Biophysical Reviews

, Volume 7, Issue 3, pp 343–352

How to test bioinformatics software?

  • Amir Hossein Kamali
  • Eleni Giannoulatou
  • Tsong Yueh Chen
  • Michael A. Charleston
  • Alistair L. McEwan
  • Joshua W. K. Ho
Review

DOI: 10.1007/s12551-015-0177-3

Cite this article as:
Kamali, A.H., Giannoulatou, E., Chen, T.Y. et al. Biophys Rev (2015) 7: 343. doi:10.1007/s12551-015-0177-3

Abstract

Bioinformatics is the application of computational, mathematical and statistical techniques to solve problems in biology and medicine. Bioinformatics programs developed for computational simulation and large-scale data analysis are widely used in almost all areas of biophysics. The appropriate choice of algorithms and correct implementation of these algorithms are critical for obtaining reliable computational results. Nonetheless, it is often very difficult to systematically test these programs as it is often hard to verify the correctness of the output, and to effectively generate failure-revealing test cases. Software testing is an important process of verification and validation of scientific software, but very few studies have directly dealt with the issues of bioinformatics software testing. In this work, we review important concepts and state-of-the-art methods in the field of software testing. We also discuss recent reports on adapting and implementing software testing methodologies in the bioinformatics field, with specific examples drawn from systems biology and genomic medicine.

Keywords

Software testing Bioinformatics Quality assurance Automated testing Cloud-based testing 

Copyright information

© International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Amir Hossein Kamali
    • 1
    • 2
  • Eleni Giannoulatou
    • 1
    • 3
  • Tsong Yueh Chen
    • 4
  • Michael A. Charleston
    • 5
  • Alistair L. McEwan
    • 2
  • Joshua W. K. Ho
    • 1
    • 3
  1. 1.Victor Chang Cardiac Research InstituteDarlinghurstAustralia
  2. 2.School of Electrical and Information EngineeringThe University of SydneySydneyAustralia
  3. 3.St. Vincent’s Clinical School, The University of New South WalesSydneyAustralia
  4. 4.Department of Computer Science and Software EngineeringSwinburne University of TechnologyMelbourneAustralia
  5. 5.School of Physical SciencesThe University of TasmaniaHobartAustralia

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