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Related Experiment Videos

Reproducible research: a bioinformatics case study.

Robert Gentleman1

  • 1Harvard University, USA. rgentlem@fhcrc.org

Statistical Applications in Genetics and Molecular Biology
|May 2, 2006
PubMed
Summary
This summary is machine-generated.

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This study introduces a new publication method for computational research, blending text and code. This "compendium" approach enhances scientific reproducibility and data accessibility for bioinformatics papers.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Scientific Publishing

Background:

  • Traditional scientific publication methods have not kept pace with technological advancements in research methodologies.
  • Current electronic journal formats largely mimic static print documents, failing to leverage computational resources.
  • A novel approach proposes documents as a mixture of text and executable code, enabling dynamic content.

Purpose of the Study:

  • To apply and demonstrate the utility of the compendium concept for publishing computational scientific research.
  • To showcase a new paradigm for scientific documents that integrates code and data.
  • To illustrate the potential of dynamic documents in scientific communication.

Main Methods:

  • The study applies the Gentleman and Temple Lang (2003) compendium methodology.

Related Experiment Videos

  • The approach is demonstrated using the seminal bioinformatics paper 'The Molecular Classification of Cancer' by Golub et al (1999).
  • The authors utilized provided data and information to reproduce key results from the original paper.

    • Main Results:

    • The study successfully demonstrates the feasibility of the compendium approach for reproducing scientific results.
    • It highlights the practical application of mixing code and text within a scientific publication.
    • The effectiveness of the compendium concept in enhancing data and software accessibility is shown.

    Conclusions:

    • The compendium model offers a powerful alternative to static scientific publications, especially for computation-heavy research.
    • This method significantly improves the reproducibility and transparency of scientific findings.
    • The compendium approach represents a substantial evolution in scientific publishing, moving towards more interactive and accessible research outputs.