Barely sufficient practices in scientific computing
- PMID: 33659915
- PMCID: PMC7892476
- DOI: 10.1016/j.patter.2021.100206
Barely sufficient practices in scientific computing
Abstract
The importance of software to modern research is well understood, as is the way in which software developed for research can support or undermine important research principles of findability, accessibility, interoperability, and reusability (FAIR). We propose a minimal subset of common software engineering principles that enable FAIRness of computational research and can be used as a baseline for software engineering in any research discipline.
© 2021 The Authors.
Similar articles
-
Applying FAIRness: Redesigning a Biomedical Informatics Research Data Management Pipeline.Methods Inf Med. 2019 Dec;58(6):229-234. doi: 10.1055/s-0040-1709158. Epub 2020 Apr 29. Methods Inf Med. 2019. PMID: 32349157
-
Reviewability and supportability: New complementary principles to empower research software practices.Comput Struct Biotechnol J. 2024 Nov 6;23:3989-3998. doi: 10.1016/j.csbj.2024.10.034. eCollection 2024 Dec. Comput Struct Biotechnol J. 2024. PMID: 39582890 Free PMC article. Review.
-
Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection.Acta Crystallogr D Struct Biol. 2024 Jun 1;80(Pt 6):439-450. doi: 10.1107/S2059798324004881. Epub 2024 Jun 4. Acta Crystallogr D Struct Biol. 2024. PMID: 38832828 Free PMC article.
-
Dental Research Data Availability and Quality According to the FAIR Principles.J Dent Res. 2022 Oct;101(11):1307-1313. doi: 10.1177/00220345221101321. Epub 2022 Jun 2. J Dent Res. 2022. PMID: 35656591 Free PMC article.
-
The FAIR guiding principles for data stewardship: fair enough?Eur J Hum Genet. 2018 Jul;26(7):931-936. doi: 10.1038/s41431-018-0160-0. Epub 2018 May 17. Eur J Hum Genet. 2018. PMID: 29777206 Free PMC article. Review.
Cited by
-
Why don't we share data and code? Perceived barriers and benefits to public archiving practices.Proc Biol Sci. 2022 Nov 30;289(1987):20221113. doi: 10.1098/rspb.2022.1113. Epub 2022 Nov 23. Proc Biol Sci. 2022. PMID: 36416041 Free PMC article.
-
Fostering reproducibility, reusability, and technology transfer in health informatics.iScience. 2021 Jul 1;24(7):102803. doi: 10.1016/j.isci.2021.102803. eCollection 2021 Jul 23. iScience. 2021. PMID: 34296072 Free PMC article. Review.
-
Landscape of 2D Deep Learning Segmentation Networks Applied to CT Scan from Lung Cancer Patients: A Systematic Review.J Imaging Inform Med. 2025 Mar 4. doi: 10.1007/s10278-025-01458-x. Online ahead of print. J Imaging Inform Med. 2025. PMID: 40038137 Review.
-
Guideline for software life cycle in health informatics.iScience. 2022 Nov 9;25(12):105534. doi: 10.1016/j.isci.2022.105534. eCollection 2022 Dec 22. iScience. 2022. PMID: 36437879 Free PMC article. Review.
-
Ten simple rules on writing clean and reliable open-source scientific software.PLoS Comput Biol. 2021 Nov 11;17(11):e1009481. doi: 10.1371/journal.pcbi.1009481. eCollection 2021 Nov. PLoS Comput Biol. 2021. PMID: 34762641 Free PMC article.
References
-
- Research Data Alliance fair for Research Software (fair4rs) wg. 2019. https://www.rd-alliance.org/groups/fair-research-software-fair4rs-wg
-
- Pinto G., Wiese I., Felipe Dias L. How do scientists develop scientific software? An external replication. ieee 25th International Conference on Software Analysis, Evolution and Reengineering (saner) 2018;2018:582–591.
-
- Chawla D.S. Influential Pandemic Simulation Verified by Code Checkers. 2020. https://media.nature.com/original/magazine-assets/d41586-020-01685-y/d41...
Publication types
LinkOut - more resources
Full Text Sources
Other Literature Sources