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Posted to hdfs-user@hadoop.apache.org by Felipe Gutierrez <fe...@gmail.com> on 2013/08/16 21:38:36 UTC
e-Science app on Hadoop
Hello,
Does anybody know an e-Science application to run on Hadoop?
Thanks.
Felipe
--
*--
-- Felipe Oliveira Gutierrez
-- Felipe.o.Gutierrez@gmail.com
-- https://sites.google.com/site/lipe82/Home/diaadia*
Re: e-Science app on Hadoop
Posted by Jeremy Lewi <je...@lewi.us>.
Contrail is a DeNovo Assembler which uses Map Reduce and Avro.
http://en.wikipedia.org/wiki/Contrail
As part of this effort, we developed an efficient FastQ InputFormat reader
for processing FastQ files in parallel.
http://kbase.science.energy.gov/about/about/ is an effort by the DOE to
create a modular platform for bioinformatics. I think its using hadoop
under the hood for job scheduling and other functions.
Dr. Michael Schatz (http://www.cbcb.umd.edu/~mschatz/) who is one of the
developers of Contrail has a bunch of work on porting bioinformatics to
Hadoop.
J
On Fri, Aug 16, 2013 at 2:42 PM, Jay Vyas <ja...@gmail.com> wrote:
> there are literally hundreds. Here is a great review article for how
> mapreduce is used in the bioinformatics algorithms space:
>
> http://www.biomedcentral.com/1471-2105/11/S12/S1
>
>
> On Fri, Aug 16, 2013 at 3:38 PM, Felipe Gutierrez <
> felipe.o.gutierrez@gmail.com> wrote:
>
>> Hello,
>>
>> Does anybody know an e-Science application to run on Hadoop?
>>
>> Thanks.
>> Felipe
>>
>> --
>> *--
>> -- Felipe Oliveira Gutierrez
>> -- Felipe.o.Gutierrez@gmail.com
>> -- https://sites.google.com/site/lipe82/Home/diaadia*
>>
>
>
>
> --
> Jay Vyas
> http://jayunit100.blogspot.com
>
Re: e-Science app on Hadoop
Posted by Jeremy Lewi <je...@lewi.us>.
Contrail is a DeNovo Assembler which uses Map Reduce and Avro.
http://en.wikipedia.org/wiki/Contrail
As part of this effort, we developed an efficient FastQ InputFormat reader
for processing FastQ files in parallel.
http://kbase.science.energy.gov/about/about/ is an effort by the DOE to
create a modular platform for bioinformatics. I think its using hadoop
under the hood for job scheduling and other functions.
Dr. Michael Schatz (http://www.cbcb.umd.edu/~mschatz/) who is one of the
developers of Contrail has a bunch of work on porting bioinformatics to
Hadoop.
J
On Fri, Aug 16, 2013 at 2:42 PM, Jay Vyas <ja...@gmail.com> wrote:
> there are literally hundreds. Here is a great review article for how
> mapreduce is used in the bioinformatics algorithms space:
>
> http://www.biomedcentral.com/1471-2105/11/S12/S1
>
>
> On Fri, Aug 16, 2013 at 3:38 PM, Felipe Gutierrez <
> felipe.o.gutierrez@gmail.com> wrote:
>
>> Hello,
>>
>> Does anybody know an e-Science application to run on Hadoop?
>>
>> Thanks.
>> Felipe
>>
>> --
>> *--
>> -- Felipe Oliveira Gutierrez
>> -- Felipe.o.Gutierrez@gmail.com
>> -- https://sites.google.com/site/lipe82/Home/diaadia*
>>
>
>
>
> --
> Jay Vyas
> http://jayunit100.blogspot.com
>
Re: e-Science app on Hadoop
Posted by Jeremy Lewi <je...@lewi.us>.
Contrail is a DeNovo Assembler which uses Map Reduce and Avro.
http://en.wikipedia.org/wiki/Contrail
As part of this effort, we developed an efficient FastQ InputFormat reader
for processing FastQ files in parallel.
http://kbase.science.energy.gov/about/about/ is an effort by the DOE to
create a modular platform for bioinformatics. I think its using hadoop
under the hood for job scheduling and other functions.
Dr. Michael Schatz (http://www.cbcb.umd.edu/~mschatz/) who is one of the
developers of Contrail has a bunch of work on porting bioinformatics to
Hadoop.
J
On Fri, Aug 16, 2013 at 2:42 PM, Jay Vyas <ja...@gmail.com> wrote:
> there are literally hundreds. Here is a great review article for how
> mapreduce is used in the bioinformatics algorithms space:
>
> http://www.biomedcentral.com/1471-2105/11/S12/S1
>
>
> On Fri, Aug 16, 2013 at 3:38 PM, Felipe Gutierrez <
> felipe.o.gutierrez@gmail.com> wrote:
>
>> Hello,
>>
>> Does anybody know an e-Science application to run on Hadoop?
>>
>> Thanks.
>> Felipe
>>
>> --
>> *--
>> -- Felipe Oliveira Gutierrez
>> -- Felipe.o.Gutierrez@gmail.com
>> -- https://sites.google.com/site/lipe82/Home/diaadia*
>>
>
>
>
> --
> Jay Vyas
> http://jayunit100.blogspot.com
>
Re: e-Science app on Hadoop
Posted by Jeremy Lewi <je...@lewi.us>.
Contrail is a DeNovo Assembler which uses Map Reduce and Avro.
http://en.wikipedia.org/wiki/Contrail
As part of this effort, we developed an efficient FastQ InputFormat reader
for processing FastQ files in parallel.
http://kbase.science.energy.gov/about/about/ is an effort by the DOE to
create a modular platform for bioinformatics. I think its using hadoop
under the hood for job scheduling and other functions.
Dr. Michael Schatz (http://www.cbcb.umd.edu/~mschatz/) who is one of the
developers of Contrail has a bunch of work on porting bioinformatics to
Hadoop.
J
On Fri, Aug 16, 2013 at 2:42 PM, Jay Vyas <ja...@gmail.com> wrote:
> there are literally hundreds. Here is a great review article for how
> mapreduce is used in the bioinformatics algorithms space:
>
> http://www.biomedcentral.com/1471-2105/11/S12/S1
>
>
> On Fri, Aug 16, 2013 at 3:38 PM, Felipe Gutierrez <
> felipe.o.gutierrez@gmail.com> wrote:
>
>> Hello,
>>
>> Does anybody know an e-Science application to run on Hadoop?
>>
>> Thanks.
>> Felipe
>>
>> --
>> *--
>> -- Felipe Oliveira Gutierrez
>> -- Felipe.o.Gutierrez@gmail.com
>> -- https://sites.google.com/site/lipe82/Home/diaadia*
>>
>
>
>
> --
> Jay Vyas
> http://jayunit100.blogspot.com
>
Re: e-Science app on Hadoop
Posted by Jay Vyas <ja...@gmail.com>.
there are literally hundreds. Here is a great review article for how
mapreduce is used in the bioinformatics algorithms space:
http://www.biomedcentral.com/1471-2105/11/S12/S1
On Fri, Aug 16, 2013 at 3:38 PM, Felipe Gutierrez <
felipe.o.gutierrez@gmail.com> wrote:
> Hello,
>
> Does anybody know an e-Science application to run on Hadoop?
>
> Thanks.
> Felipe
>
> --
> *--
> -- Felipe Oliveira Gutierrez
> -- Felipe.o.Gutierrez@gmail.com
> -- https://sites.google.com/site/lipe82/Home/diaadia*
>
--
Jay Vyas
http://jayunit100.blogspot.com
Re: e-Science app on Hadoop
Posted by Jay Vyas <ja...@gmail.com>.
there are literally hundreds. Here is a great review article for how
mapreduce is used in the bioinformatics algorithms space:
http://www.biomedcentral.com/1471-2105/11/S12/S1
On Fri, Aug 16, 2013 at 3:38 PM, Felipe Gutierrez <
felipe.o.gutierrez@gmail.com> wrote:
> Hello,
>
> Does anybody know an e-Science application to run on Hadoop?
>
> Thanks.
> Felipe
>
> --
> *--
> -- Felipe Oliveira Gutierrez
> -- Felipe.o.Gutierrez@gmail.com
> -- https://sites.google.com/site/lipe82/Home/diaadia*
>
--
Jay Vyas
http://jayunit100.blogspot.com
Re: e-Science app on Hadoop
Posted by Jay Vyas <ja...@gmail.com>.
there are literally hundreds. Here is a great review article for how
mapreduce is used in the bioinformatics algorithms space:
http://www.biomedcentral.com/1471-2105/11/S12/S1
On Fri, Aug 16, 2013 at 3:38 PM, Felipe Gutierrez <
felipe.o.gutierrez@gmail.com> wrote:
> Hello,
>
> Does anybody know an e-Science application to run on Hadoop?
>
> Thanks.
> Felipe
>
> --
> *--
> -- Felipe Oliveira Gutierrez
> -- Felipe.o.Gutierrez@gmail.com
> -- https://sites.google.com/site/lipe82/Home/diaadia*
>
--
Jay Vyas
http://jayunit100.blogspot.com
Re: e-Science app on Hadoop
Posted by Jay Vyas <ja...@gmail.com>.
there are literally hundreds. Here is a great review article for how
mapreduce is used in the bioinformatics algorithms space:
http://www.biomedcentral.com/1471-2105/11/S12/S1
On Fri, Aug 16, 2013 at 3:38 PM, Felipe Gutierrez <
felipe.o.gutierrez@gmail.com> wrote:
> Hello,
>
> Does anybody know an e-Science application to run on Hadoop?
>
> Thanks.
> Felipe
>
> --
> *--
> -- Felipe Oliveira Gutierrez
> -- Felipe.o.Gutierrez@gmail.com
> -- https://sites.google.com/site/lipe82/Home/diaadia*
>
--
Jay Vyas
http://jayunit100.blogspot.com