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Kamali AH, Giannoulatou E, Chen TY, et al. How to test bioinformatics software?. Biophys Rev. 2015;7(3):343-352doi: 10.1007/s12551-015-0177-3.
Kamali, A. H., Giannoulatou, E., Chen, T. Y., Charleston, M. A., McEwan, A. L., & Ho, J. W. K. (2015). How to test bioinformatics software?. Biophysical reviews, 7(3), 343-352. https://doi.org/10.1007/s12551-015-0177-3
Kamali, Amir Hossein, et al. "How to test bioinformatics software?." Biophysical reviews vol. 7,3 (2015): 343-352. doi: https://doi.org/10.1007/s12551-015-0177-3
Kamali AH, Giannoulatou E, Chen TY, Charleston MA, McEwan AL, Ho JWK. How to test bioinformatics software?. Biophys Rev. 2015 Sep;7(3):343-352. doi: 10.1007/s12551-015-0177-3. Epub 2015 Aug 13. PMID: 28510230; PMCID: PMC5425734.
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Biophys Rev. 2015 Sep;7(3):343-352. doi: 10.1007/s12551-015-0177-3. Epub 2015 Aug 13.

How to test bioinformatics software?.

Biophysical reviews

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

Affiliations

  1. Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia.
  2. School of Electrical and Information Engineering, The University of Sydney, Sydney, NSW, 2006, Australia.
  3. St. Vincent's Clinical School, The University of New South Wales, Sydney, NSW, 2010, Australia.
  4. Department of Computer Science and Software Engineering, Swinburne University of Technology, Melbourne, VIC, Australia.
  5. School of Physical Sciences, The University of Tasmania, Hobart, TAS, Australia.
  6. Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia. [email protected].
  7. St. Vincent's Clinical School, The University of New South Wales, Sydney, NSW, 2010, Australia. [email protected].

PMID: 28510230 PMCID: PMC5425734 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: Automated testing; Bioinformatics; Cloud-based testing; Quality assurance; Software testing

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