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The BioExtract Server: a web-based bioinformatic workflow platform

The BioExtract Server (bioextract.org) is an open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These task...

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Detalles Bibliográficos
Autores principales: Lushbough, Carol M., Jennewein, Douglas M., Brendel, Volker P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125737/
https://www.ncbi.nlm.nih.gov/pubmed/21546552
http://dx.doi.org/10.1093/nar/gkr286
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author Lushbough, Carol M.
Jennewein, Douglas M.
Brendel, Volker P.
author_facet Lushbough, Carol M.
Jennewein, Douglas M.
Brendel, Volker P.
author_sort Lushbough, Carol M.
collection PubMed
description The BioExtract Server (bioextract.org) is an open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet.
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spelling pubmed-31257372011-07-05 The BioExtract Server: a web-based bioinformatic workflow platform Lushbough, Carol M. Jennewein, Douglas M. Brendel, Volker P. Nucleic Acids Res Articles The BioExtract Server (bioextract.org) is an open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet. Oxford University Press 2011-07-01 2011-05-05 /pmc/articles/PMC3125737/ /pubmed/21546552 http://dx.doi.org/10.1093/nar/gkr286 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Lushbough, Carol M.
Jennewein, Douglas M.
Brendel, Volker P.
The BioExtract Server: a web-based bioinformatic workflow platform
title The BioExtract Server: a web-based bioinformatic workflow platform
title_full The BioExtract Server: a web-based bioinformatic workflow platform
title_fullStr The BioExtract Server: a web-based bioinformatic workflow platform
title_full_unstemmed The BioExtract Server: a web-based bioinformatic workflow platform
title_short The BioExtract Server: a web-based bioinformatic workflow platform
title_sort bioextract server: a web-based bioinformatic workflow platform
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125737/
https://www.ncbi.nlm.nih.gov/pubmed/21546552
http://dx.doi.org/10.1093/nar/gkr286
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