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BioCASE: Accelerating Software Development of Genome-Wide Filtering Applications

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Book cover Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living (IWANN 2009)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 5518))

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Abstract

Due to the high pace that algorithms for scanning genome-wide datasets are produced, most of the software is quickly released. As a consequence, they usually lack in system portability and only provide a text-based user interface. BioCASE is an open-source tool developed to assist bioinformaticians in the task of producing software to perform any kind of computationally-expensive genome-wide scanning. BioCASE will produce efficient software with some other added features such as to be portable, to have a graphical user interface (GUI) and to be easily set up. A first version of BioCASE (http://bios.ugr.es/biocase) has been completed and it is being currently used in the design of a genome- wide tool to perform variable selection of genotype data sets based on multivariate association and transmission-disequilibrium tests.

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References

  1. Gentleman, R.C., et al.: Bioconductor: open software development for computational biology and bioinformatics. Genome Biology 5(5), 1–16 (2004)

    Google Scholar 

  2. Kim, T.M., Jung, Y.C., Rhyu, M.G., Jung, M.H., Chung, Y.J.: Gear: genomic enrichment analysis of regional dna copy number changes. Bioinformatics 24(3), 420–421 (2008)

    Article  Google Scholar 

  3. Sebastiani, P., Abad-Grau, M.M.: Bayesian estimates of linkage disequilibrium. BMC Genetics 8, 1–13 (2007)

    Article  Google Scholar 

  4. Scheet, P., Stephens, M.: A fast and flexible statistical model for large-scale population genotype. data: Applications to inferring missing genotypes and haplotypic phase. Am. J. Hum. Genet. 78, 629–644 (2006)

    Article  Google Scholar 

  5. Abad-Grau, M.M., Montes, R., Sebastiani, P.: Building chromosome-wide LD maps. Bioinformatics 22(16), 1933–1934 (2006)

    Article  Google Scholar 

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Author information

Authors and Affiliations

  1. Departamento de Lenguajes y Sistemas Informáticos, ETS Ingeniería Informática y de Telecomunicaciones, Universidad de Granada, c/ Periodista Daniel Saucedo Aranda s/n, 18071, Granada, Spain

    Rosana Montes & María M. Abad-Grau

Authors
  1. Rosana Montes
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  2. María M. Abad-Grau
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Editor information

Editors and Affiliations

  1. Graduate School of Engineering, Osaka Prefecture University, Osaka, Japan

    Sigeru Omatu

  2. Department of Informatics / CCTC, University of Minho, Braga, Portugal

    Miguel P. Rocha

  3. MAmI Research Lab, University of Castilla-La Mancha,, Ciudad Real, Spain

    José Bravo

  4. Department of Informatics, University of Vigo, Ourense, Spain

    Florentino Fernández

  5. Grupo de Investigación GICAP, Área de Lenguajes Higher Polytechnic School, Universidad de Burgos, Burgos, Spain

    Emilio Corchado

  6. Higher Polytechnic School, University of Burgos, Burgos, Spain

    Andrés Bustillo

  7. Department of Informatics, University of Salamanca, Salamanca, Spain

    Juan M. Corchado

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© 2009 Springer-Verlag Berlin Heidelberg

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Montes, R., Abad-Grau, M.M. (2009). BioCASE: Accelerating Software Development of Genome-Wide Filtering Applications. In: Omatu, S., et al. Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living. IWANN 2009. Lecture Notes in Computer Science, vol 5518. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02481-8_166

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  • DOI: https://doi.org/10.1007/978-3-642-02481-8_166

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-02480-1

  • Online ISBN: 978-3-642-02481-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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