Verification and validation of bioinformatics software without a gold standard: a case study of BWA and Bowtie

E Giannoulatou, SH Park, DT Humphreys, JWK Ho - BMC bioinformatics, 2014 - Springer
Background Bioinformatics software quality assurance is essential in genomic medicine.
Systematic verification and validation of bioinformatics software is difficult because it is often …

How to test bioinformatics software?

AH Kamali, E Giannoulatou, TY Chen… - Biophysical …, 2015 - Springer
Bioinformatics is the application of computational, mathematical and statistical techniques to
solve problems in biology and medicine. Bioinformatics programs developed for …

An innovative approach for testing bioinformatics programs using metamorphic testing

TY Chen, JWK Ho, H Liu, X Xie - BMC bioinformatics, 2009 - Springer
Background Recent advances in experimental and computational technologies have fueled
the development of many sophisticated bioinformatics programs. The correctness of such …

[HTML][HTML] Scalability and validation of big data bioinformatics software

A Yang, M Troup, JWK Ho - Computational and structural biotechnology …, 2017 - Elsevier
This review examines two important aspects that are central to modern big data
bioinformatics analysis–software scalability and validity. We argue that not only are the …

Evaluating genomic tests from bench to bedside: a practical framework

JS Lin, M Thompson, KAB Goddard, MA Piper… - BMC medical informatics …, 2012 - Springer
The development of genomic tests is one of the most significant technological advances in
medical testing in recent decades. As these tests become increasingly available, so does …

Quality assurance of bioinformatics software: a case study of testing a biomedical text processing tool using metamorphic testing

M Srinivasan, MP Shahri, I Kahanda… - Proceedings of the 3rd …, 2018 - dl.acm.org
Bioinformatics software plays a very important role in making critical decisions within many
areas including medicine and health care. However, most of the research is directed …

On best practices in the development of bioinformatics software

FV Leprevost, VC Barbosa, EL Francisco… - Frontiers in …, 2014 - frontiersin.org
Bioinformatics is one of the major areas of study in modern biology. Mediumand large-scale
quantitative biology studies have created a demand for professionals with proficiency in …

[HTML][HTML] General guidelines for biomedical software development

LB Silva, RC Jimenez, N Blomberg, JL Oliveira - F1000Research, 2017 - ncbi.nlm.nih.gov
Most bioinformatics tools available today were not written by professional software
developers, but by people that wanted to solve their own problems, using computational …

Translational bioinformatics applications in genome medicine

AJ Butte - Genome Medicine, 2009 - Springer
Although investigators using methodologies in bioinformatics have always been useful in
genomic experimentation in analytic, engineering, and infrastructure support roles, only …

A quick guide to genomics and bioinformatics training for clinical and public audiences

MD Brazas, F Lewitter, MV Schneider… - PLoS computational …, 2014 - journals.plos.org
Traditionally, bioinformatics tools and training programs have focused on life science
audiences. Though heterogeneous, their needs are at least fairly well understood. Driven by …