From 783a38929423964a106c18a699ff923b65a6a134 Mon Sep 17 00:00:00 2001 From: Thomas Vuillaume Date: Wed, 11 Feb 2026 17:00:33 +0100 Subject: [PATCH 1/2] add tools references in FAIR task page --- pages/tasks/fair_rs.md | 71 +++++++++++------------------------------- 1 file changed, 18 insertions(+), 53 deletions(-) diff --git a/pages/tasks/fair_rs.md b/pages/tasks/fair_rs.md index 804928cf..36b5fbbe 100644 --- a/pages/tasks/fair_rs.md +++ b/pages/tasks/fair_rs.md @@ -1,11 +1,12 @@ --- -title: Adopting FAIR software practices +title: Adopting FAIR Research Software Practices description: What practices and tools can help improve FAIRness of software? -contributors: ["Aleksandra Nenadic", "Daniel Garijo"] +contributors: ["Aleksandra Nenadic", "Daniel Garijo", "Thomas Vuillaume"] page_id: fair_rs -indicators: [] -related_pages: - tasks: [software_metadata, citing_software, licensing_software, software_documentation, documenting_code, archiving_software, organising_software_projects] +related_pages: + tasks: [software_metadata, citing_software, licensing_software, software_documentation, documenting_code, archiving_software, organising_software_projects, testing_software] +child_pages: [] +quality_indicators: [] keywords: ["fair software", "fair"] --- @@ -27,14 +28,14 @@ Let's have a quick look into what each of the above principle means in practice. ### How can we Make our Software Findable? - [Create a description of your software][software_metadata] to make it discoverable by search engines and other search tools -- Use standards (such as [CodeMeta][codemeta]) to describe interoperable metadata for your software (see [Research Software Metadata Guidelines][rsmd-g1]) +- Use standards (such as {% tool "codemeta" %}) to describe interoperable metadata for your software (see [Research Software Metadata Guidelines][rsmd-g1]) - Place your software in a public software repository (and ideally register it in a [general-purpose or domain-specific software registry][software-registries]) -- Use a unique and persistent identifiers for your software, such as **Digital Object Identifiers** (DOIs) provided by [Zenodo][zenodo], [FigShare][figshare], or **SoftWare Heritage persistent IDentifiers** ([SWHID](swhid)) provided by [Software Heritage][software-heritage]. +- Use a unique and persistent identifiers for your software, such as **Digital Object Identifiers** (DOIs) provided by {% tool "zenodo" %}, {% tool "figshare" %}, or **SoftWare Heritage persistent IDentifiers** ({% tool "swhid" %}) provided by {% tool "software-heritage" %}. In addition to findability of your software, identifiers can help you get credit for your work by providing citable references. - More broadly, use software sharing and collaborative platforms, as they facilitate code publication, sharing and findability: - - general-purpose software repositories - [GitHub][github] and [GitLab][gitlab] - - programming language-specific software repositories - [PyPi][pypi] (for Python) and [CRAN][cran] (for R) - - software registries - [BioTools][biotools] (for biosciences) and [Awesome Research Software Registries][awesome-rs-registries], providing a list of research software registries (by country, organisation, domain and programming language) where research software can be registered to help promote its discovery + - general-purpose software repositories - {% tool "github" %} and {% tool "gitlab" %} + - programming language-specific software repositories - {% tool "pypi" %} (for Python) and {% tool "cran" %} (for R) + - software registries - {% tool "biotools" %} (for biosciences) and {% tool "awesome-research-software-registries" %}, providing a list of research software registries (by country, organisation, domain and programming language) where research software can be registered to help promote its discovery ### How can we Make our Software Accessible? @@ -43,7 +44,7 @@ In addition to findability of your software, identifiers can help you get credit ### How can we Make our Software Interoperable? -- Use community-agreed standard formats for inputs and outputs of [your software and its metadata][software_metadata] (e.g. [CodeMeta][codemeta]) +- Use community-agreed standard formats for inputs and outputs of [your software and its metadata][software_metadata] (e.g. {% tool "codemeta" %}) - Communicate with other software and tools via standard protocols and APIs - Using standard data exchange, input and output formats and communication protocols helps create interoperable software that can more readily integrate with other tools into more complex pipelines - More broadly - explain the [functionality of your software and protocols (e.g command line interface) for interaction with it][documenting_code] @@ -51,7 +52,7 @@ In addition to findability of your software, identifiers can help you get credit ### How can we Make our Software Reusable? - [Document your software][software_documentation] (including its functionality, how to install and run it) to make it more understandable by others who may wish to reuse or extend it -- [Give a licence to your software][licensing_software] clearly stating how it can be reused (check the [open source licence guide][opensource-licence-guide] or [choosealicense.com][choosealicense] on choosing the licence most appropriate for your needs) +- [Give a licence to your software][licensing_software] clearly stating how it can be reused (check the {% tool "opensource-licence-guide" %} or {% tool "choosealicense" %} on choosing the licence most appropriate for your needs) - State how to [cite your software][citing_software], so people can give you credit when they reuse it - More broadly, follow best practices for software development, e.g. [structure your software][organising_software_projects] using common patterns and use coding conventions to make your code readable and understandable by people @@ -74,11 +75,11 @@ This mean that software may be FAIR, but still not very good in terms of what it Tools and frameworks exist for assessing software FAIRness: -- [FAIRsoft evaluator][fair-rs-evaluator] -- [FAIR software test][fair-rs-test] -- [FAIR Software Checklist][fair-rs-checklist] - a self-assessment tool developed by the Australian Research Data Commons (ARDC) and the Netherlands eScience Center -- ["How FAIR is your software"][howfairis] - a command line tool to evaluate a software repository's compliance with the FAIR principles -- [CODECHECK][codecheck] - an approach for independent execution of computations underlying research articles +- {% tool "fairsoft-evaluator" %} +- {% tool "fair-software-test" %} +- {% tool "fair-software-checklist" %} - a self-assessment tool developed by the Australian Research Data Commons (ARDC) and the Netherlands eScience Center +- {% tool "howfairis" %} - a command line tool to evaluate a software repository's compliance with the FAIR principles +- {% tool "codecheck" %} - an approach for independent execution of computations underlying research articles - [Common metrics for Research Software][fair-metrics] that may used to assess each of the FAIR4RS principles They not meant to criticise or discredit software or its authors. @@ -86,39 +87,3 @@ Their role is to make quality aspects visible, help researchers identify strengt In the context of research software, such assessments are diagnostic rather than evaluative — they guide reflection, transparency, and learning, not scoring or ranking. By using them, researchers can better understand how their software performs across different aspects of FAIRness and make informed decisions about how to improve it. -[awesome-rs-registries]: https://github.com/NLeSC/awesome-research-software-registries -[biotools]: https://bio.tools -[cff]: https://citation-file-format.github.io/ -[choosealicense]: https://choosealicense.com/ -[codecheck]: https://codecheck.org.uk/project/ -[codemeta]: (https://codemeta.github.io/) -[cran]: https://cran.r-project.org/web/packages/ -[fair-cookbook]: https://faircookbook.elixir-europe.org/content/home.html -[fair-rs-evaluator]: https://openebench.bsc.es/observatory/Evaluation -[fair-rs-test]: https://github.com/marioa/fair-test?tab=readme-ov-file -[fair-rs-checklist]: https://fairsoftwarechecklist.net -[fair4ml]: https://www.rd-alliance.org/groups/fair-machine-learning-fair4ml-ig/activity/ -[figshare]: https://figshare.com/ -[github]: https://github.com -[gitlab]: https://about.gitlab.com/ -[howfairis]: https://github.com/fair-software/howfairis/ -[opensource-licence-guide]: https://opensource.guide/legal/#which-open-source-license-is-appropriate-for-my-project -[rsmd-g1]: https://fair-impact.github.io/RSMD-guidelines/1.General/ -[swhid]: https://docs.softwareheritage.org/devel/swh-model/persistent-identifiers.html -[pypi]: https://pypi.org/ -[software-heritage]: https://www.softwareheritage.org/ -[software-registries]: https://github.com/NLeSC/awesome-research-software-registries -[zenodo]: https://zenodo.org/ -[fair-data]: https://doi.org/10.1038/sdata.2016.18 -[fair-workflows]: https://doi.org/10.1038/s41597-025-04451-9 -[fair-rs]: https://doi.org/10.15497/RDA00068 -[rs-quality]: ./quality -[fair-metrics]: https://doi.org/10.5281/zenodo.15535629 -[software_metadata]: ./software_metadata -[software_documentation]: ./software_documentation -[licensing_software]: ./licensing_software -[documenting_code]: ./documenting_code -[archiving_software.md]: ./archiving_software -[testing_software]: ./testing_software -[citing_software]: ./citing_software -[organising_software_projects]: ./organising_software_projects From b2699ba22eb01ce5e7b9d86aa48a4b3cfa1d0846 Mon Sep 17 00:00:00 2001 From: Thomas Vuillaume Date: Wed, 11 Feb 2026 17:19:37 +0100 Subject: [PATCH 2/2] fix tools names --- pages/tasks/fair_rs.md | 42 +++++++++++++++++++++++++++++++++++------- 1 file changed, 35 insertions(+), 7 deletions(-) diff --git a/pages/tasks/fair_rs.md b/pages/tasks/fair_rs.md index 36b5fbbe..937c8234 100644 --- a/pages/tasks/fair_rs.md +++ b/pages/tasks/fair_rs.md @@ -30,12 +30,12 @@ Let's have a quick look into what each of the above principle means in practice. - [Create a description of your software][software_metadata] to make it discoverable by search engines and other search tools - Use standards (such as {% tool "codemeta" %}) to describe interoperable metadata for your software (see [Research Software Metadata Guidelines][rsmd-g1]) - Place your software in a public software repository (and ideally register it in a [general-purpose or domain-specific software registry][software-registries]) -- Use a unique and persistent identifiers for your software, such as **Digital Object Identifiers** (DOIs) provided by {% tool "zenodo" %}, {% tool "figshare" %}, or **SoftWare Heritage persistent IDentifiers** ({% tool "swhid" %}) provided by {% tool "software-heritage" %}. +- Use a unique and persistent identifiers for your software, such as **Digital Object Identifiers** (DOIs) provided by {% tool "zenodo" %}, {% tool "figshare" %}, or **SoftWare Heritage persistent IDentifiers** ([SWHID](swhid)) provided by {% tool "software-heritage" %}. In addition to findability of your software, identifiers can help you get credit for your work by providing citable references. - More broadly, use software sharing and collaborative platforms, as they facilitate code publication, sharing and findability: - general-purpose software repositories - {% tool "github" %} and {% tool "gitlab" %} - - programming language-specific software repositories - {% tool "pypi" %} (for Python) and {% tool "cran" %} (for R) - - software registries - {% tool "biotools" %} (for biosciences) and {% tool "awesome-research-software-registries" %}, providing a list of research software registries (by country, organisation, domain and programming language) where research software can be registered to help promote its discovery + - programming language-specific software repositories - {% tool "pypi" %} (for {% tool "python" %}) and {% tool "cran" %} (for R) + - software registries - {% tool "biotools" %} (for biosciences) and [Awesome Research Software Registries][awesome-rs-registries], providing a list of research software registries (by country, organisation, domain and programming language) where research software can be registered to help promote its discovery ### How can we Make our Software Accessible? @@ -52,7 +52,7 @@ In addition to findability of your software, identifiers can help you get credit ### How can we Make our Software Reusable? - [Document your software][software_documentation] (including its functionality, how to install and run it) to make it more understandable by others who may wish to reuse or extend it -- [Give a licence to your software][licensing_software] clearly stating how it can be reused (check the {% tool "opensource-licence-guide" %} or {% tool "choosealicense" %} on choosing the licence most appropriate for your needs) +- [Give a licence to your software][licensing_software] clearly stating how it can be reused (check the [open source licence guide][opensource-licence-guide] or {% "choosealicense" %} on choosing the licence most appropriate for your needs) - State how to [cite your software][citing_software], so people can give you credit when they reuse it - More broadly, follow best practices for software development, e.g. [structure your software][organising_software_projects] using common patterns and use coding conventions to make your code readable and understandable by people @@ -75,9 +75,9 @@ This mean that software may be FAIR, but still not very good in terms of what it Tools and frameworks exist for assessing software FAIRness: -- {% tool "fairsoft-evaluator" %} -- {% tool "fair-software-test" %} -- {% tool "fair-software-checklist" %} - a self-assessment tool developed by the Australian Research Data Commons (ARDC) and the Netherlands eScience Center +- {% tool "fair-rs-evaluator" %} +- {% tool "fair-rs-test" %} +- {% tool "fair-rs-checklist" %} - a self-assessment tool developed by the Australian Research Data Commons (ARDC) and the Netherlands eScience Center - {% tool "howfairis" %} - a command line tool to evaluate a software repository's compliance with the FAIR principles - {% tool "codecheck" %} - an approach for independent execution of computations underlying research articles - [Common metrics for Research Software][fair-metrics] that may used to assess each of the FAIR4RS principles @@ -87,3 +87,31 @@ Their role is to make quality aspects visible, help researchers identify strengt In the context of research software, such assessments are diagnostic rather than evaluative — they guide reflection, transparency, and learning, not scoring or ranking. By using them, researchers can better understand how their software performs across different aspects of FAIRness and make informed decisions about how to improve it. +[awesome-rs-registries]: https://github.com/NLeSC/awesome-research-software-registries +[biotools]: https://bio.tools +[cff]: https://citation-file-format.github.io/ +[codecheck]: https://codecheck.org.uk/project/ +[cran]: https://cran.r-project.org/web/packages/ +[fair-cookbook]: https://faircookbook.elixir-europe.org/content/home.html +[fair-rs-evaluator]: https://openebench.bsc.es/observatory/Evaluation +[fair-rs-test]: https://github.com/marioa/fair-test?tab=readme-ov-file +[fair-rs-checklist]: https://fairsoftwarechecklist.net +[fair4ml]: https://www.rd-alliance.org/groups/fair-machine-learning-fair4ml-ig/activity/ +[opensource-licence-guide]: https://opensource.guide/legal/#which-open-source-license-is-appropriate-for-my-project +[rsmd-g1]: https://fair-impact.github.io/RSMD-guidelines/1.General/ +[swhid]: https://docs.softwareheritage.org/devel/swh-model/persistent-identifiers.html +[software-registries]: https://github.com/NLeSC/awesome-research-software-registries +[zenodo]: https://zenodo.org/ +[fair-data]: https://doi.org/10.1038/sdata.2016.18 +[fair-workflows]: https://doi.org/10.1038/s41597-025-04451-9 +[fair-rs]: https://doi.org/10.15497/RDA00068 +[rs-quality]: ./quality +[fair-metrics]: https://doi.org/10.5281/zenodo.15535629 +[software_metadata]: ./software_metadata +[software_documentation]: ./software_documentation +[licensing_software]: ./licensing_software +[documenting_code]: ./documenting_code +[archiving_software.md]: ./archiving_software +[testing_software]: ./testing_software +[citing_software]: ./citing_software +[organising_software_projects]: ./organising_software_projects \ No newline at end of file