Scipediacontent: Scipediacontent moved page Draft Content 474150789 to Wilson Yu 2008a

2021-02-01T14:51:34Z

Scipediacontent moved page Draft Content 474150789 to Wilson Yu 2008a

Scipediacontent: Created page with " == Abstract == Bioinformatics pipelines enable life scientists to effectively analyze biological data through automated multi-step processes constructed by individual progra..."

2021-02-01T14:51:29Z

Created page with " == Abstract == Bioinformatics pipelines enable life scientists to effectively analyze biological data through automated multi-step processes constructed by individual progra..."

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== Abstract ==

Bioinformatics pipelines enable life scientists to effectively analyze biological data through automated multi-step processes constructed by individual programs and databases. The huge amount of data and time consuming computations require effectively parallelized pipelines to provide results within a reasonable time. To reduce researchers' programming burden for pipeline creation and parallelization, we developed the bioinformatics pipeline generation and parallelization toolkit (BioGent). A user needs only to create a pipeline definition file that describes the data processing sequence and input/output files. A program termed schedpipe in the BioGent toolkit takes the definition file and executes the designed procedure. Schedpipe automatically parallelizes the pipeline execution by performing independent data processing steps on multiple CPUs, and by decomposing big datasets into small chunks and processing them in parallel. Schedpipe controls program execution on multiple CPUs through a simple application programming interface (API) of the Parallel Job Manager (PJM) library. As a part of the BioGent toolkit, PJM was developed to effectively launch and monitor programs on multiple CPUs using a message passing interface (MPI) protocol. The PJM API can also be used to parallelize other serial programs. A demonstration using PJM for parallelization shows 10% to 50% savings in time compared to an indigenous parallelization through a batch queuing system.

== Original document ==

The different versions of the original document can be found in:

* [http://bhsai.org/pubs/Yu_2007_A_Tool_for_Creating.pdf http://bhsai.org/pubs/Yu_2007_A_Tool_for_Creating.pdf]

* [http://xplorestaging.ieee.org/ielx5/4437948/4437949/04438020.pdf?arnumber=4438020 http://xplorestaging.ieee.org/ielx5/4437948/4437949/04438020.pdf?arnumber=4438020],
: [http://dx.doi.org/10.1109/hpcmp-ugc.2007.5 http://dx.doi.org/10.1109/hpcmp-ugc.2007.5]

* [http://yadda.icm.edu.pl/yadda/element/bwmeta1.element.ieee-000004438020 http://yadda.icm.edu.pl/yadda/element/bwmeta1.element.ieee-000004438020],
: [https://apps.dtic.mil/dtic/tr/fulltext/u2/a480822.pdf https://apps.dtic.mil/dtic/tr/fulltext/u2/a480822.pdf],
: [https://dl.acm.org/citation.cfm?id=1335093 https://dl.acm.org/citation.cfm?id=1335093],
: [https://apps.dtic.mil/docs/citations/ADA480822 https://apps.dtic.mil/docs/citations/ADA480822],
: [https://ieeexplore.ieee.org/document/4438020 https://ieeexplore.ieee.org/document/4438020],
: [http://www.dtic.mil/cgi-bin/GetTRDoc?AD=ADP023782&Location=U2&doc=GetTRDoc.pdf http://www.dtic.mil/cgi-bin/GetTRDoc?AD=ADP023782&Location=U2&doc=GetTRDoc.pdf],
: [https://academic.microsoft.com/#/detail/2095598813 https://academic.microsoft.com/#/detail/2095598813]

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Wilson Yu 2008a - Revision history

Scipediacontent: Scipediacontent moved page Draft Content 474150789 to Wilson Yu 2008a

Scipediacontent: Created page with " == Abstract == Bioinformatics pipelines enable life scientists to effectively analyze biological data through automated multi-step processes constructed by individual progra..."