diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml index d8d8ed1a..5e16bda9 100644 --- a/.github/workflows/check.yml +++ b/.github/workflows/check.yml @@ -19,7 +19,7 @@ jobs: uses: actions/checkout@v4 with: repository: esciencecenter-digital-skills/NEBULA - ref: v0.4.0 + ref: v0.4.2 path: ./NEBULA - name: Checkout content diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index 0f2dadae..0014bdea 100644 --- a/.github/workflows/deploy.yml +++ b/.github/workflows/deploy.yml @@ -12,8 +12,8 @@ jobs: with: content_organization: esciencecenter-digital-skills content_repository: research-software-support - content_ref: v0.1.1 + content_ref: main base_url: research-software-support - nebula_ref: v0.4.1 + nebula_ref: v0.4.2 diff --git a/modules/citation/citationcff.md b/modules/citation/citationcff.md index cc207caf..50d67596 100644 --- a/modules/citation/citationcff.md +++ b/modules/citation/citationcff.md @@ -1,5 +1,5 @@ --- -title: The `CITATION.cff` file +title: CITATION.cff file type: reading order: 4 --- diff --git a/modules/citation/create_citation_file.md b/modules/citation/create_citation_file.md index 8534987b..1b84bd1f 100644 --- a/modules/citation/create_citation_file.md +++ b/modules/citation/create_citation_file.md @@ -1,5 +1,5 @@ --- -title: Using cffinit to create `CITATION.cff` +title: CFFinit tool type: exercise order: 5 --- diff --git a/modules/citation/ex_when_to_cite.md b/modules/citation/ex_when_to_cite.md index 658223fa..118ccf53 100644 --- a/modules/citation/ex_when_to_cite.md +++ b/modules/citation/ex_when_to_cite.md @@ -1,5 +1,5 @@ --- -title: Which software should I cite? +title: What to cite? type: exercise order: 6 --- diff --git a/modules/citation/further_reading.md b/modules/citation/further_reading.md index 13ec9204..eadbed3c 100644 --- a/modules/citation/further_reading.md +++ b/modules/citation/further_reading.md @@ -1,5 +1,5 @@ --- -title: Reading material +title: Further reading type: reading order: 7 --- diff --git a/modules/citation/index.md b/modules/citation/index.md index 4afc17ec..c1852918 100644 --- a/modules/citation/index.md +++ b/modules/citation/index.md @@ -1,5 +1,5 @@ --- -id: 0 +id: 3 trl: medium category: Publishing & Citing title: Software citation diff --git a/modules/citation/principles.md b/modules/citation/principles.md index 7b26cb0e..5e2bd9cb 100644 --- a/modules/citation/principles.md +++ b/modules/citation/principles.md @@ -4,9 +4,8 @@ type: reading order: 3 --- -## The FORCE11 working group published the [Software Citation Principles](https://force11.org/info/software-citation-principles-published-2016/) - -### The principles +### The software citation principles +The FORCE11 working group published the [Software Citation Principles](https://force11.org/info/software-citation-principles-published-2016/) **Importance**: Software should be considered a legitimate and citable product of research. Software citations should be accorded the same importance in the scholarly record as citations of other research products, such as publications and data; they should be included in the metadata of the citing work, for example in the reference list of a journal article, and should not be omitted or separated. Software should be cited on the same basis as any other research product such as a paper or a book, that is, authors should cite the appropriate set of software products just as they cite the appropriate set of papers. diff --git a/modules/fairsoftware/exercise1.md b/modules/fairsoftware/exercise1.md index 80910950..353d4646 100644 --- a/modules/fairsoftware/exercise1.md +++ b/modules/fairsoftware/exercise1.md @@ -4,9 +4,7 @@ type: exercise order: 2 --- -# Exercise 1 - -## What is FAIR? +## Exercise: What is FAIR? ### FAIR principles (15 minutes) diff --git a/modules/fairsoftware/exercise2.md b/modules/fairsoftware/exercise2.md index 3348f67e..4302818b 100644 --- a/modules/fairsoftware/exercise2.md +++ b/modules/fairsoftware/exercise2.md @@ -4,9 +4,7 @@ type: exercise order: 3 --- -# Exercise 2 - -## Mapping the principles +## Exercise: Mapping the principles ### The FAIR4RS Principles are: @@ -45,7 +43,7 @@ The following three examples of software have been described with statements tha #### Example 1: [Comet](https://doi.org/10.1002/pmic.201200439) -Comet is a command-line tool and desktop application for tandem mass spectrometry sequence database search6. +[Comet](https://doi.org/10.1002/pmic.201200439) is a command-line tool and desktop application for tandem mass spectrometry sequence database search6. - Comet is licensed under the Apache 2.0 open source licence. - Comet is registered in the bio.tools catalogue of bioinformatics tools, where it has a globally unique and persistent identifier, and rich metadata that includes the identifier and is searchable and indexable. @@ -57,7 +55,7 @@ Comet is a command-line tool and desktop application for tandem mass spectrometr #### Example 2: [PureGoMe](https://doi.org/10.5281/zenodo.4337242) -PuReGoMe is a project aimed at understanding Dutch public sentiment during the COVID-19 outbreak period by analysing real-time Twitter data. It provides a collection of Python scripts and Jupyter notebooks for this purpose. +[PureGoMe](https://doi.org/10.5281/zenodo.4337242) is a project aimed at understanding Dutch public sentiment during the COVID-19 outbreak period by analysing real-time Twitter data. It provides a collection of Python scripts and Jupyter notebooks for this purpose. - PureGoMe can be downloaded from the project repository, while metadata is accessible independently from the registry. - PuReGoMe's GitHub repository has detailed records of the development history. @@ -70,7 +68,7 @@ PuReGoMe is a project aimed at understanding Dutch public sentiment during the C #### Example 3: [gammaShiny](https://doi.org/10.5281/zenodo.4139005) -gammaShiny is an application that provides enhanced graphical user interfaces for the R gamma package8. It is used to process in-situ gamma-ray spectrometry measurements for luminescence dating. +[gammaShiny](https://doi.org/10.5281/zenodo.4139005) is an application that provides enhanced graphical user interfaces for the R gamma package8. It is used to process in-situ gamma-ray spectrometry measurements for luminescence dating. - gammaShiny has been deposited in the HAL French national archive and it has a persistent globally unique identifier, with the HAL identifier of the metadata record and a SWHID, identifying specifically the software artefact on the Software Heritage universal software source code archive. - Thanks to the HAL platform, where a licence is mandatory, gammaShiny is under a GNU General Public Licence v3.0. diff --git a/modules/fairsoftware/exercise3.md b/modules/fairsoftware/exercise3.md index e3d11eb2..ec97fef4 100644 --- a/modules/fairsoftware/exercise3.md +++ b/modules/fairsoftware/exercise3.md @@ -4,9 +4,7 @@ type: exercise order: 4 --- -# Exercise 3 - -## FAIR in practice +## Exercise: FAIR in practice Role playing exercise: One person presents the software, the other person gives feedback. diff --git a/modules/fairsoftware/reading.md b/modules/fairsoftware/reading.md index 410217b4..d1d5d88d 100644 --- a/modules/fairsoftware/reading.md +++ b/modules/fairsoftware/reading.md @@ -1,5 +1,5 @@ --- -title: Reading material +title: Further reading type: reading order: 5 --- @@ -11,4 +11,5 @@ Follow the links below to read about other resources related to FAIR research so ### FAIR Research Software Principles adoption The FAIR4RS Principles were [released in 2022](https://doi.org/10.15497/RDA00068), and since then there have been many efforts for adopting them. + The blog post [The FAIR for Research Software Principles after two years: an adoption update](https://www.researchsoft.org/blog/2024-03/) contains a summary of these efforts. \ No newline at end of file diff --git a/modules/licenses/ex_choose_a_license.md b/modules/licenses/ex_choose_a_license.md index 3c3bf2a9..b30f6ecb 100644 --- a/modules/licenses/ex_choose_a_license.md +++ b/modules/licenses/ex_choose_a_license.md @@ -1,5 +1,5 @@ --- -title: Choose a license for or using your policy +title: Choose a license type: exercise order: 5 --- diff --git a/modules/licenses/ex_have_licensing_policy.md b/modules/licenses/ex_have_licensing_policy.md index d19212e8..77d70662 100644 --- a/modules/licenses/ex_have_licensing_policy.md +++ b/modules/licenses/ex_have_licensing_policy.md @@ -1,5 +1,5 @@ --- -title: Does your university have a software licensing policy? +title: Is there a policy? type: exercise order: 6 --- diff --git a/modules/licenses/ex_licenses_in_use.md b/modules/licenses/ex_licenses_in_use.md index 7c7b02f4..fae99d9c 100644 --- a/modules/licenses/ex_licenses_in_use.md +++ b/modules/licenses/ex_licenses_in_use.md @@ -1,5 +1,5 @@ --- -title: What licenses do researchers at your university use? +title: What's used? type: exercise order: 7 --- diff --git a/modules/licenses/university_policy.md b/modules/licenses/university_policy.md index 400df28d..6af8e35b 100644 --- a/modules/licenses/university_policy.md +++ b/modules/licenses/university_policy.md @@ -1,5 +1,5 @@ --- -title: University software policies +title: University Policies type: reading order: 3 --- diff --git a/modules/publication/automating_software_publication.md b/modules/publication/automating_software_publication.md index 84323810..205e5f2b 100644 --- a/modules/publication/automating_software_publication.md +++ b/modules/publication/automating_software_publication.md @@ -1,5 +1,5 @@ --- -title: Automating software publication +title: Automating publication type: exercise order: 4 --- diff --git a/modules/publication/discussion.md b/modules/publication/discussion.md index 376fa457..27a6b93e 100644 --- a/modules/publication/discussion.md +++ b/modules/publication/discussion.md @@ -1,12 +1,10 @@ --- -title: Discussion -type: reading +title: Before we dive in... +type: exercise order: 1 --- -# Discussion - -## Before we dive in... +## Discussion: Before we dive in... What do you already know about software publication? diff --git a/modules/publication/index.md b/modules/publication/index.md index 94a2ece2..ca087ebc 100644 --- a/modules/publication/index.md +++ b/modules/publication/index.md @@ -1,5 +1,5 @@ --- -id: 8 +id: 1 trl: medium category: Publishing & Citing title: Software publication diff --git a/modules/publication/media/fair.png b/modules/publication/media/fair.png new file mode 100644 index 00000000..77343956 Binary files /dev/null and b/modules/publication/media/fair.png differ diff --git a/modules/publication/reading.md b/modules/publication/reading.md index d41ffcbb..b63b4112 100644 --- a/modules/publication/reading.md +++ b/modules/publication/reading.md @@ -1,5 +1,5 @@ --- -title: Reading material +title: Further reading type: reading order: 6 --- diff --git a/modules/publication/slides-publication.pmd b/modules/publication/slides-publication.pmd index bbcf19e8..ffce3a94 100644 --- a/modules/publication/slides-publication.pmd +++ b/modules/publication/slides-publication.pmd @@ -31,15 +31,11 @@ The goal is to allow others to find and use your code, if they so wish, without ## Why Publish? -### Major scientific considerations -* Citability -* Reproducibility - - -### FAIRness -