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 -
- -
+* Major scientific considerations + * Citability + * Reproducibility +* FAIRness + Note: diff --git a/modules/publication/software_publication_pipeline.md b/modules/publication/software_publication_pipeline.md index 4c7743a6..409bec91 100644 --- a/modules/publication/software_publication_pipeline.md +++ b/modules/publication/software_publication_pipeline.md @@ -1,5 +1,5 @@ --- -title: Software publication pipeline +title: Publication pipeline type: reading order: 3 --- diff --git a/modules/researchsoftware/exercise-is-it-research-software.md b/modules/researchsoftware/exercise-is-it-research-software.md index 78fe79d4..c94df799 100644 --- a/modules/researchsoftware/exercise-is-it-research-software.md +++ b/modules/researchsoftware/exercise-is-it-research-software.md @@ -1,7 +1,7 @@ --- -title: Is it research software? +title: Research software? type: exercise -order: 3 +order: 5 --- ## Exercise: Is it research software? diff --git a/modules/researchsoftware/exercise-research-life-cycle.md b/modules/researchsoftware/exercise-research-life-cycle.md index 4c289ee1..c8dda175 100644 --- a/modules/researchsoftware/exercise-research-life-cycle.md +++ b/modules/researchsoftware/exercise-research-life-cycle.md @@ -1,14 +1,14 @@ --- -title: Where does software fit in the research life cycle? +title: Research life cycle type: exercise -order: 4 +order: 6 --- ## Exercise: Where does software fit in the research life cycle? Take a look at the research life cycle below. -The Research Life Cycle +The Research Life Cycle Think of a piece of research software you have used or developed. diff --git a/modules/researchsoftware/research-software.md b/modules/researchsoftware/research-software.md index 214f1877..2b6c170a 100644 --- a/modules/researchsoftware/research-software.md +++ b/modules/researchsoftware/research-software.md @@ -1,7 +1,7 @@ --- -title: The role of research software +title: Research software type: reading -order: 5 +order: 4 --- ## The role of research software (10 minutes) diff --git a/modules/researchsoftware/slides-researchsoftware.pmd b/modules/researchsoftware/slides-researchsoftware.pmd index 77f767ec..831b798b 100644 --- a/modules/researchsoftware/slides-researchsoftware.pmd +++ b/modules/researchsoftware/slides-researchsoftware.pmd @@ -1,7 +1,7 @@ --- title: Research Software type: slides -order: 2 +order: 3 --- @@ -41,7 +41,7 @@ The data can be converted into an image using custom software. ## The research lifecycle
-The Research Life Cycle +The Research Life Cycle
Software is used all across the research lifecycle @@ -55,7 +55,7 @@ Software is used all across the research life cycle.
- +
definition of Research Software from the FAIR4RS working group diff --git a/modules/researchsoftware/slides-software.pmd b/modules/researchsoftware/slides-software.pmd index 78ac6227..ad105fd8 100644 --- a/modules/researchsoftware/slides-software.pmd +++ b/modules/researchsoftware/slides-software.pmd @@ -16,9 +16,9 @@ order: 1 ## Software is data -Computer scientist: *"Software is just data"* +Some data enthousiasts might say: *"Software is just data"*
- +
Photo by Alexander Sinn on Unsplash @@ -53,12 +53,11 @@ Software is stored as bits and read from disk, loaded into memory and processed ## Software is not data -Everyone but computer scientists: *"Software is not data"* - +Everyone but the data enthousiast: *"Software is not data"*
- +
Photo by Barn Images on Unsplash diff --git a/modules/researchsoftware/software-and-data.md b/modules/researchsoftware/software-and-data.md index 0d0147a1..61fed1f0 100644 --- a/modules/researchsoftware/software-and-data.md +++ b/modules/researchsoftware/software-and-data.md @@ -1,7 +1,7 @@ --- -title: Software is data +title: Software and data type: reading -order: 6 +order: 2 --- ### Software is data (10 minutes, optional) @@ -11,7 +11,7 @@ Read the following blogpost about why this concept is so powerful: https://www.blackliszt.com/2014/04/fundamental-concepts-of-computing-software-is-data.html -### Software is a special type of data () +### Software is a special type of data (10 minutes, optional) However for most practical purposes in most domains of scientific research (except maybe the domain of computer science) it is useful to make a distinction between the data that is software and other data. From now on, when we use the word data, we mean the kind fo data which is not software and which we use to store more static information. - Software is executable, data is not. @@ -27,5 +27,4 @@ https://doi.org/10.7287/peerj.preprints.2630v1 ### Discussion -- - Can you think of examples where the line between software and data becomes fuzzy? diff --git a/modules/smp/index.md b/modules/softwaremanagementplans/index.md similarity index 100% rename from modules/smp/index.md rename to modules/softwaremanagementplans/index.md diff --git a/modules/smp/info.md b/modules/softwaremanagementplans/info.md similarity index 100% rename from modules/smp/info.md rename to modules/softwaremanagementplans/info.md diff --git a/modules/smp/media/documentation.png b/modules/softwaremanagementplans/media/documentation.png similarity index 100% rename from modules/smp/media/documentation.png rename to modules/softwaremanagementplans/media/documentation.png diff --git a/modules/smp/media/engineering.png b/modules/softwaremanagementplans/media/engineering.png similarity index 100% rename from modules/smp/media/engineering.png rename to modules/softwaremanagementplans/media/engineering.png diff --git a/modules/smp/media/groupedrequirements.png b/modules/softwaremanagementplans/media/groupedrequirements.png similarity index 100% rename from modules/smp/media/groupedrequirements.png rename to modules/softwaremanagementplans/media/groupedrequirements.png diff --git a/modules/smp/media/maintenance.png b/modules/softwaremanagementplans/media/maintenance.png similarity index 100% rename from modules/smp/media/maintenance.png rename to modules/softwaremanagementplans/media/maintenance.png diff --git a/modules/smp/media/nlesc-dummy.png b/modules/softwaremanagementplans/media/nlesc-dummy.png similarity index 100% rename from modules/smp/media/nlesc-dummy.png rename to modules/softwaremanagementplans/media/nlesc-dummy.png diff --git a/modules/smp/media/projectmanagement.png b/modules/softwaremanagementplans/media/projectmanagement.png similarity index 100% rename from modules/smp/media/projectmanagement.png rename to modules/softwaremanagementplans/media/projectmanagement.png diff --git a/modules/smp/media/purpose.png b/modules/softwaremanagementplans/media/purpose.png similarity index 100% rename from modules/smp/media/purpose.png rename to modules/softwaremanagementplans/media/purpose.png diff --git a/modules/smp/media/researchcycle.png b/modules/softwaremanagementplans/media/researchcycle.png similarity index 100% rename from modules/smp/media/researchcycle.png rename to modules/softwaremanagementplans/media/researchcycle.png diff --git a/modules/smp/media/smpguide.png b/modules/softwaremanagementplans/media/smpguide.png similarity index 100% rename from modules/smp/media/smpguide.png rename to modules/softwaremanagementplans/media/smpguide.png diff --git a/modules/smp/media/softwarespectrum.png b/modules/softwaremanagementplans/media/softwarespectrum.png similarity index 100% rename from modules/smp/media/softwarespectrum.png rename to modules/softwaremanagementplans/media/softwarespectrum.png diff --git a/modules/smp/media/threelevels.png b/modules/softwaremanagementplans/media/threelevels.png similarity index 100% rename from modules/smp/media/threelevels.png rename to modules/softwaremanagementplans/media/threelevels.png diff --git a/modules/smp/media/thumbnail-smp.jpg b/modules/softwaremanagementplans/media/thumbnail-smp.jpg similarity index 100% rename from modules/smp/media/thumbnail-smp.jpg rename to modules/softwaremanagementplans/media/thumbnail-smp.jpg diff --git a/modules/smp/media/venn_fairsmp.png b/modules/softwaremanagementplans/media/venn_fairsmp.png similarity index 100% rename from modules/smp/media/venn_fairsmp.png rename to modules/softwaremanagementplans/media/venn_fairsmp.png diff --git a/modules/smp/media/viaappia.png b/modules/softwaremanagementplans/media/viaappia.png similarity index 100% rename from modules/smp/media/viaappia.png rename to modules/softwaremanagementplans/media/viaappia.png diff --git a/modules/smp/exercise1.md b/modules/softwaremanagementplans/practicalguide.md similarity index 92% rename from modules/smp/exercise1.md rename to modules/softwaremanagementplans/practicalguide.md index 55034b06..8b4041e3 100644 --- a/modules/smp/exercise1.md +++ b/modules/softwaremanagementplans/practicalguide.md @@ -1,12 +1,11 @@ --- -title: Exercise 1 -type: exercise +title: Practical Guide +type: reading order: 2 --- -# Exercise 1 -## Software Management Plans (10 minutes) +## Practical Guide to Software Management Plans (15 minutes) Research software plays a crucial role in academic research and has become a key output of many research projects. A software management plan helps to implement best practices during software development and ensures that software is accessible and reusable in the short and longer term. It also contributes to the reproducibility of results and stimulates collaborative work on open-source software for research. diff --git a/modules/smp/reading.md b/modules/softwaremanagementplans/reading.md similarity index 100% rename from modules/smp/reading.md rename to modules/softwaremanagementplans/reading.md diff --git a/modules/smp/slides-smp.pmd b/modules/softwaremanagementplans/slides-smp.pmd similarity index 100% rename from modules/smp/slides-smp.pmd rename to modules/softwaremanagementplans/slides-smp.pmd diff --git a/modules/smp/exercise3.md b/modules/softwaremanagementplans/smpvsfair.md similarity index 97% rename from modules/smp/exercise3.md rename to modules/softwaremanagementplans/smpvsfair.md index b96cd8cf..b29e7a27 100644 --- a/modules/smp/exercise3.md +++ b/modules/softwaremanagementplans/smpvsfair.md @@ -1,11 +1,9 @@ --- -title: Exercise 3 +title: SMP vs FAIR type: exercise order: 4 --- -# Exercise 3 - ## SMP vs FAIR ### Why do we care? diff --git a/modules/smp/exercise2.md b/modules/softwaremanagementplans/softwareassessment.md similarity index 97% rename from modules/smp/exercise2.md rename to modules/softwaremanagementplans/softwareassessment.md index 0979f527..0c8ec91b 100644 --- a/modules/smp/exercise2.md +++ b/modules/softwaremanagementplans/softwareassessment.md @@ -1,10 +1,10 @@ --- -title: Exercise 2 +title: Software Assessment type: exercise order: 3 --- -# Exercise 2 +# Assess your software *In a live setting, this exercise is done in groups. Each group will be assigned a software project.