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          Institute: MPI für molekulare Genetik     Collection: Department of Vertebrate Genomics     Display Documents

ID: 552746.0, MPI für molekulare Genetik / Department of Vertebrate Genomics
Data integration using scanners with SQL output--the bioscanners project at sourceforge
Authors:Groth, D.; Hartmann, S.; Friemel, M.; Hill, N.; Muller, S.; Poustka, A. J.; Panopoulou, G.
Date of Publication (YYYY-MM-DD):2010
Title of Journal:Journal of Integrative Bioinformatics
Journal Abbrev.:J Integr Bioinform
Issue / Number:3
Start Page:e122
End Page:e122
Review Status:not specified
Audience:Experts Only
Abstract / Description:There is currently no standardized approach for parsing output that the numerous bioinformatical tools generate. Because the framework approach of the Bio-toolkits has some shortcomings, we searched for alternative approaches. To this end, we evaluated scanner generators for various programming languages with respect to their potential of standalone, small and fast applications that can easily delivered on any modern and many ancient operating system. We developed sample applications that generate standard SQL database code and thereby greatly simplify the parsing work of data integration and data analysis. At the sourceforge project page the source code and some binaries for a selection of our applications are freely available at http://bioscanners.sourceforge.net.
Free Keywords:Computational Biology/methods; Databases, Factual; Internet; Programming Languages; Statistics as Topic; Time Factors
External Publication Status:published
Document Type:Article
Communicated by:Hans Lehrach
Affiliations:MPI für molekulare Genetik
MPI für Pflanzenzüchtungsforschung
External Affiliations:University of Potsdam, Bioinformatics Group, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
Identifiers:ISSN:1613-4516 (Electronic) [ID No:1]
DOI:10.2390/biecoll-jib-2010-122 [ID No:2]
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