Software testing in microbial bioinformatics: a call to action-Reference-Cited by-同舟云学术

Software testing in microbial bioinformatics: a call to action

Published:2022-03-08 Issue:3 Volume:8 Page:
ISSN:2057-5858
Container-title:Microbial Genomics
language:en
Short-container-title:

Author:

van der Putten Boas C.L.¹²^ORCID,Mendes C. I.³^ORCID,Talbot Brooke M.⁴^ORCID,de Korne-Elenbaas Jolinda⁵²^ORCID,Mamede Rafael³^ORCID,Vila-Cerqueira Pedro³^ORCID,Coelho Luis Pedro⁶⁷^ORCID,Gulvik Christopher A.⁸,Katz Lee S.⁹¹⁰^ORCID,

Affiliation:

1. Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, the Netherlands

2. Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, the Netherlands

3. Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal

4. Department of Biological and Biomedical Sciences, Emory University, Atlanta, GA, USA

5. Department of Infectious Diseases, Public Health Laboratory, Public Health Service of Amsterdam, the Netherlands

6. Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, PR China

7. Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, PR China

8. Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA

9. Center for Food Safety, University of Georgia, Griffin, GA, USA

10. Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA

Abstract

Computational algorithms have become an essential component of research, with great efforts by the scientific community to raise standards on development and distribution of code. Despite these efforts, sustainability and reproducibility are major issues since continued validation through software testing is still not a widely adopted practice. Here, we report seven recommendations that help researchers implement software testing in microbial bioinformatics. We have developed these recommendations based on our experience from a collaborative hackathon organised prior to the American Society for Microbiology Next Generation Sequencing (ASM NGS) 2020 conference. We also present a repository hosting examples and guidelines for testing, available from https://github.com/microbinfie-hackathon2020/CSIS.

Funder

Fundação para a Ciência e a Tecnologia

Shanghai Municipal Science and Technology Major Project

ZJLab

Publisher

Microbiology Society

Subject

General Medicine

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3. Retraction

4. Retraction: Measures of Clade Confidence Do Not Correlate with Accuracy of Phylogenetic Trees

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