted by "Mattmann, Chris A (388J)" <ch...@jpl.nasa.gov>.
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" <gs...@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
---------------------------------------------------------------------
To unsubscribe, e-mail: general-unsubscribe@incubator.apache.org
For additional commands, e-mail: general-help@incubator.apache.org
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Chris Mattmann, Ph.D.
Senior Computer Scientist
NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
Office: 171-266B, Mailstop: 171-246
Email: Chris.Mattmann@jpl.nasa.gov
WWW: http://sunset.usc.edu/~mattmann/
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Adjunct Assistant Professor, Computer Science Department
University of Southern California, Los Angeles, CA 90089 USA
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Re: Anyone using ASF software in bio-informatics?
Posted by Grant Ingersoll <gs...@apache.org>.
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: general-unsubscribe@incubator.apache.org
For additional commands, e-mail: general-help@incubator.apache.org
Re: Anyone using ASF software in bio-informatics?
Posted by Marshall Schor <ms...@schor.com>.
Apache UIMA is used by many projects in this space. Here are 2:
The Open Health Natural Language Processing (OHNLP) Consortium [1] says,
under "goals", "The Consortium promotes the open source UIMA framework
and SDK <http://incubator.apache.org/uima/> as the basis for biomedical
NLP systems. Applications created within UIMA consist of software
components (referred to as annotators) and their associated
configuration files and external resources. Within the framework, one
can also create complete pipelines composed of a sequence of annotators
and the data flow between them.
Another is the u-compare web-site, [2] which is an integrated text
mining/natural language processing system based on the UIMA Framework,
with annotators mainly in the Bio-informatics space
-Marshall
[1]
https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/Open_Health_Natural_Language_Processing_%28OHNLP%29_Consortium
[2] http://u-compare.org/
On 3/10/2010 6:29 AM, Tommaso Teofili wrote:
> Hi,
> As far as I know the Center for Computational Pharmacology at the University
> of Colorodo is using Apache UIMA for biomedical text processing.
> http://incubator.apache.org/uima/external-resources.html
> http://bionlp-uima.sourceforge.net/
> Cheers,
> Tommaso
>
> 2010/3/10 Francis De Brabandere <fr...@gmail.com>
>
>
>> Cropdesign (BASF) is using Apache Wicket for their internal experiment
>> statistics reporting website. But I don't work there any more...
>>
>> Cheers,
>> Francis
>>
>> On Wed, Mar 10, 2010 at 11:07 AM, Antonio Petrelli
>> <an...@gmail.com> wrote:
>>
>>> 2010/3/10 Ross Gardler <rg...@apache.org>:
>>>
>>>> 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?
>>>>
>>> You might try to ask the Commons Math people, I guess they are the
>>> right ones to ask:
>>> http://commons.apache.org/math/mail-lists.html
>>>
>>> Antonio
>>>
>>> ---------------------------------------------------------------------
>>> To unsubscribe, e-mail: general-unsubscribe@incubator.apache.org
>>> For additional commands, e-mail: general-help@incubator.apache.org
>>>
>>>
>>>
>>
>>
>> --
>> http://www.somatik.be
>> Microsoft gives you windows, Linux gives you the whole house.
>>
>> ---------------------------------------------------------------------
>> To unsubscribe, e-mail: general-unsubscribe@incubator.apache.org
>> For additional commands, e-mail: general-help@incubator.apache.org
>>
>>
>>
>
---------------------------------------------------------------------
To unsubscribe, e-mail: general-unsubscribe@incubator.apache.org
For additional commands, e-mail: general-help@incubator.apache.org
Re: Anyone using ASF software in bio-informatics?
Posted by Tommaso Teofili <to...@gmail.com>.
Hi,
As far as I know the Center for Computational Pharmacology at the University
of Colorodo is using Apache UIMA for biomedical text processing.
http://incubator.apache.org/uima/external-resources.html
http://bionlp-uima.sourceforge.net/
Cheers,
Tommaso
2010/3/10 Francis De Brabandere <fr...@gmail.com>
> Cropdesign (BASF) is using Apache Wicket for their internal experiment
> statistics reporting website. But I don't work there any more...
>
> Cheers,
> Francis
>
> On Wed, Mar 10, 2010 at 11:07 AM, Antonio Petrelli
> <an...@gmail.com> wrote:
> > 2010/3/10 Ross Gardler <rg...@apache.org>:
> >> 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?
> >
> > You might try to ask the Commons Math people, I guess they are the
> > right ones to ask:
> > http://commons.apache.org/math/mail-lists.html
> >
> > Antonio
> >
> > ---------------------------------------------------------------------
> > To unsubscribe, e-mail: general-unsubscribe@incubator.apache.org
> > For additional commands, e-mail: general-help@incubator.apache.org
> >
> >
>
>
>
> --
> http://www.somatik.be
> Microsoft gives you windows, Linux gives you the whole house.
>
> ---------------------------------------------------------------------
> To unsubscribe, e-mail: general-unsubscribe@incubator.apache.org
> For additional commands, e-mail: general-help@incubator.apache.org
>
>
Re: Anyone using ASF software in bio-informatics?
Posted by Francis De Brabandere <fr...@gmail.com>.
Cropdesign (BASF) is using Apache Wicket for their internal experiment
statistics reporting website. But I don't work there any more...
Cheers,
Francis
On Wed, Mar 10, 2010 at 11:07 AM, Antonio Petrelli
<an...@gmail.com> wrote:
> 2010/3/10 Ross Gardler <rg...@apache.org>:
>> 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?
>
> You might try to ask the Commons Math people, I guess they are the
> right ones to ask:
> http://commons.apache.org/math/mail-lists.html
>
> Antonio
>
> ---------------------------------------------------------------------
> To unsubscribe, e-mail: general-unsubscribe@incubator.apache.org
> For additional commands, e-mail: general-help@incubator.apache.org
>
>
--
http://www.somatik.be
Microsoft gives you windows, Linux gives you the whole house.
---------------------------------------------------------------------
To unsubscribe, e-mail: general-unsubscribe@incubator.apache.org
For additional commands, e-mail: general-help@incubator.apache.org
Re: Anyone using ASF software in bio-informatics?
Posted by Antonio Petrelli <an...@gmail.com>.
2010/3/10 Ross Gardler <rg...@apache.org>:
> 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?
You might try to ask the Commons Math people, I guess they are the
right ones to ask:
http://commons.apache.org/math/mail-lists.html
Antonio
---------------------------------------------------------------------
To unsubscribe, e-mail: general-unsubscribe@incubator.apache.org
For additional commands, e-mail: general-help@incubator.apache.org
Re: Anyone using ASF software in bio-informatics?
Posted by "Mattmann, Chris A (388J)" <ch...@jpl.nasa.gov>.
Hi Ross,
Though we just started and technically aren¹t officially endorsed ASF
software, OODT has been used for 7+ years to implement a national virtual
data system for the U.S. National Cancer Institute¹s Early Detection
Research Network (EDRN), a network of 40+ institutions sharing biomarker,
study (protocol) information, raw science data and specimens amongst the
laboratories and information systems of those participating in the EDRN.
Cheers,
Chris
On 3/10/10 1:55 AM, "Ross Gardler" <rg...@apache.org> 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: general-unsubscribe@incubator.apache.org
> For additional commands, e-mail: general-help@incubator.apache.org
>
>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Chris Mattmann, Ph.D.
Senior Computer Scientist
NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
Office: 171-266B, Mailstop: 171-246
Email: Chris.Mattmann@jpl.nasa.gov
WWW: http://sunset.usc.edu/~mattmann/
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Adjunct Assistant Professor, Computer Science Department
University of Southern California, Los Angeles, CA 90089 USA
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
---------------------------------------------------------------------
To unsubscribe, e-mail: general-unsubscribe@incubator.apache.org
For additional commands, e-mail: general-help@incubator.apache.org