Reference health
Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software
9/9 checkable references clean · checked 2026-07-14
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a publisher retraction, withdrawal, or removal notice.
45 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
The 9 checked references that resolve
resolves10.1186/2047-217X-2-15
Ten recommendations for creating usable bioinformatics command line software
resolves10.1093/bioinformatics/btz278
ORCA: a comprehensive bioinformatics container environment for education and research
resolves10.1093/gigascience/giy016
Boutiques: a flexible framework to integrate command-line applications in computing platforms
resolves10.12688/f1000research.15140.2
Recommendations for the packaging and containerizing of bioinformatics software
resolves10.1101/655456
The Mastery Rubric for Bioinformatics: supporting design and evaluation of career-spanning education and training
resolves10.12688/f1000research.11407.1
Four simple recommendations to encourage best practices in research software
The 45 references without a DOI — listed, not checked
no DOI — not checked1,500 scientists lift the lid on reproducibility
no DOI — not checkedSoftware Carpentry: lessons learned
no DOI — not checkedBest practices for scientific computing
no DOI — not checkedLack of software engineering practices in the development of bioinformatics software
no DOI — not checkedICCGI 2013: Eighth International Multi-Conference on Computing in the Global Information Technology, Nice, France
no DOI — not checkedDeveloping scientific software
no DOI — not checkedError: why scientific programming does not compute
no DOI — not checkedTroubling trends in scientific software use
no DOI — not checkedScientific software development is not an oxymoron
no DOI — not checkedEngineering bioinformatics: building reliability, performance and productivity into bioinformatics software
no DOI — not checkedTen simple rules for developing usable software in computational biology
no DOI — not checkedTen simple rules for making research software more robust
no DOI — not checkedToward effective software solutions for big biology
no DOI — not checkedUnderstanding the scientific software ecosystem and its impact: current and future measures
no DOI — not checkedOn best practices in the development of bioinformatics software
no DOI — not checkedA large-scale analysis of bioinformatics code on GitHub
no DOI — not checkedTen simple rules for biologists learning to program
no DOI — not checkedOrchestrating high-throughput genomic analysis with Bioconductor
no DOI — not checkedBioconda: sustainable and comprehensive software distribution for the life sciences
no DOI — not checkedDocker. https://www.docker.com/. Accessed 8 July 2019.
no DOI — not checkedBioboxes: standardised containers for interchangeable bioinformatics software
no DOI — not checkedThe Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows
no DOI — not checkedThe Software Sustainability Institute: changing research software attitudes and practices
no DOI — not checkedGreenfeld
AR
. Cookiecutter. https://github.com/audreyr/cookiecutter. Accessed 8 July 2019.
no DOI — not checkedTravis CI - Test and Deploy Your Code with Confidence. https://travis-ci.org/. Accessed 21 March 2019.
no DOI — not checkedThe Git Project. Git. https://git-scm.com/. Accessed 14 April 2019.
no DOI — not checkedThe Open Group Base Specifications Issue 7, 2018 edition
no DOI — not checkedFree Software Foundation, Inc. GNU Coding Standards. 2019; https://www.gnu.org/prep/standards/standards.html.
no DOI — not checkedTen simple rules for documenting scientific software
no DOI — not checkedUNIX Time-Sharing System: Foreword
no DOI — not checkedThe Pragmatic Programmer: From Journeyman to Master
no DOI — not checkedBiopython: freely available Python tools for computational molecular biology and bioinformatics
no DOI — not checkedTop considerations for creating bioinformatics software documentation
no DOI — not checkedPreston-Werner
T
. Semantic Versioning 2.0.0. https://semver.org/spec/v2.0.0.html. Accessed 4 March 2019.
no DOI — not checkedThe Art of UNIX Programming
no DOI — not checkedChoose an open source license. https://choosealicense.com/. Accessed 4 March 2019.
no DOI — not checkedBuilding a better ReadMe
no DOI — not checkedTen simple rules for taking advantage of Git and GitHub
no DOI — not checkedFacts and Fallacies of Software Engineering
no DOI — not checkedThe Curl developers. Curl: command line tool and library for transferring data with URLs. https://curl.haxx.se/. Accessed 12 April 2019.
no DOI — not checkedbionitio boot https://cloud.docker.com/u/bionitio/repository/docker/bionitio/bionitio-boot.
no DOI — not checkedAustralian Bioinformatics and Computational Biology Society (ABACBS) 2018 Annual Conference. https://www.abacbs.org/conference2018/about. Accessed 18 June 2019.
no DOI — not checkedThe FAIR Guiding Principles for scientific data management and stewardship
no DOI — not checkedZenodo. https://zenodo.org/. Accessed 18 June 2019.
no DOI — not checkedGeorgeson P, Syme A, Sloggett C, et al., Supporting data for “Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software.”. GigaScience Database. 2019. 10.5524/100640.
What this badge says. CiteStamped means the CHECKABLE references of this
work were clean at the dated check: each resolved to a known work in a public registry, and none
carried a publisher retraction notice at that time. It says nothing about the quality, findings,
or importance of the work itself, and nothing about references deposited without a DOI.
checked 2026-07-14 — re-checked daily as this page is visited; titles and statuses come from Crossref and DataCite and are not part of the signed record
Embed this badge
Both snippets point at the live badge image and link back to this page. The badge re-renders from the daily check, so an embed never goes stale by more than a day of visits.
<a href="https://citestamp.com/citestamped/10.1093/gigascience/giz109"><img src="https://citestamp.com/citestamped/10.1093/gigascience/giz109/badge.svg" alt="CiteStamped reference-health badge" width="460" height="64"></a>
[](https://citestamp.com/citestamped/10.1093/gigascience/giz109)