Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome

Garijo Verdejo, Daniel; Kinnings, Sarah; Xie, Li; Xie, Lei; Zhang, Yinliang; Bourne, Philip E. y Gil, Yolanda (2013). Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome. "Plos one" ; ISSN 1932-6203. https://doi.org/10.1371/journal.pone.0080278.

Descripción

Título: Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome
Autor/es:
  • Garijo Verdejo, Daniel
  • Kinnings, Sarah
  • Xie, Li
  • Xie, Lei
  • Zhang, Yinliang
  • Bourne, Philip E.
  • Gil, Yolanda
Tipo de Documento: Artículo
Título de Revista/Publicación: Plos one
Fecha: 2013
Materias:
Escuela: Facultad de Informática (UPM) [antigua denominación]
Departamento: Inteligencia Artificial
Grupo Investigación UPM: oeg
Licencias Creative Commons: Ninguna

Texto completo

[img]
Vista Previa
PDF (Document Portable Format) - Se necesita un visor de ficheros PDF, como GSview, Xpdf o Adobe Acrobat Reader
Descargar (363kB) | Vista Previa

Resumen

How easy is it to reproduce the results found in a typical computational biology paper? Either through experience or intuition the reader will already know that the answer is with difficulty or not at all. In this paper we attempt to quantify this difficulty by reproducing a previously published paper for different classes of users (ranging from users with little expertise to domain experts) and suggest ways in which the situation might be improved. Quantification is achieved by estimating the time required to reproduce each of the steps in the method described in the original paper and make them part of an explicit workflow that reproduces the original results. Reproducing the method took several months of effort, and required using new versions and new software that posed challenges to reconstructing and validating the results. The quantification leads to “reproducibility maps” that reveal that novice researchers would only be able to reproduce a few of the steps in the method, and that only expert researchers with advance knowledge of the domain would be able to reproduce the method in its entirety. The workflow itself is published as an online resource together with supporting software and data. The paper concludes with a brief discussion of the complexities of requiring reproducibility in terms of cost versus benefit, and a desiderata with our observations and guidelines for improving reproducibility. This has implications not only in reproducing the work of others from published papers, but reproducing work from one’s own laboratory.

Más información

ID de Registro: 21853
Identificador DC: http://oa.upm.es/21853/
Identificador OAI: oai:oa.upm.es:21853
Identificador DOI: 10.1371/journal.pone.0080278
URL Oficial: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0080278
Depositado por: Dr Oscar Corcho
Depositado el: 03 Dic 2013 12:35
Ultima Modificación: 21 Abr 2016 12:38
  • Open Access
  • Open Access
  • Sherpa-Romeo
    Compruebe si la revista anglosajona en la que ha publicado un artículo permite también su publicación en abierto.
  • Dulcinea
    Compruebe si la revista española en la que ha publicado un artículo permite también su publicación en abierto.
  • Recolecta
  • e-ciencia
  • Observatorio I+D+i UPM
  • OpenCourseWare UPM