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How to test bioinformatics software?

Citation

Kamali, AH and Giannoulatou, E and Chen, TY and Charleston, MA and McEwan, AL and Ho, JWK, How to test bioinformatics software?, Biophysical Reviews, 7, (3) pp. 343-352. ISSN 1867-2450 (2015) [Refereed Article]

Copyright Statement

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

DOI: 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.

Item Details

Item Type:Refereed Article
Keywords:software testing, bioinformatics, quality assurance, automated testing, cloud-based testing
Research Division:Information and Computing Sciences
Research Group:Computer Software
Research Field:Bioinformatics Software
Objective Division:Expanding Knowledge
Objective Group:Expanding Knowledge
Objective Field:Expanding Knowledge in the Biological Sciences
Author:Charleston, MA (Associate Professor Michael Charleston)
ID Code:106987
Year Published:2015
Deposited By:Mathematics and Physics
Deposited On:2016-02-29
Last Modified:2017-11-01
Downloads:0

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