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Software testing in microbial bioinformatics: a call to action
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 t...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Microbiology Society
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9176277/ https://www.ncbi.nlm.nih.gov/pubmed/35259087 http://dx.doi.org/10.1099/mgen.0.000790 |
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author | van der Putten, Boas C.L. Mendes, C. I. Talbot, Brooke M. de Korne-Elenbaas, Jolinda Mamede, Rafael Vila-Cerqueira, Pedro Coelho, Luis Pedro Gulvik, Christopher A. Katz, Lee S. |
author_facet | van der Putten, Boas C.L. Mendes, C. I. Talbot, Brooke M. de Korne-Elenbaas, Jolinda Mamede, Rafael Vila-Cerqueira, Pedro Coelho, Luis Pedro Gulvik, Christopher A. Katz, Lee S. |
author_sort | van der Putten, Boas C.L. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-9176277 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Microbiology Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-91762772022-06-09 Software testing in microbial bioinformatics: a call to action van der Putten, Boas C.L. Mendes, C. I. Talbot, Brooke M. de Korne-Elenbaas, Jolinda Mamede, Rafael Vila-Cerqueira, Pedro Coelho, Luis Pedro Gulvik, Christopher A. Katz, Lee S. Microb Genom Personal Views 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. Microbiology Society 2022-03-08 /pmc/articles/PMC9176277/ /pubmed/35259087 http://dx.doi.org/10.1099/mgen.0.000790 Text en https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License. |
spellingShingle | Personal Views van der Putten, Boas C.L. Mendes, C. I. Talbot, Brooke M. de Korne-Elenbaas, Jolinda Mamede, Rafael Vila-Cerqueira, Pedro Coelho, Luis Pedro Gulvik, Christopher A. Katz, Lee S. Software testing in microbial bioinformatics: a call to action |
title | Software testing in microbial bioinformatics: a call to action |
title_full | Software testing in microbial bioinformatics: a call to action |
title_fullStr | Software testing in microbial bioinformatics: a call to action |
title_full_unstemmed | Software testing in microbial bioinformatics: a call to action |
title_short | Software testing in microbial bioinformatics: a call to action |
title_sort | software testing in microbial bioinformatics: a call to action |
topic | Personal Views |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9176277/ https://www.ncbi.nlm.nih.gov/pubmed/35259087 http://dx.doi.org/10.1099/mgen.0.000790 |
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