Kamali Amir Hossein, Giannoulatou Eleni, Chen Tsong Yueh, Charleston Michael A, McEwan Alistair L, Ho Joshua W K
Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia.
School of Electrical and Information Engineering, The University of Sydney, Sydney, NSW, 2006, Australia.
Biophys Rev. 2015 Sep;7(3):343-352. doi: 10.1007/s12551-015-0177-3. Epub 2015 Aug 13.
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.
生物信息学是应用计算、数学和统计技术来解决生物学和医学问题的学科。为计算模拟和大规模数据分析而开发的生物信息学程序广泛应用于生物物理学的几乎所有领域。算法的恰当选择以及这些算法的正确实现对于获得可靠的计算结果至关重要。然而，系统地测试这些程序通常非常困难，因为往往难以验证输出的正确性，也难以有效地生成能揭示故障的测试用例。软件测试是科学软件验证和确认的重要过程，但很少有研究直接涉及生物信息学软件测试的问题。在这项工作中，我们回顾了软件测试领域的重要概念和最新方法。我们还讨论了关于在生物信息学领域采用和实施软件测试方法的近期报告，并从系统生物学和基因组医学中选取了具体实例。
