General guidelines for biomedical software development [version 2; referees: 2 approved]
Most bioinformatics tools available today were not written by professional software developers, but by people that wanted to solve their own problems, using computational solutions and spending the minimum time and effort possible, since these were just the means to an end. Consequently, a vast numb...
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doaj-7909def3d8984cc08a603023c4ad4fff2020-11-25T04:00:12ZengF1000 Research LtdF1000Research2046-14022017-07-01610.12688/f1000research.10750.212745General guidelines for biomedical software development [version 2; referees: 2 approved]Luis Bastiao Silva0Rafael C. Jimenez1Niklas Blomberg2José Luis Oliveira3BMD Software, Aveiro, PortugalELIXIR Hub, Wellcome Trust Genome Campus, Hinxton, UKELIXIR Hub, Wellcome Trust Genome Campus, Hinxton, UKInstitute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, Aveiro, PortugalMost bioinformatics tools available today were not written by professional software developers, but by people that wanted to solve their own problems, using computational solutions and spending the minimum time and effort possible, since these were just the means to an end. Consequently, a vast number of software applications are currently available, hindering the task of identifying the utility and quality of each. At the same time, this situation has hindered regular adoption of these tools in clinical practice. Typically, they are not sufficiently developed to be used by most clinical researchers and practitioners. To address these issues, it is necessary to re-think how biomedical applications are built and adopt new strategies that ensure quality, efficiency, robustness, correctness and reusability of software components. We also need to engage end-users during the development process to ensure that applications fit their needs. In this review, we present a set of guidelines to support biomedical software development, with an explanation of how they can be implemented and what kind of open-source tools can be used for each specific topic.https://f1000research.com/articles/6-273/v2Bioinformatics |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Luis Bastiao Silva Rafael C. Jimenez Niklas Blomberg José Luis Oliveira |
spellingShingle |
Luis Bastiao Silva Rafael C. Jimenez Niklas Blomberg José Luis Oliveira General guidelines for biomedical software development [version 2; referees: 2 approved] F1000Research Bioinformatics |
author_facet |
Luis Bastiao Silva Rafael C. Jimenez Niklas Blomberg José Luis Oliveira |
author_sort |
Luis Bastiao Silva |
title |
General guidelines for biomedical software development [version 2; referees: 2 approved] |
title_short |
General guidelines for biomedical software development [version 2; referees: 2 approved] |
title_full |
General guidelines for biomedical software development [version 2; referees: 2 approved] |
title_fullStr |
General guidelines for biomedical software development [version 2; referees: 2 approved] |
title_full_unstemmed |
General guidelines for biomedical software development [version 2; referees: 2 approved] |
title_sort |
general guidelines for biomedical software development [version 2; referees: 2 approved] |
publisher |
F1000 Research Ltd |
series |
F1000Research |
issn |
2046-1402 |
publishDate |
2017-07-01 |
description |
Most bioinformatics tools available today were not written by professional software developers, but by people that wanted to solve their own problems, using computational solutions and spending the minimum time and effort possible, since these were just the means to an end. Consequently, a vast number of software applications are currently available, hindering the task of identifying the utility and quality of each. At the same time, this situation has hindered regular adoption of these tools in clinical practice. Typically, they are not sufficiently developed to be used by most clinical researchers and practitioners. To address these issues, it is necessary to re-think how biomedical applications are built and adopt new strategies that ensure quality, efficiency, robustness, correctness and reusability of software components. We also need to engage end-users during the development process to ensure that applications fit their needs. In this review, we present a set of guidelines to support biomedical software development, with an explanation of how they can be implemented and what kind of open-source tools can be used for each specific topic. |
topic |
Bioinformatics |
url |
https://f1000research.com/articles/6-273/v2 |
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