IDEAS home Printed from https://ideas.repec.org/a/bpj/sagmbi/v4y2005i1n2.html
   My bibliography  Save this article

Reproducible Research: A Bioinformatics Case Study

Author

Listed:
  • Gentleman Robert

    (Harvard University)

Abstract

While scientific research and the methodologies involved have gone through substantial technological evolution the technology involved in the publication of the results of these endeavors has remained relatively stagnant. Publication is largely done in the same manner today as it was fifty years ago. Many journals have adopted electronic formats, however, their orientation and style is little different from a printed document. The documents tend to be static and take little advantage of computational resources that might be available. Recent work, Gentleman and Temple Lang (2003), suggests a methodology and basic infrastructure that can be used to publish documents in a substantially different way. Their approach is suitable for the publication of papers whose message relies on computation. Stated quite simply, Gentleman and Temple Lang (2003) propose a paradigm where documents are mixtures of code and text. Such documents may be self-contained or they may be a component of a compendium which provides the infrastructure needed to provide access to data and supporting software. These documents, or compendiums, can be processed in a number of different ways. One transformation will be to replace the code with its output -- thereby providing the familiar, but limited, static document. In this paper we apply these concepts to a seminal paper in bioinformatics, namely The Molecular Classification of Cancer, Golub et al (1999). The authors of that paper have generously provided data and other information that have allowed us to largely reproduce their results. Rather than reproduce this paper exactly we demonstrate that such a reproduction is possible and instead concentrate on demonstrating the usefulness of the compendium concept itself.

Suggested Citation

  • Gentleman Robert, 2005. "Reproducible Research: A Bioinformatics Case Study," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 4(1), pages 1-25, January.
  • Handle: RePEc:bpj:sagmbi:v:4:y:2005:i:1:n:2
    DOI: 10.2202/1544-6115.1034
    as

    Download full text from publisher

    File URL: https://doi.org/10.2202/1544-6115.1034
    Download Restriction: For access to full text, subscription to the journal or payment for the individual article is required.

    File URL: https://libkey.io/10.2202/1544-6115.1034?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Ingemar André & Jacob Corn, 2013. "The RosettaCon 2012 Special Collection: Code Writ on Water, Documentation Writ in Stone," PLOS ONE, Public Library of Science, vol. 8(9), pages 1-3, September.
    2. Jorge Faleiro & Edward Tsang, 2018. "Supporting Crowd-Powered Science in Economics: FRACTI, a Conceptual Framework for Large-Scale Collaboration and Transparent Investigation in Financial Markets," Papers 1808.07959, arXiv.org.
    3. Ben Marwick & Carl Boettiger & Lincoln Mullen, 2018. "Packaging Data Analytical Work Reproducibly Using R (and Friends)," The American Statistician, Taylor & Francis Journals, vol. 72(1), pages 80-88, January.
    4. Giovanni Baiocchi, 2007. "Reproducible research in computational economics: guidelines, integrated approaches, and open source software," Computational Economics, Springer;Society for Computational Economics, vol. 30(1), pages 19-40, August.
    5. Jorge Faleiro, 2018. "A Language for Large-Scale Collaboration in Economics: A Streamlined Computational Representation of Financial Models," Papers 1809.06471, arXiv.org.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:bpj:sagmbi:v:4:y:2005:i:1:n:2. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Peter Golla (email available below). General contact details of provider: https://www.degruyter.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.