ArticlePeerJ. Computer science2022
Improving bioinformatics software quality through incorporation of software engineering practices.
Article in PeerJ. Computer science, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 1 of them a synthesis that pooled it.
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Who cites it
11 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Assessment of the functionality and usability of open-source rare variant analysis pipelines.Briefings in bioinformatics · 2025Pooled it
- BioTester: an AI-driven automated testing framework for identifying potential quality risks in bioinformatics software.Briefings in bioinformatics · 2026Article
- A scoping review of approaches to evaluating workflow management systems for bioinformatics users.Briefings in bioinformatics · 2026Article
- Mapping the bioinformatics resource landscape: an analysis of LibGuides across Canadian universities.The journal of the Canadian Health Libraries Association · 2025Article
- Steering veridical large language model analyses by correcting and enriching generated database queries: first steps toward ChatGPT bioinformatics.Briefings in bioinformatics · 2024Article
- Improving bioinformatics software quality through teamwork.Bioinformatics (Oxford, England) · 2024Article
- Bioinformatics in Russia: history and present-day landscape.Briefings in bioinformatics · 2024Review
- A choice, not an obligation : Releasing scientific software as open source should be the responsibility of the authors.EMBO reports · 2024Article
- The five pillars of computational reproducibility: bioinformatics and beyond.Briefings in bioinformatics · 2023Article
- Application of Model-Building Based on Arterial Ultrasound Imaging Evaluation to Predict CHD Risk.Computational and mathematical methods in medicine · 2022Article
- A Data-Driven Medical Decision Framework for Associating Adverse Drug Events with Drug-Drug Interaction Mechanisms.Journal of healthcare engineering · 2022Article
Corrections and comments
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBioinformatics software is developed for collecting, analyzing, integrating, and interpreting life science datasets that are often enormous. Bioinformatics engineers often lack the software engineering skills necessary for developing robust, maintainable, reusable software. This study presents review and discussion of the findings and efforts made to improve the quality of bioinformatics software. METHODOLOGY: A systematic review was conducted of related literature that identifies core software engineering concepts for improving bioinformatics software development: requirements gathering, documentation, testing, and integration. The findings are presented with the aim of illuminating trends within the research that could lead to viable solutions to the struggles faced by bioinformatics engineers when developing scientific software.
resultsThe findings suggest that bioinformatics engineers could significantly benefit from the incorporation of software engineering principles into their development efforts. This leads to suggestion of both cultural changes within bioinformatics research communities as well as adoption of software engineering disciplines into the formal education of bioinformatics engineers. Open management of scientific bioinformatics development projects can result in improved software quality through collaboration amongst both bioinformatics engineers and software engineers.
conclusionsWhile strides have been made both in identification and solution of issues of particular import to bioinformatics software development, there is still room for improvement in terms of shifts in both the formal education of bioinformatics engineers as well as the culture and approaches of managing scientific bioinformatics research and development efforts.
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