Reference health

Ten simple rules for making research software more robust

https://doi.org/10.1371/journal.pcbi.1005412
CiteStamped reference-health badge
18/18 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.

9 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 18 checked references that resolve
resolves10.1038/nbt.3240
Toward effective software solutions for big biology
resolves10.1038/533452a
1,500 scientists lift the lid on reproducibility
resolves10.1145/2063348.2063374
A survey of the practice of computational science
resolves10.1080/21655979.2015.1050162
Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software
resolves10.1093/nar/gkv1116
Tools and data services registry: a community effort to document bioinformatics resources
resolves10.1101/gr.361602
The Bioperl Toolkit: Perl Modules for the Life Sciences
resolves10.1186/2047-217X-2-15
Ten recommendations for creating usable bioinformatics command line software
resolves10.1038/nrg3305
Next-generation sequencing data interpretation: enhancing reproducibility and accessibility
resolves10.1109/MS.2008.84
Dealing with Risk in Scientific Software Development
resolves10.1093/nar/gkw343
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update
resolves10.1109/MCSE.2012.62
Virtual Appliances, Cloud Computing, and Reproducible Research
resolves10.1186/gb-2004-5-10-r80
Bioconductor: open software development for computational biology and bioinformatics
resolves10.1371/journal.pbio.1001745
Best Practices for Scientific Computing
resolves10.1371/journal.pcbi.1005510
Good enough practices in scientific computing
resolves10.1371/journal.pcbi.1000424
A Quick Guide to Organizing Computational Biology Projects
resolves10.1371/journal.pcbi.1004668
A Quick Introduction to Version Control with Git and GitHub
resolves10.1038/nprot.2016.095
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
resolves10.1016/j.infsof.2014.11.001
A systematic literature review on the barriers faced by newcomers to open source software projects
The 9 references without a DOI — listed, not checked
no DOI — not checkedA decade of web server updates at the bioinformatics links directory: 2003–2012
no DOI — not checkedGOBLET: The Global Organisation for Bioinformatics Learning, Education and Training
no DOI — not checkedVaroquaux G. Software for reproducible science: let’s not have a misunderstanding; 2015. <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://gael-varoquaux.info/programming/software-for-reproducible-science-lets-not-have-a-misunderstanding.html" xlink:type="simple">http://gael-varoquaux.info/programming/software-for-reproducible-science-lets-not-have-a-misunderstanding.html</ext-link>.
no DOI — not checkedBrown CT. Replication, reproduction, and remixing in research software; 2013. <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://ivory.idyll.org/blog/research-software-reuse.html" xlink:type="simple">http://ivory.idyll.org/blog/research-software-reuse.html</ext-link>.
no DOI — not checkedTop considerations for creating bioinformatics software documentation
no DOI — not checkedBuilding a Better ReadMe
no DOI — not checkedFree Software Foundation. GNU Coding Standards; 2016. <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://www.gnu.org/prep/standards/standards.html" xlink:type="simple">https://www.gnu.org/prep/standards/standards.html</ext-link>.
no DOI — not checkedThe IEEE, The Open Group. The Open Group Base Specifications Issue 7 IEEE Std 1003.1-2008. 12. Utility Conventions; 2016. <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap12.html" xlink:type="simple">http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap12.html</ext-link>.
no DOI — not checkedPreston-Werner T. Semantic Versioning 2.0.0; 2016. <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://semver.org/spec/v2.0.0.html" xlink:type="simple">http://semver.org/spec/v2.0.0.html</ext-link>.
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

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