diff --git a/.github/spellignore.txt b/.github/spellignore.txt new file mode 100644 index 0000000..888464a --- /dev/null +++ b/.github/spellignore.txt @@ -0,0 +1,161 @@ +ADDME +AllDigital +anonymise +APIs +artifacts +aspirational +backend +Badging +BioExcel +BIOEXCEL-FRAMEWORK +bioinformatician +bioinformatics +Bioschemas +Braunschweig +BSSW +CASTIEL +Carpentries +CarpentriesData +CarpentriesLibrary +CarpentriesSoftware +Center +CHAOSS +codebase +CodeRefinery +comp-lvls-se +Coursera +CRSP +CSE +cybersecurity +DALIA +DaLiJe +de +DFG +DigComp +DigCompEdu +DigCompOrg +DigiFlex +digitalisation +DigitalSkillsGap +distributable +DMP +DOCBB +DOMREP +EBI +ECTS +EduTrain +edX +EMBL +EMBL-EBI +eng +ENCCS +EOR +Erlangen-Nürnberg +ERuDIte +EuroCC +EuroHPC +examplemaster +exascale +ExCALIBUR +EXCELERATE +executables +FAIRness +FAU +findability +findable +FIXME +Forschung +Friedrich +Fortran +franca +funders +FutureUniversity +genomic +GitHub +GitLab +GDPR +GPL +habilitation +HAI +Hannay +HIDA +HIFIS +HMC +HPC +HPC-Akademie +HPC-CF +HPC-oriented +HTC +IDEs +Ing +ISCB +Jena +JOSS +JU +Kanban +KDL-CAREERS +KSA +KSAs +LIBS +lingua +LLM +LLMs +LRZIntroCpp +LRZModernCpp +matplotlib +MATSE +MOOCs +MPI +multicore +multithreading +NFDI +NFDI4Ing +numpy +OECD +OER +OpenScience +Orithena +OSI-approved +Paderborn +pdf +PerMedCoE +PhDs +PRACE +pre-recorded +pre-requisite +proto +PRs +RDM +RDM-RSE +repos +reproducibility +ReproHack +researchology +researchonomy +reusability +RSE +RSE's +rse-specialisations +RTPs +scipy +SeniorCC +SRU +SSI +sth +SureSoft +SusTrainable +SWLC +swrepo +swrepos +SWREPOS +SysOps +tbl +TeSS +teams-se +TrainingMaterial +UofO +un-deRSE +US-RSE +WIP +Wissenschaft +Zenodo diff --git a/.github/workflows/compile.yml b/.github/workflows/compile.yml new file mode 100644 index 0000000..791228e --- /dev/null +++ b/.github/workflows/compile.yml @@ -0,0 +1,48 @@ +name: compilepaper +on: [push] +jobs: + paper: + runs-on: ubuntu-latest + env: + DIR: . + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Install pandoc + run: | + sudo apt-get update && sudo apt-get install -y --no-install-recommends \ + texlive texlive-latex-extra pandoc latexmk \ + texlive-bibtex-extra biber \ + texlive-fonts-recommended texlive-fonts-extra lmodern fonts-linuxlibertine \ + python3 python3-yaml \ + xz-utils make gpg-agent + python3 -m pip install -r ${{ env.DIR }}/002/requirements.txt + - name: pandoc compile + working-directory: ${{ env.DIR }}/002/ + run: make all + - name: move + run: mkdir -p github_artifacts && mv ${{ env.DIR }}/002/*.pdf ./github_artifacts/ + - name: Upload pdf as artifact + uses: actions/upload-artifact@v3 + with: + name: PDF files + path: ./github_artifacts + deploy: + needs: [paper] + runs-on: ubuntu-latest + if: ${{ github.repository == 'CaptainSifff/paper_teaching-learning-RSE' && github.ref == 'refs/heads/main' }} + steps: + - name: Checkout + uses: actions/checkout@v4 + - uses: actions/download-artifact@v3 + with: + path: github_artifacts + - name: move + run: mkdir -p github_deploy && mv github_artifacts/*/* github_deploy + - name: deploy on orphan branch + uses: peaceiris/actions-gh-pages@v3 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: ./github_deploy + publish_branch: build + force_orphan: true diff --git a/.github/workflows/spellcheck.yml b/.github/workflows/spellcheck.yml new file mode 100644 index 0000000..25cced4 --- /dev/null +++ b/.github/workflows/spellcheck.yml @@ -0,0 +1,42 @@ +name: 'spellcheck' +on: + workflow_dispatch: + pull_request: + push: + branches: + - main + +jobs: + spellcheck: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: "populate spellignore" + run: | + for file in "*.md" + do + # strip citations and references + sed -ri 's/\[@[A-Za-z0-9_ ;@-]+\]//g' $file + sed -ri 's/[^#\[][@#][A-Za-z0-9_ ;@-]+:[A-Za-z0-9_ ;@-]+}*//g' $file + sed -ri 's/@[A-Za-z0-9_]+//g' $file + # strip words that escape the spellchecker allowlist + sed -i 's/Dr.-Ing.//g; s/Ph.D.//g; s/M.Sc.//g; s/B.Sc.//g; s/Fortran//g;' $file + # latex commands + grep -P -oh -e "(?<=[\\\\\{])[A-Za-z]+" $file | sort | uniq >> .github/spellignore.txt + # RSE compositions + grep -P -oh -e "[\w-]*RSE[\w-]*" $file | sort | uniq >> .github/spellignore.txt + # remove header + sed -i '1,/---/{/^---$/,/^---$/d}' $file + done + - name: "populate spellignore with author names" + uses: mikefarah/yq@master + with: + cmd: | + yq '.authors[] | .lastName' contributors.yml | sed 's/ /\n/g; /null/d' >> .github/spellignore.txt + yq '.authors[] | .firstName' contributors.yml | sed 's/ /\n/g; /null/d' >> .github/spellignore.txt + yq '.authors[] | .suffixName' contributors.yml | sed 's/ /\n/g; /null/d' >> .github/spellignore.txt + - uses: eschercloudai/md-spellcheck-action@v0.0.2 + with: + files-to-check: "competencies.md|call_to_action.md|survey.md|institutionalised_education.md|intro.md" + files-to-exclude: "CONTRIBUTING.md\nREADME.md" + words-to-ignore-file: .github/spellignore.txt diff --git a/002/.gitignore b/002/.gitignore new file mode 100644 index 0000000..906c9b6 --- /dev/null +++ b/002/.gitignore @@ -0,0 +1,6 @@ +call_to_action.pdf +competencies.pdf +institutionalised_education.pdf +intro.pdf +survey.pdf +build/ diff --git a/002/CODE_OF_CONDUCT.md b/002/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..5e6a41e --- /dev/null +++ b/002/CODE_OF_CONDUCT.md @@ -0,0 +1,128 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, race, religion, or sexual identity +and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the + overall community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or + advances of any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email + address, without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official e-mail address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at +Florian Goth . +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series +of actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or +permanent ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within +the community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.0, available at +https://www.contributor-covenant.org/version/2/0/code_of_conduct.html. + +Community Impact Guidelines were inspired by [Mozilla's code of conduct +enforcement ladder](https://github.com/mozilla/diversity). + +[homepage]: https://www.contributor-covenant.org + +For answers to common questions about this code of conduct, see the FAQ at +https://www.contributor-covenant.org/faq. Translations are available at +https://www.contributor-covenant.org/translations. diff --git a/002/CONTRIBUTING.md b/002/CONTRIBUTING.md new file mode 100644 index 0000000..da9179a --- /dev/null +++ b/002/CONTRIBUTING.md @@ -0,0 +1,54 @@ +# Contributing to our project on teaching RSE + +This paper is intended as a collaborative effort and we are looking for input from you! + +You can contribute in various ways: + +- Propose content/text via pull request +- Improve existing content via pull request +- Review or comment on pull requests of others + +Nevertheless we follow some rules: + +## We Develop with GitHub + +We use GitHub to host the paper, to track issues and feature requests, as well as accept pull requests. + +## We Use GitHub Flow, So All Code Changes Happen Through Pull Requests + +Pull requests are the best way to propose changes to the source material (we use Github Flow). +We actively welcome your pull requests: + +- optional: open issue describing what you want to do +- Fork this repository +- Create your changes in your fork +- Go to the [pull requests](https://github.com/CaptainSifff/paper_teaching-learning-RSE/pulls) page of this repository and push `new pull request` +- You can add DRAFT, or WIP to indicate work-in-progress PRs. +- Add a short description + +#### How to review existing pull requests + +- Go to the [pull requests](https://github.com/CaptainSifff/paper_teaching-learning-RSE/pulls) page of this repository +- Click on any of the open pull requests +- Leave comments under `Conversation` or do a full review under `Files changed` + +## Formatting, etc +For writing text, **Please utilise semantic line breaks!** +We utilise tags to categorise issues and PRs to the respective paper. +Please also note, that we use British english instead of American english. + +## Becoming an Author +If you want to become an author of the project open a PR that adds the relevant information +to [contributors.yml](contributors.yml) (At the end of the file you find a template for the fields) +Make sure the name provided in the "author:" field matches +exactly with the name in the Markdown preamble author list. + +We aim to be inclusive for everyone who wants to become a contributor. + +## Publication +We currently have split the topic of teaching RSEs in Germany across four papers. +We aim for a publication of most of these papers. +All people that have participated in discussions with us, +e.g. at deRSE23 or undeRSE23 are at least eligible for contributor status. +If you have participated regularly at our weekly working meetings(try to reach out to fgoth@physik.uni-wuerzburg.de) you are eligible for +authorship. diff --git a/002/LICENSE.md b/002/LICENSE.md new file mode 100644 index 0000000..4ea99c2 --- /dev/null +++ b/002/LICENSE.md @@ -0,0 +1,395 @@ +Attribution 4.0 International + +======================================================================= + +Creative Commons Corporation ("Creative Commons") is not a law firm and +does not provide legal services or legal advice. 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Except for the limited purpose of indicating that +material is shared under a Creative Commons public license or as +otherwise permitted by the Creative Commons policies published at +creativecommons.org/policies, Creative Commons does not authorize the +use of the trademark "Creative Commons" or any other trademark or logo +of Creative Commons without its prior written consent including, +without limitation, in connection with any unauthorized modifications +to any of its public licenses or any other arrangements, +understandings, or agreements concerning use of licensed material. For +the avoidance of doubt, this paragraph does not form part of the +public licenses. + +Creative Commons may be contacted at creativecommons.org. diff --git a/002/Makefile b/002/Makefile new file mode 100644 index 0000000..ade5215 --- /dev/null +++ b/002/Makefile @@ -0,0 +1,52 @@ +.DEFAULT_GOAL := all + +MAKE_PDFA := true + +objects := competencies.pdf + +all: $(objects) + +%.pdf: %.md bibliography/bibliography.bib contributors.yml preamble.sty build/template.tex glossary.tex filter.py Makefile + @mkdir -p build + @mkdir -p build/svg-inkscape + @rm -f build/pdfa.xmpi + cp --update preamble.sty build/ + cp --update bibliography/bibliography.bib build/ + cp --update glossary.tex build/ + python3 filter.py --input="${<}" --output="build/${<}" --contributors="contributors.yml" + pandoc \ + --standalone \ + --number-sections \ + --filter pandoc-xnos \ + --bibliography=bibliography.bib \ + --biblatex \ + --toc \ + --template="build/template.tex" \ + -f markdown-latex_macros \ + -M pdfa-$(MAKE_PDFA)=1 \ + -M date="`date "+%F"`" \ + -M datexmp="`date "+%F"`" \ + -M linkcolor=darkgray \ + -V hyperrefoptions=pdfa \ + -V colorlinks=true \ + -V papersize=a4 \ + -o "build/${@:.pdf=}.tex" \ + "build/$<" + @sed -i '/\\author{}/d' "build/${@:.pdf=}.tex" + if grep -q "\\makeglossaries" "${<}"; then \ + cd build; \ + pdflatex -shell-escape --jobname="${@:.pdf=}" "${@:.pdf=}.tex"; \ + makeglossaries "${@:.pdf=}"; \ + fi + latexmk \ + -pdflatex -shell-escape -bibtex -halt-on-error \ + -jobname="${@:.pdf=}" -cd "build/${@:.pdf=}.tex" + @mv "build/${@}" "${@}" + +build/template.tex: template.py + @mkdir -p build + pandoc --print-default-template=latex > "${@}" + python3 "${<}" "${@}" + +clean: + rm -f $(objects) diff --git a/002/README.md b/002/README.md new file mode 100644 index 0000000..180a79c --- /dev/null +++ b/002/README.md @@ -0,0 +1,38 @@ +# Position Paper 002 +## The teachingRSE project: "Teaching and Learning Research Software Engineering" [![CC BY 4.0](https://img.shields.io/badge/License-CC%20BY%204.0-lightgrey.svg)](http://creativecommons.org/licenses/by/4.0/) + +It started all at a workshop at deRSE23 in Paderborn where the community came together to discuss what to teach to future RSEs +and in which institutions to bring up the next generation of RSEs. + +As we discovered, the scope of this task is so big that +we had to split the paper in different subpapers highlighting different aspects + +Get the latest version of the respective PDF files here: + +* "Foundational competencies and responsibilities of an RSE" ([competencies.pdf](https://github.com/CaptainSifff/paper_teaching-learning-RSE/blob/build/competencies.pdf)) + +## How to build from this repo: +- make sure you have the necessary system dependencies: apt-get install xz-utils make sed gpg-agent pandoc latexmk biber texlive-bibtex-extra +- let's get the required pandoc modules via pip: python3 -m pip install -r requirements.txt +- execute make from the top-level-folder + +## Publication +We currently have split the topic of teaching RSEs in Germany across four papers. +We aim for a publication of most of these papers. +All people that have participated in discussions with us, +e.g. at deRSE23 or undeRSE23 are at least eligible for contributor status. +If you have participated regularly at our weekly working meetings you are eligible for +authorship. + +The first paper, +_Foundational Competencies and Responsibilities of a Research Software Engineer_, +is now available as a pre-print: https://arxiv.org/abs/2311.11457 +Feedback is welcome as an issue on this repository. + +## License + +[![Creative Commons License](https://i.creativecommons.org/l/by/4.0/88x31.png)](http://creativecommons.org/licenses/by/4.0/) + +Each file in this repository is licensed under a [Creative Commons Attribution 4.0 International License](http://creativecommons.org/licenses/by/4.0/). + +When re-using material from this repository, please attribute it with the information given in the file [attribution.md](attribution.md). diff --git a/002/bibliography/.gitignore b/002/bibliography/.gitignore new file mode 100644 index 0000000..e964244 --- /dev/null +++ b/002/bibliography/.gitignore @@ -0,0 +1,301 @@ +## Core latex/pdflatex auxiliary files: +*.aux +*.lof +*.log +*.lot +*.fls +*.out +*.toc +*.fmt +*.fot +*.cb +*.cb2 +.*.lb + +## Intermediate documents: +*.dvi +*.xdv +*-converted-to.* +# these rules might exclude image files for figures etc. +# *.ps +# *.eps +# *.pdf + +## Generated if empty string is given at "Please type another file name for output:" +.pdf + +## Bibliography auxiliary files (bibtex/biblatex/biber): +*.bbl +*.bcf +*.blg +*-blx.aux +*-blx.bib +*.run.xml + +## Build tool auxiliary files: +*.fdb_latexmk +*.synctex +*.synctex(busy) +*.synctex.gz +*.synctex.gz(busy) +*.pdfsync + +## Build tool directories for auxiliary files +# latexrun +latex.out/ + +## Auxiliary and intermediate files from other packages: +# algorithms +*.alg +*.loa + +# achemso +acs-*.bib + +# amsthm +*.thm + +# beamer +*.nav +*.pre +*.snm +*.vrb + +# changes +*.soc + +# comment +*.cut + +# cprotect +*.cpt + +# elsarticle (documentclass of Elsevier journals) +*.spl + +# endnotes +*.ent + +# fixme +*.lox + +# feynmf/feynmp +*.mf +*.mp +*.t[1-9] +*.t[1-9][0-9] +*.tfm + +#(r)(e)ledmac/(r)(e)ledpar +*.end +*.?end +*.[1-9] +*.[1-9][0-9] +*.[1-9][0-9][0-9] +*.[1-9]R +*.[1-9][0-9]R +*.[1-9][0-9][0-9]R +*.eledsec[1-9] +*.eledsec[1-9]R +*.eledsec[1-9][0-9] +*.eledsec[1-9][0-9]R +*.eledsec[1-9][0-9][0-9] +*.eledsec[1-9][0-9][0-9]R + +# glossaries +*.acn +*.acr +*.glg +*.glo +*.gls +*.glsdefs +*.lzo +*.lzs +*.slg +*.slo +*.sls + +# uncomment this for glossaries-extra (will ignore makeindex's style files!) +# *.ist + +# gnuplot +*.gnuplot +*.table + +# gnuplottex +*-gnuplottex-* + +# gregoriotex +*.gaux +*.glog +*.gtex + +# htlatex +*.4ct +*.4tc +*.idv +*.lg +*.trc +*.xref + +# hyperref +*.brf + +# knitr +*-concordance.tex +# TODO Uncomment the next line if you use knitr and want to ignore its generated tikz files +# *.tikz +*-tikzDictionary + +# listings +*.lol + +# luatexja-ruby +*.ltjruby + +# makeidx +*.idx +*.ilg +*.ind + +# minitoc +*.maf +*.mlf +*.mlt +*.mtc[0-9]* +*.slf[0-9]* +*.slt[0-9]* +*.stc[0-9]* + +# minted +_minted* +*.pyg + +# morewrites +*.mw + +# newpax +*.newpax + +# nomencl +*.nlg +*.nlo +*.nls + +# pax +*.pax + +# pdfpcnotes +*.pdfpc + +# sagetex +*.sagetex.sage +*.sagetex.py +*.sagetex.scmd + +# scrwfile +*.wrt + +# svg +svg-inkscape/ + +# sympy +*.sout +*.sympy +sympy-plots-for-*.tex/ + +# pdfcomment +*.upa +*.upb + +# pythontex +*.pytxcode +pythontex-files-*/ + +# tcolorbox +*.listing + +# thmtools +*.loe + +# TikZ & PGF +*.dpth +*.md5 +*.auxlock + +# titletoc +*.ptc + +# todonotes +*.tdo + +# vhistory +*.hst +*.ver + +# easy-todo +*.lod + +# xcolor +*.xcp + +# xmpincl +*.xmpi + +# xindy +*.xdy + +# xypic precompiled matrices and outlines +*.xyc +*.xyd + +# endfloat +*.ttt +*.fff + +# Latexian +TSWLatexianTemp* + +## Editors: +# WinEdt +*.bak +*.sav + +# Texpad +.texpadtmp + +# LyX +*.lyx~ + +# Kile +*.backup + +# gummi +.*.swp + +# KBibTeX +*~[0-9]* + +# TeXnicCenter +*.tps + +# auto folder when using emacs and auctex +./auto/* +*.el + +# expex forward references with \gathertags +*-tags.tex + +# standalone packages +*.sta + +# Makeindex log files +*.lpz + +# xwatermark package +*.xwm + +# REVTeX puts footnotes in the bibliography by default, unless the nofootinbib +# option is specified. Footnotes are the stored in a file with suffix Notes.bib. +# Uncomment the next line to have this generated file ignored. +#*Notes.bib diff --git a/002/bibliography/README.md b/002/bibliography/README.md new file mode 100644 index 0000000..48bfbfc --- /dev/null +++ b/002/bibliography/README.md @@ -0,0 +1,14 @@ +# Teaching RSE: bibliography database + +We use a single, shared BibTeX bibliography file for all papers in the teaching RSE project. This is imported as a Git submodule from this repository. If you want to contribute new entries to the bibliography, you need to add them there. + +After adding the entries here, update the submodules in your branch of the respective repository that uses this submodule: + +```shell +git submodule update --remote --merge +git add bibliography +git commit -m "Update bibliography submodule" +git push +``` + +In your pull request, you should see `bibliography` as a one-line modification, with the comment `Submodule bibliography added at `. Make sure that this commit hash points to the state of the bibliography repository you want to. This means that it should not point to a commit in your fork not on the main repository. Be careful also to not point to a commit that you later squash. diff --git a/002/bibliography/bibliography.bib b/002/bibliography/bibliography.bib new file mode 100644 index 0000000..afde99e --- /dev/null +++ b/002/bibliography/bibliography.bib @@ -0,0 +1,6128 @@ +@Online{AcademicProgrammesHPC, + author = {{High-Performance Computing in Europe}}, + title = {Academic Programmes}, + url = {https://hpc-portal.eu/academic-programmes}, + urldate = {2023-08-25}, +} + +@Article{Ahn2014, + author = {Ahn, June and Pellicone, Anthony and Butler, Brian S.}, + title = {Open badges for education: what are the implications at the intersection of open systems and badging?}, + journal = {Research in Learning Technology}, + year = {2014}, + volume = {22}, + month = aug, + issn = {2156-7077}, + doi = {10.3402/rlt.v22.23563}, + publisher = {Association for Learning Technology}, +} + +@Article{Ahsan2023, + author = {Ahsan, Kamrul and Akbar, Suraiyah and Kam, Booi and Abdulrahman, Muhammad Dan-Asabe}, + title = {Implementation of micro-credentials in higher education: A systematic literature review}, + journal = {Education and Information Technologies}, + year = {2023}, + month = mar, + doi = {10.1007/s10639-023-11739-z}, + publisher = {Springer Science and Business Media {LLC}}, +} + +@InProceedings{Akoh2017, + author = {Akoh, Ben}, + title = {Determinants of Mobile Learning in {I}ndigenous/Cultural Contexts: The Phenomenon in {C}anadian {F}irst {N}ations}, + booktitle = {Tomorrow's Learning: Involving Everyone}, + year = {2017}, + editor = {Tatnall, Arthur and Webb, Mary}, + booksubtitle = {Learning with and about Technologies and Computing}, + volume = {515}, + series = {{IFIP} Advances in Information and Communication Technology}, + publisher = {Springer International Publishing}, + isbn = {978-3-319-74310-3}, + pages = {24--34}, + doi = {10.1007/978-3-319-74310-3_4}, + address = {Cham, Switzerland}, + issn = {1868-422X}, + lccn = {2018930742}, + eventdate = {2017-07-03/2017-07-06}, + venue = {Dublin, Ireland}, +} + +@InProceedings{Alghamdi2017, + author = {Alghamdi, Jawaher and Holland, Charlotte}, + title = {Game-Play: Effects of Online Gamified and Game-Based Learning on Dispositions, Abilities and Behaviours of Primary Learners}, + booktitle = {Tomorrow's Learning: Involving Everyone}, + year = {2017}, + editor = {Tatnall, Arthur and Webb, Mary}, + booksubtitle = {Learning with and about Technologies and Computing}, + volume = {515}, + series = {{IFIP} Advances in Information and Communication Technology}, + publisher = {Springer International Publishing}, + isbn = {978-3-319-74310-3}, + pages = {55--63}, + doi = {10.1007/978-3-319-74310-3_7}, + address = {Cham, Switzerland}, + issn = {1868-422X}, + lccn = {2018930742}, + eventdate = {2017-07-03/2017-07-06}, + venue = {Dublin, Ireland}, +} + +@Online{AlgorithmicBattle, + author = {{RWTH Aachen University}}, + title = {Algorithmic Battle}, + url = {https://tcs.rwth-aachen.de/lehre/algobattle/WS2023/}, + urldate = {2023-07-03}, +} + +@TechReport{Alibay2022, + author = {Alibay, Irfan and Barnoud, Jonathan and Beckstein, Oliver and Gowers, Richard J. and Naughton, Fiona and Wang, Lily}, + title = {{MDAK}its: Supporting and promoting the development of community packages leveraging the {MDA}nalysis library [v0.1.0]}, + institution = {MDAnalysis}, + year = {2022}, + type = {White Paper}, + month = aug, + doi = {10.6084/m9.figshare.20520726.v1}, +} + +@TechReport{AllDigital2022, + author = {{ALL DIGITAL} and {HUAWEI} and {EY}}, + title = {Strategies to address the digital skills gap in the {EU}}, + institution = {Europeandigitalskills.eu}, + year = {2022}, + type = {White Paper}, + month = apr, + url = {https://www.europeandigitalskills.eu/white-paper/}, + publisher = {Huawei Technologies Co., Ltd}, +} + +@Article{Alt2021, + author = {Alt, Dorit}, + title = {Who benefits from digital badges? Motivational precursors of digital badge usages in higher education}, + journal = {Current Psychology}, + year = {2021}, + volume = {42}, + number = {8}, + month = jun, + pages = {6629--6640}, + doi = {10.1007/s12144-021-02002-0}, + publisher = {Springer Science and Business Media {LLC}}, +} + +@Misc{Alves2021, + author = {Alves, Daniel and Isasi, Jennifer}, + title = {Publica{\c{c}}{\~a}o do {P}rogramming {H}istorian em portugu{\^e}s}, + year = {2021}, + howpublished = {The Programming Historian blog}, + month = jan, + url = {https://programminghistorian.org/posts/launch-portuguese}, + urldate = {2023-08-23}, +} + +@Article{Ambite2021, + author = {Ambite, Jos{\'e} Luis and Fierro, Lily and Gordon, Jonathan and Burns, Gully A. P. C. and Geigl, Florian and Lerman, Kristina and Van Horn, John D.}, + title = {{BD2K} Training Coordinating Center's {ERuDIte}: The Educational Resource Discovery Index for Data Science}, + journal = {{IEEE} Transactions on Emerging Topics in Computing}, + year = {2021}, + volume = {9}, + number = {1}, + month = jan, + pages = {316--328}, + doi = {10.1109/tetc.2019.2903466}, + publisher = {Institute of Electrical and Electronics Engineers ({IEEE})}, +} + +@Book{Anderson2001, + author = {Anderson, Lorin W. and Krathwohl, David R.}, + title = {A Taxonomy for Learning, Teaching, and Assessing}, + year = {2001}, + editor = {Airasian, Peter W. and Cruikshank, Kathleen A. and Mayer, Richard E. and Pintrich, Paul R. and Raths, James and Wittrock, Merlin C.}, + subtitle = {A Revision of {B}loom's Taxonomy of Educational Objectives}, + titleaddon = {Abridged Edition}, + publisher = {Addison Wesley Longman}, + isbn = {0-8013-1903-X}, + lccn = {00063423}, +} + +@Article{Anzt2021, + author = {Anzt, Hartwig and Bach, Felix and Druskat, Stephan and L\"{o}ffler, Frank and Loewe, Axel and Renard, Bernhard Y. and Seemann, Gunnar and Struck, Alexander and Achhammer, Elke and Aggarwal, Piush and Appel, Franziska and Bader, Michael and Brusch, Lutz and Busse, Christian and Chourdakis, Gerasimos and Dabrowski, Piotr Wojciech and Ebert, Peter and Flemisch, Bernd and Friedl, Sven and Fritzsch, Bernadette and Funk, Maximilian D. and Gast, Volker and Goth, Florian and Grad, Jean-No\"{e}l and Hegewald, Jan and Hermann, Sibylle and Hohmann, Florian and Janosch, Stephan and Kutra, Dominik and Linxweiler, Jan and Muth, Thilo and Peters-Kottig, Wolfgang and Rack, Fabian and Raters, Fabian H.C. and Rave, Stephan and Reina, Guido and Rei\ss{}ig, Malte and Ropinski, Timo and Schaarschmidt, Joerg and Seibold, Heidi and Thiele, Jan P. and Uekermann, Benjamin and Unger, Stefan and Weeber, Rudolf}, + title = {An environment for sustainable research software in {G}ermany and beyond: current state, open challenges, and call for action [version 2; peer review: 2 approved]}, + journal = {F1000Research}, + year = {2021}, + volume = {9}, + number = {295}, + doi = {10.12688/f1000research.23224.2}, +} + +@TechReport{Appel2021, + author = {Appel, Franziska and Loewe, Axel}, + title = {{F}orschungssoftware - Nachhaltige {E}ntwicklung und {U}nterst\"{u}tzung}, + year = {2021}, + type = {IAMO Policy Brief}, + number = {42}, + address = {Halle (Saale), Saxony-Anhalt, Germany}, + isbn = {978-3-95992-124-4}, + publisher = {Leibniz Institute of Agricultural Development in Transition Economies (IAMO)}, + url = {https://hdl.handle.net/10419/240937}, +} + +@TechReport{Aragon2023, + author = {Aragon, Selina and Antonioletti, Mario and Walker, Johanna and Chue Hong, Neil}, + title = {Understanding the software and data used in the social sciences: {A} study for the {E}conomics and {S}ocial {R}esearch {C}ouncil}, + institution = {Software Sustainability Institute}, + year = {2023}, + month = nov, + doi = {10.5281/zenodo.7785706}, +} + +@Online{ARCHERDrivingTest2022, + author = {{ARCHER2 Training Team}}, + title = {{ARCHER2} {D}riving {T}est launched}, + year = {2022}, + url = {https://www.archer2.ac.uk/news/2022/01/24/driving-test.html}, + month = jan, + urldate = {2024-02-22}, + day = {24}, +} + +@Online{ARCHERDrivingTest2021, + author = {Barrass, Clair}, + title = {{ARCHER} {D}riving {T}est retrospective}, + year = {2021}, + url = {https://www.archer2.ac.uk/news/2021/02/03/archer-driving-test.html}, + month = feb, + urldate = {2024-02-22}, + day = {3}, +} + +@Online{ARCHERDrivingTest, + title = {{ARCHER2} {D}riving {T}est}, + url = {https://www.archer2.ac.uk/training/driving-test.html}, + organization = {ARCHER2 Training Team}, + urldate = {2024-02-22}, +} + +@Article{Artaza2016, + author = {Artaza, Haydee and Chue Hong, Neil and Corpas, Manuel and Corpuz, Angel and Hooft, Rob W. W. and Jim{\'{e}}nez, Rafael C. and Lesko{\v{s}}ek, Brane and Olivier, Brett G. and Stourac, Jan and Svobodov{\'{a}} Va{\v{r}}ekov{\'{a}}, Radka and Van Parys, Thomas and Vaughan, Daniel}, + title = {Top 10 metrics for life science software good practices}, + journal = {F1000Research}, + year = {2016}, + volume = {5}, + pages = {2000}, + month = aug, + doi = {10.12688/f1000research.9206.1}, + publisher = {F1000 Research Ltd}, +} + +@Article{Astigarraga2022, + author = {Astigarraga, Julen and Cruz-Alonso, Ver{\'{o}}nica}, + title = {{\textexclamdown}Se puede entender c{\'{o}}mo funcionan {G}it y {G}it{H}ub!}, + journal = {Ecosistemas}, + year = {2022}, + volume = {31}, + number = {1}, + pages = {2332}, + month = apr, + issn = {1697-2473}, + doi = {10.7818/ecos.2332}, + publisher = {Asociacion Espanola de Ecologia Terrestre ({AEET})}, +} + +@misc{Athalye2023, + title = {The Missing Semester of Your {CS} Education}, + url = {https://missing.csail.mit.edu/}, + urldate = {2023-08-11}, + howpublished = {MIT, Computer Science \& Artificial Intelligence Laboratory}, + author = {Athalye, Anish and Gjengset, Jon and Gonzalez Ortiz, Jose Javier}, +} + +@Article{Attwood2015b, + author = {Attwood, Teresa K. and Bongcam-Rudloff, Erik and Brazas, Michelle E. and Corpas, Manuel and Gaudet, Pascale and Lewitter, Fran and Mulder, Nicola and Palagi, Patricia M. and Schneider, Maria Victoria and van Gelder, Celia W. G. and {GOBLET Consortium}}, + title = {Correction: {GOBLET}: The Global Organisation for Bioinformatics Learning, Education and Training}, + journal = {{PLOS} Computational Biology}, + year = {2015}, + volume = {11}, + number = {5}, + month = may, + pages = {e1004281}, + doi = {10.1371/journal.pcbi.1004281}, + publisher = {Public Library of Science ({PLoS})}, +} + +@Article{Attwood2017, + author = {Attwood, Teresa K. and Blackford, Sarah and Brazas, Michelle D. and Davies, Angela and Schneider, Maria Victoria}, + title = {A global perspective on evolving bioinformatics and data science training needs}, + journal = {Briefings in Bioinformatics}, + year = {2019}, + volume = {20}, + number = {2}, + month = mar, + pages = {398--404}, + issn = {1477-4054}, + doi = {10.1093/bib/bbx100}, + publisher = {Oxford University Press ({OUP})}, +} + +@Article{Atwood2015a, + author = {Atwood, Teresa K. and Bongcam-Rudloff, Erik and Brazas, Michelle E. and Corpas, Manuel and Gaudet, Pascale and Lewitter, Fran and Mulder, Nicola and Palagi, Patricia M. and Schneider, Maria Victoria and van Gelder, Celia W. G. and {GOBLET Consortium}}, + title = {{GOBLET}: The Global Organisation for Bioinformatics Learning, Education and Training}, + journal = {{PLOS} Computational Biology}, + year = {2015}, + editor = {Welch, Lonnie}, + volume = {11}, + number = {4}, + month = apr, + pages = {e1004143}, + doi = {10.1371/journal.pcbi.1004143}, + publisher = {Public Library of Science ({PLoS})}, + related = {Attwood2015b}, + relatedstring = {Corrected in}, +} + +@Online{AwesomeRSEEducationalResources, + author = {{Helmholtz Federated IT Services}}, + title = {Awesome Educational Resources for Research Software Engineering}, + url = {https://github.com/hifis-net/awesome-rse-education}, + urldate = {2023-08-25}, +} + +@Online{AwesomeRSEPoliciesGuidelines, + author = {{Helmholtz Federated IT Services}}, + title = {Awesome Research Software Engineering Policies and Guidelines}, + url = {https://github.com/hifis-net/awesome-rse-policies}, + urldate = {2023-08-25}, +} + +@Article{Bacall2023, + author = {Bacall, Finn and Apaolaza, Aitor and Andrabi, Munazah and Child, Chris and Goble, Carole and Sand, Olivier and Botzki, Alexander}, + title = {Making Bioinformatics Training Events and Material More Discoverable Using {TeSS}, the {ELIXIR} Training Portal}, + journal = {Current Protocols}, + year = {2023}, + volume = {3}, + number = {2}, + month = feb, + issn = {2691-1299}, + doi = {10.1002/cpz1.682}, + publisher = {Wiley}, +} + +@InProceedings{Badreddin2019, + author = {Badreddin, Omar and Hamou-Lhadj, Wahab and Chauhan, Swapnil}, + title = {Susereum: Towards a Reward Structure for Sustainable Scientific Research Software}, + booktitle = {Proceedings of the 2019 {IEEE}/{ACM} 14\textsuperscript{th} International Workshop on Software Engineering for Science ({SE}4{S}cience)}, + year = {2019}, + month = may, + publisher = {IEEE}, + doi = {10.1109/se4science.2019.00015}, + isbn = {978-1-7281-2276-2}, + eventdate = {2019-05-28/2019-05-28}, + venue = {Montr{\'e}al, Qu{\'e}bec, Canada}, +} + +@Article{Bain2020, + author = {Bain, Stevie A. and Meagher, Thomas R. and Barker, Daniel}, + title = {Design, delivery and evaluation of a bioinformatics education workshop for 13-16-year-olds}, + journal = {Journal of Biological Education}, + year = {2020}, + volume = {56}, + number = {5}, + pages = {570--580}, + month = dec, + doi = {10.1080/00219266.2020.1858932}, + publisher = {Informa {UK} Limited}, +} + +@Article{Bain2022, + author = {Bain, Stevie A. and Plaisier, Heleen and Anderson, Felicity and Cook, Nicola and Crouch, Kathryn and Meagher, Thomas R. and Ritchie, Michael G. and Wallace, Edward W. 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{Paris, France}, + institution = {UNESCO}, +} + +@Article{Chang2021, + author = {Chang, Hui-Yin and Colby, Sean M. and Du, Xiuxia and Gomez, Javier D. and Helf, Maximilian J. and Kechris, Katerina and Kirkpatrick, Christine R. and Li, Shuzhao and Patti, Gary J. and Renslow, Ryan S. and Subramaniam, Shankar and Verma, Mukesh and Xia, Jianguo and Young, Jamey D.}, + title = {A Practical Guide to Metabolomics Software Development}, + journal = {Analytical Chemistry}, + year = {2021}, + volume = {93}, + number = {4}, + pages = {1912--1923}, + month = jan, + doi = {10.1021/acs.analchem.0c03581}, + publisher = {American Chemical Society ({ACS})}, +} + +@Misc{CHAOSSDEIBadging, + author = {{CHAOSS}}, + title = {Overview of {D\&{}I} Badging}, + year = {2020}, + howpublished = {CHAOSS Community Handbook}, + month = nov, + url = {https://handbook.chaoss.community/badging/}, + urldate = {2023-06-23}, +} + +@Article{Cheng2019, + author = {Cheng, Zui and Richardson, Jennifer C. and Newby, Timothy J.}, + title = {Using digital badges as goal-setting facilitators: a multiple case study}, + journal = {Journal of Computing in Higher Education}, + year = {2019}, + volume = {32}, + number = {2}, + month = oct, + pages = {406--428}, + doi = {10.1007/s12528-019-09240-z}, + publisher = {Springer Science and Business Media {LLC}}, +} + +@InProceedings{Cherubini2007, + author = {Cherubini, Mauro and Venolia, Gina and DeLine, Rob and Ko, Amy J.}, + title = {Let's Go to the Whiteboard: How and Why Software Developers Use Drawings}, + booktitle = {Proceedings of the {SIGCHI} Conference on Human Factors in Computing Systems}, + year = {2007}, + eventdate = {2007-04-28/2007-05-03}, + venue = {San Jose, California, USA}, + publisher = {ACM}, + month = apr, + isbn = {978-1-59593-593-9}, + doi = {10.1145/1240624.1240714}, + address = {New York, New York, USA}, +} + +@Article{Chicco2023, + author = {Chicco, Davide and Jurman, Giuseppe}, + title = {Ten simple rules for providing bioinformatics 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Debt}, + year = {2020}, + eventdate = {2020-06-28/2020-06-30}, + venue = {Seoul, Republic of Korea}, + publisher = {Association for Computing Machinery}, + month = sep, + isbn = {978-1-4503-7960-1}, + pages = {62--66}, + doi = {10.1145/3387906.3388628}, + address = {New York, New York, USA}, +} + +@Article{Crick2017, + author = {Crick, Tom and Hall, Benjamin A. and Ishtiaq, Samin}, + title = {Reproducibility in Research: Systems, Infrastructure, Culture}, + journal = {Journal of Open Research Software}, + year = {2017}, + volume = {5}, + number = {1}, + month = nov, + pages = {32}, + doi = {10.5334/jors.73}, + publisher = {Ubiquity Press, Ltd.}, +} + +@Article{Crouch2013, + author = {Crouch, Stephen and Chue Hong, Neil and Hettrick, Simon and Jackson, Mike and Pawlik, Aleksandra and Sufi, Shoaib and Carr, Les and De Roure, David and Goble, Carole and Parsons, Mark}, + title = {The Software Sustainability Institute: Changing Research Software Attitudes and Practices}, + journal = 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Skills. 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R. and Grandgenett, Neal and Morgan, William and Rosenwald, Anne and Tapprich, William and Triplett, Eric W. and Pauley, Mark A.}, + title = {{NIBLSE}: A Network for Integrating Bioinformatics into Life Sciences Education}, + journal = {{CBE}---Life Sciences Education}, + year = {2015}, + volume = {14}, + number = {4}, + month = dec, + pages = {le3}, + issn = {1931-7913}, + doi = {10.1187/cbe.15-06-0123}, + publisher = {American Society for Cell Biology ({ASCB})}, +} + +@InCollection{Donnelly2018, + author = {Donnelly, Roisin and Maguire, Terry}, + title = {{I}reland's Higher Education Teachers Have a National Professional Development Framework, Now What?}, + booktitle = {Transforming our World Through Design, Diversity and Education}, + year = {2018}, + editor = {Craddock, Gerald and Doran, Cormac and McNutt, Larry and Rice, D{\'o}nal}, + volume = {256}, + series = {Studies in Health Technology and Informatics}, + publisher = {IOS Press}, + isbn = {978-1-61499-923-2}, + pages = {655--666}, + doi = {10.3233/978-1-61499-923-2-655}, +} + +@Misc{Drac2023a, + author = {{Digital Research Alliance of Canada, National Research Software Strategy Working Group}}, + title = {National Research Software Strategy 2023}, + year = {2023}, + howpublished = {Zenodo}, + month = aug, + doi = {10.5281/zenodo.10214741}, +} + +@Misc{Drac2023b, + author = {{Alliance de recherche num{\'e}rique du Canada, Groupe de travail sur la strat{\'e}gie nationale en mati{\`e}re de logiciels de recherche}}, + title = {Strat{\'e}gie nationale en mati{\`e}re de logiciels de recherche 2023}, + year = {2023}, + howpublished = {Zenodo}, + month = aug, + doi = {10.5281/zenodo.10214856}, + related = {Drac2023a}, + relatedstring = {Translation of}, +} + +@TechReport{Duckles2016, + author = {Duckles, Beth M.}, + title = {Value of Software Carpentry to Instructors Report}, + year = {2016}, + month = jan, + url = {https://software-carpentry.org/files/bib/duckles-instructor-engagement-2016.pdf}, +} + +@online{ECTS, +organization = {European Education Area}, +title = {European Credit Transfer and Accumulation System ({ECTS})}, +url = {https://education.ec.europa.eu/education-levels/higher-education/inclusive-and-connected-higher-education/european-credit-transfer-and-accumulation-system}, +urldate = {2023-07-20}, +} + +@Online{EdinburghRSECollaborationCall2023, + organization = {{The Royal Society of Edinburgh}}, + title = {{RSE} Research Collaboration Grants}, + url = {https://rse.org.uk/funding-collaboration/award/rse-research-collaboration-grants/}, + urldate = {2023-08-11}, +} + +@Online{EdinburghRSEFellowshipCall2023, + organization = {{The Royal Society of Edinburgh}}, + title = {{RSE} Personal Research Fellowships}, + url = {https://rse.org.uk/funding-collaboration/award/rse-personal-research-fellowships/}, + urldate = {2023-08-11}, +} + +@online{EDUTRAIN, +organization = {German National Research Data Infrastructure (NFDI)}, +title={{NFDI}: Section Training \& Education}, +url={https://www.nfdi.de/section-edutrain/?lang=en}, +urldate={2023-07-27} +} + +@misc{EduTrain2022, +author = {Herres-Pawlis, Sonja and Pelz, Peter and Kockmann, Norbert and Gl\"{a}ser, Roger and Richter, Manuela and Liermann, Johannes and Ortmeyer, Jochen and Heine, Ina and Metzmacher, Amelie and Andres, Ann-Christin and M\"{u}nzmay, Andreas and Heuer, Jan-Ocko and Hagener, Malte and Dierkes, Jens and Wiljes, Cord and Lindst\"{a}dt, Birte and Danabalan, Renita and Jolliffe, John D.}, +title = {{S}ektionskonzept {T}raining \& {E}ducation zur {E}inrichtung einer {S}ektion im {V}erein {N}ationale {F}orschungsdateninfrastruktur ({NFDI}) {e.V.}}, +month = apr, +year = 2022, +publisher = {Zenodo}, +version = {2.0}, +doi = {10.5281/zenodo.6475541}, +} + +@online{edX, +organization = {{digital education company 2U}}, +title = {{edx} - online learning platform}, +url = {https://www.edx.org/}, +urldate = {2023-07-20} +} + +@online{ENCCS, +author = {{EuroCC National Competence Centre Sweden}}, +title = {{ENCCS - Supercomputer access and training for your business/organisation}}, +url = {https://enccs.se/}, +urldate = {2023-10-27} +} + +@TechReport{ENCCS2022, + author = {{ENCCS}}, + title = {{ENCCS} Instructor Training}, + institution = {{EuroCC National Competence Center Sweden}}, + year = {2022}, + type = {Training Material to Train the Trainer}, + month = nov, + url = {https://www.eurocc-access.eu/wp-content/uploads/2022/12/EuroCC_NCC_Sweden_instructor_training_workshop.pdf}, +} + +@online{ENCCSInstructorTraining, +author = {ENCCS}, +title = {{ENCCS} Instructor Training}, +url = {https://enccs.github.io/instructor-training/}, +urldate = {2023-06-16} +} + +@online{ENCCSLessons, +author = {{EuroCC National Competence Center Sweden}}, +title = {{ENCCS} Lessons}, +url = {https://enccs.se/lessons/}, +urldate = {2024-07-25} +} + +@Online{ESDCConsulation2023, + title = {More information about {EDSC}}, + url = {https://edsc-consultation.eu/about-edsc/}, + urldate = {2023-08-28}, + publisher = {ESDC Consulation}, +} + +@InProceedings{EuroCC2022, + author = {{CASTIEL} and {EuroCC Network}}, + title = {Best Practice Guide: How to Find New Attendees for Training Courses}, + booktitle = {Training Best Practice Seminar ({CASTIEL})}, + year = {2022}, + eventdate = {2022-01-20}, + publisher = {EuroCC}, + month = jan, + url = {https://www.eurocc-access.eu/wp-content/uploads/2022/04/20220401_Best_Practice_Guide-Training_Best_Practice_Seminar_final.pdf}, +} + +@online{EuroCCTraining, + author = {{EuroCC}}, + title = {{EuroCC} Training}, + url = {https://www.eurocc-access.eu/services/training/}, + urldate = {2023-06-16} +} + +@TechReport{EuroHPCJU2023, + author = {{Governing Board of the EuroHPC Joint Undertaking}}, + title = {Amending the {J}oint {U}ndertaking's Work Programme and Budget for the year 2023 (Work Programme and Budget Amendment no. 1)}, + institution = {EuroHPC Joint Undertaking}, + year = {2023}, + type = {{E}uro{HPC} {JU} {D}ecision}, + number = {No 03/2023}, + month = mar, + url = {https://eurohpc-ju.europa.eu/system/files/2023-03/Decision%203.2023.-%201st%20Amendment%20WP%202023.pdf}, +} + +@TechReport{EuropeanCommissionDGRI2024, + author = {{European Commission, Directorate-General for Research and Innovation}}, + title = {Access to and preservation of scientific information in {E}urope -- 2023 report on the implementation of the {C}ommission {R}ecommendation 2018/790}, + year = {2024}, + doi = {10.2777/223623}, + address = {Luxembourg}, + isbn = {978-92-68-09795-3}, + publisher = {Publications Office of the European Union}, +} + +@Article{EuropeanCommissionRecommendation2018, + author = {{European Commission}}, + title = {{C}ommission {R}ecommendation ({EU}) 2018/790 of 25 {A}pril 2018 on access to and preservation of scientific information}, + journal = {Official Journal of the European Union}, + year = {2018}, + volume = {61}, + number = {134}, + month = may, + issn = {1977-0677}, + url = {http://data.europa.eu/eli/reco/2018/790/oj}, + pages = {12--18}, +} + +@online{EXCALIBUR, +author = {ExCALIBUR}, +title = {{E}xascale {C}omputing {AL}gorithms \& {I}nfrastructures {B}enefiting {UK} {R}esearch}, +url = {https://excalibur.ac.uk}, +urldate = {2023-06-16} +} + +@online{ExportControl, +organization = {Federal Office for Economic Affairs and Export Control (BAFA)}, +title = {Export Control in Science \& Research}, +url = {https://www.bafa.de/SharedDocs/Downloads/EN/Foreign_Trade/ec_awareness_academia.html}, +urldate = {2023-08-04} +} + +@InProceedings{FaceyShaw2018, + author = {Facey-Shaw, Lisa and Specht, Marcus and Bartley-Bryan, Jeanette}, + title = {Digital Badges for Motivating Introductory Programmers: Qualitative Findings from Focus Groups}, + booktitle = {2018 {IEEE} Frontiers in Education Conference ({FIE})}, + year = {2018}, + publisher = {IEEE}, + month = oct, + isbn = {978-1-5386-1174-6}, + doi = {10.1109/fie.2018.8659227}, + issn = {2377-634X}, + eventdate = {2018-10-03/2018-10-06}, + venue = {San Jose, California, USA}, +} + +@Article{FAIR, + author = {Wilkinson, Mark D. and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and da Silva Santos, Luiz Bonino and Bourne, Philip E. and Bouwman, Jildau and Brookes, Anthony J. and Clark, Tim and Crosas, Merc{\`e} and Dillo, Ingrid and Dumon, Olivier and Edmunds, Scott and Evelo, Chris T. and Finkers, Richard and Gonzalez-Beltran, Alejandra and Gray, Alasdair J. 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Linxweiler, Jan and Schwarzmeier, Moritz and Seibold, Heidi and Thiele, Jan Philipp and von Waldow, Harald and Wittke, Samantha}, + title = {Foundational Competencies and Responsibilities of a Research Software Engineer}, + year = {2023}, + howpublished = {arXiv}, + month = nov, + doi = {10.48550/arXiv.2311.11457}, + eprint = {2311.11457}, + archiveprefix = {arXiv}, + primaryclass = {cs.SE}, +} + +@article{Gotterbarn1999, +author = {Gotterbarn, Don and Miller, Keith and Rogerson, Simon}, +title = {Software Engineering Code of Ethics is Approved}, +year = {1999}, +publisher = {Association for Computing Machinery}, +address = {New York, New York, USA}, +volume = {42}, +number = {10}, +issn = {0001-0782}, +doi = {10.1145/317665.317682}, +journal = {Communications of the ACM}, +month = oct, +pages = {102--107}, +numpages = {6} +} + +@InCollection{Grant2016, + author = {Grant, Sheryl}, + title = {Building Collective Belief in Badges: Designing Trust Networks}, + booktitle = {Foundation of Digital Badges and Micro-Credentials}, + year = {2016}, + editor = {Ifenthaler, Dirk and Bellin-Mularski, Nicole and Mah, Dana-Kristin}, + booksubtitle = {Demonstrating and Recognizing Knowledge and Competencies}, + publisher = {Springer International Publishing}, + isbn = {978-3-319-15425-1}, + pages = {97--114}, + doi = {10.1007/978-3-319-15425-1_6}, + address = {Cham, Switzerland}, + month = jun, +} + +@Article{Grossfield2022, + author = {Grossfield, Alan}, + title = {How to be a Good Member of a Scientific Software Community [Article v1.0]}, + journal = {Living Journal of Computational Molecular Science}, + year = {2022}, + volume = {3}, + number = {1}, + month = jan, + pages = {1473}, + doi = {10.33011/livecoms.3.1.1473}, + address = {Boulder, Colorado, USA}, +} + +@Article{Grossmann2023, + author = {Grossmann, Yves Vincent and Franke, Michael}, + title = {{S}oftware ist kein {B}eiprodukt!}, + journal = {b.i.t.online}, + year = {2023}, + subtitle = {Nachhaltige 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A field experiment on the effects of gamification}, + journal = {Computers in Human Behavior}, + year = {2017}, + volume = {71}, + month = jun, + pages = {469--478}, + doi = {10.1016/j.chb.2015.03.036}, + publisher = {Elsevier {BV}}, +} + +@InProceedings{Hannay2009, + author = {Hannay, Jo Erskine and MacLeod, Carolyn and Singer, Janice and Langtangen, Hans Petter and Pfahl, Dietmar and Wilson, Greg}, + title = {How do scientists develop and use scientific software?}, + booktitle = {Proceedings of the 2009 {ICSE} Workshop on Software Engineering for Computational Science and Engineering}, + year = {2009}, + month = may, + publisher = {IEEE}, + doi = {10.1109/secse.2009.5069155}, + isbn = {978-1-4244-3737-5}, + eventdate = {2009-05-23/2009-05-23}, + venue = {Vancouver, British Columbia, Canada}, +} + +@Article{Hansch2015, + author = {Hansch, Anna and Newman, Christopher and Schildhauer, Thomas}, + title = {Fostering Engagement with Gamification: Review of Current Practices on Online Learning Platforms}, + journal = {{SSRN} Electronic Journal}, + year = {2015}, + month = nov, + doi = {10.2139/ssrn.2694736}, + publisher = {Elsevier {BV}}, +} + +@InProceedings{Haupt2017, + author = {Haupt, Carina and Schlauch, Tobias}, + title = {Track 1 Paper: The Software Engineering Community at {DLR} --- How we got where we are}, + booktitle = {Proceedings of the Workshop on Sustainable Software for Science: Practice and Experiences ({WSSSPE5.1})}, + year = {2017}, + editor = {Chue Hong, Neil and Druskat, Stephan and Haines, Robert and Jay, Caroline and Katz, Daniel S. and Sufi, Shoaib}, + eventdate = {2017-09-06/2017-09-06}, + venue = {University of Manchester, Manchester, United Kingdom}, + publisher = {figshare}, + month = sep, + doi = {10.6084/m9.figshare.5331703}, +} + +@InProceedings{Haupt2018, + author = {Haupt, Carina and Schlauch, Tobias and Meinel, Michael}, + title = {The software engineering initiative of {DLR}}, + booktitle = {Proceedings of the {SE4S}cience '18: 2018 {IEEE}/{ACM} 13\textsuperscript{th} International Workshop on Software Engineering for Science}, + year = {2018}, + editor = {Bilof, Randall}, + eventdate = {2018-06-02/2018-06-02}, + venue = {Gothenburg, Sweden}, + publisher = {ACM}, + month = jun, + isbn = {978-1-4503-5748-7}, + pages = {16--19}, + doi = {10.1145/3194747.3194749}, + address = {New York, New York, USA}, +} + +@TechReport{Hedinger2022, + author = {Hedinger, Franziska}, + title = {Microcertifications: d{\'e}veloppements r{\'e}cents en {S}uisse et {\`a} l'{\'e}chelle internationale}, + institution = {Swiss Federation for Adult Learning}, + year = {2022}, + type = {Rapport de fond}, + month = mar, + address = {Zurich, Switzerland}, +} + +@Article{Hennah2017, + author = {Hennah, Naomi and Seery, Michael K.}, + title = {Using Digital Badges for Developing High School Chemistry Laboratory Skills}, + journal = {Journal of Chemical Education}, + year = {2017}, + volume = {94}, + number = {7}, + month = may, + pages = {844--848}, + doi = {10.1021/acs.jchemed.7b00175}, + publisher = {American Chemical Society ({ACS})}, +} + +@Article{Heroux2022, + author = {Heroux, Michael A.}, + title = {Research Software Science: Expanding the Impact of Research Software Engineering}, + journal = {Computing in Science \& Engineering}, + year = {2022}, + volume = {24}, + number = {6}, + pages = {22--27}, + month = nov, + doi = {10.1109/mcse.2023.3260475}, + publisher = {Institute of Electrical and Electronics Engineers ({IEEE})}, +} + +@Misc{Hettrick2016, + author = {Hettrick, Simon}, + title = {A not-so-brief history of Research Software Engineers}, + year = {2016}, + month = aug, + howpublished = {Software Susitainability Institute}, + url = {https://www.software.ac.uk/blog/2016-08-17-not-so-brief-history-research-software-engineers-0}, + urldate = {2023-06-16}, +} + +@Article{Hickey2019, + author = {Hickey, Daniel T. and Chartrand, Grant T.}, + title = {Recognizing competencies vs. completion vs. participation: Ideal roles for web-enabled digital badges}, + journal = {Education and Information Technologies}, + year = {2019}, + volume = {25}, + number = {2}, + month = sep, + pages = {943--956}, + doi = {10.1007/s10639-019-10000-w}, + publisher = {Springer Science and Business Media {LLC}}, +} + +@online{HIDA, +author = {Helmholtz}, +title = {Helmholtz Information \& Data Science Academy ({HIDA})}, +url = {https://www.helmholtz-hida.de}, +urldate = {2023-06-16} +} + +@online{HIFIS, +author = {Helmholtz}, +title = {Helmholtz Federated {IT} Services ({HIFIS})}, +url = {https://hifis.net}, +urldate = {2023-06-16} +} + +@Article{Higashi2020, + author = {Higashi, Ross and Schunn, Christian D.}, + title = {Perceived relevance of digital badges predicts longitudinal change in program engagement}, + journal = {Journal of Educational Psychology}, + year = {2020}, + volume = {112}, + number = {5}, + month = jul, + pages = {1020--1041}, + doi = {10.1037/edu0000401}, + publisher = {American Psychological Association ({APA})}, +} + +@Article{Hiltemann2023, + author = {Hiltemann, Saskia and Rasche, Helena and Gladman, Simon and Hotz, Hans-Rudolf and Larivi{\`e}re, Delphine and Blankenberg, Daniel and Jagtap, Pratik D. and Wollmann, Thomas and Bretaudeau, Anthony and Gou{\'{e}}, Nadia and Griffin, Timothy J. and Royaux, Coline and Le Bras, Yvan and Mehta, Subina and Syme, Anna and Coppens, Frederik and Droesbeke, Bert and Soranzo, Nicola and Bacon, Wendi and Psomopoulos, Fotis and Gallardo-Alba, Crist{\'{o}}bal and Davis, John and F{\"o}ll, Melanie Christine and Fahrner, Matthias and Doyle, Maria A. and Serrano-Solano, Beatriz and Fouilloux, Anne Claire and van Heusden, Peter and Maier, Wolfgang and Clements, Dave and Heyl, Florian and {Galaxy Training Network} and Gr{\"u}ning, Bj{\"o}rn and Batut, B{\'e}r{\'e}nice}, + title = {Galaxy Training: A powerful framework for teaching!}, + journal = {{PLOS} Computational Biology}, + year = {2023}, + editor = {Ouellette, Francis}, + volume = {19}, + number = {1}, + month = jan, + pages = {e1010752}, + doi = {10.1371/journal.pcbi.1010752}, + publisher = {Public Library of Science ({PLoS})}, +} + +@online{HImaging, +author = {Helmholtz}, +title = {Helmholtz Imaging}, +url = {https://helmholtz-imaging.de/}, +urldate = {2023-06-16} +} + +@book{Hirvela2022, + title = {Right to Respect for Private and Family Life, Home and Correspondence}, + subtitle = {A Practical Guide to the Article 8 Case-Law of the European Court of Human Rights}, + isbn = {978-1-83970-323-2}, + publisher = {Intersentia}, + author = {Hirvel{\"a}, P{\"a}ivi and Heikkil{\"a}, Satu}, + month = oct, + year = {2022}, + doi = {10.1017/9781839703232}, +} + +@online{HMC, +author = {Helmholtz}, +title = {Helmholtz Metadata Collaboration (HMC)}, +url = {https://helmholtz-metadaten.de}, +urldate = {2023-06-16} +} + +@Article{Holinski2020, + author = {Holinski, Alexandra and Burke, Melissa L. and Morgan, Sarah L. and McQuilton, Peter and Palagi, Patricia M.}, + title = {Biocuration - mapping resources and needs [version 2; peer review: 2 approved]}, + journal = {F1000Research}, + year = {2020}, + volume = {9}, + month = dec, + pages = {1094}, + doi = {10.12688/f1000research.25413.2}, + publisher = {F1000 Research Ltd}, +} + +@online{HPCAkademie, +organization = {HLRS}, +title = {Die {S}upercomputing {A}kademie}, +url={https://www.supercomputing-akademie.de/}, +urldate={2023-07-27} +} + +@online{HPCCF, + author = {{The HPC Certification Forum}}, + title = {HPC Certification Forum}, + url = {https://www.hpc-certification.org}, + urldate = {2023-11-01}, +} + +@online{HPCCFCompetencies, + author = {{The HPC Certification Forum}}, + title = {Competencies}, + url = {https://www.hpc-certification.org/cs/}, + urldate = {2023-06-16}, +} + +@book{humphreys_extending_2004, + title = {Extending Ourselves: Computational Science, Empiricism, and Scientific Method}, + isbn = {978-0-19-978596-4}, + shorttitle = {Extending Ourselves}, + publisher = {Oxford University Press}, + author = {Humphreys, Paul}, + date = {2004-08-12}, + doi = {10.1093/0195158709.001.0001}, +} + +@Article{HunterZinck2021, + author = {Hunter-Zinck, Haley and de Siqueira, Alexandre Fioravante and V{\'{a}}squez, V{\'{a}}leri N. and Barnes, Richard and Martinez, Ciera C.}, + title = {Ten simple rules on writing clean and reliable open-source scientific software}, + journal = {{PLOS} Computational Biology}, + year = {2021}, + volume = {17}, + number = {11}, + pages = {e1009481}, + month = nov, + doi = {10.1371/journal.pcbi.1009481}, + editor = {Markel, Scott}, + publisher = {Public Library of Science ({PLoS})}, +} + +@Article{Hurst2015, + author = {Hurst, Emily Josephine}, + title = {Digital Badges: Beyond Learning Incentives}, + journal = {Journal of Electronic Resources in Medical Libraries}, + year = {2015}, + volume = {12}, + number = {3}, + month = jul, + pages = {182--189}, + doi = {10.1080/15424065.2015.1065661}, + publisher = {Informa {UK} Limited}, +} + +@Online{IBMBadges, + author = {{IBM}}, + title = {{IBM} Training / Badges}, + url = {https://www.ibm.com/training/search?query=*&trainingType=Badge}, + urldate = {2023-07-03}, +} + +@TechReport{ICDLEurope2021, + author = {ICDL}, + title = {{DigComp} and {ICDL}}, + institution = {ICDL Europe}, + year = {2021}, + subtitle = {Mapping {ICDL} to the {E}uropean {D}igital {C}ompetence {F}ramework}, + month = jan, + url = {https://icdleurope.org/policy-and-publications/digcomp-and-icdl/}, +} + +@Book{Ifenthaler2016, + title = {Foundation of Digital Badges and Micro-Credentials}, + year = {2016}, + editor = {Ifenthaler, Dirk and Bellin-Mularski, Nicole and Mah, Dana-Kristin}, + subtitle = {Demonstrating and Recognizing Knowledge and Competencies}, + publisher = {Springer International Publishing}, + isbn = {978-3-319-15425-1}, + doi = {10.1007/978-3-319-15425-1}, + address = {Cham, Switzerland}, + month = jun, +} + +@Article{InamoratodosSantos2023, + author = {Inamorato dos Santos, Andreia and Chinkes, Ernesto and Carvalho, Marco A. G. and Sol{\'{o}}rzano, Claudia M. V. and Marroni, Lilian S.}, + title = {The digital competence of academics in higher education: is the glass half empty or half full?}, + journal = {International Journal of Educational Technology in Higher Education}, + year = {2023}, + volume = {20}, + number = {1}, + month = feb, + issn = {2365-9440}, + doi = {10.1186/s41239-022-00376-0}, + publisher = {Springer Science and Business Media {LLC}}, +} + +@Online{INTERSECTOnlineResources, + author = {{INTERSECT}}, + title = {Existing Research Software Engineering Training Material}, + year = {2023}, + url = {https://intersect-training.org/training-links/}, + urldate = {2023-07-12}, +} + +@Book{Irving2021, + author = {Irving, Damien and Hertweck, Kate and Johnston, Luke and Ostblom, Joel and Wickham, Charlotte and Wilson, Greg}, + title = {Research Software Engineering with {P}ython}, + year = {2021}, + subtitle = {Building software that makes research possible}, + publisher = {CRC Press}, + isbn = {978-1-003-14348-2}, + doi = {10.1201/9781003143482}, +} + +@Article{Isik2023, + author = {I{\c s}{\i}k, Esra B{\"u}{\c s}ra and Brazas, Michelle D. and Schwartz, Russell and Gaeta, Bruno and Palagi, Patricia M. and Gelder, Celia W. G. van and Suravajhala, Prashanth and Singh, Harpreet and Morgan, Sarah L. and Zahroh, Hilyatuz and Ling, Maurice and Satagopam, Venkata P. and McGrath, Annette and Nakai, Kenta and Tan, Tin Wee and Gao, Ge and Mulder, Nicola and Sch{\"o}nbach, Christian and Zheng, Yun and De Las Rivas, Javier and Khan, Asif M.}, + title = {Grand challenges in bioinformatics education and training}, + journal = {Nature Biotechnology}, + year = {2023}, + volume = {41}, + number = {8}, + month = aug, + pages = {1171--1174}, + doi = {10.1038/s41587-023-01891-9}, + publisher = {Springer Science and Business Media {LLC}}, +} + +@Article{Jaana2019, + author = {Kullaslahti, Jaana and Ruhalahti, Sanna and Brauer, Sanna}, + title = {Professional Development of Digital Competences: Standardised Frameworks Supporting Evolving Digital Badging Practices}, + journal = {Journal of Siberian Federal University. Humanities \& Social Sciences}, + year = {2019}, + volume = {12}, + number = {2}, + month = feb, + pages = {175--186}, + doi = {10.17516/1997-1370-0387}, + publisher = {Siberian Federal University}, +} + +@TechReport{Jackson2011a, + author = {Jackson, Mike and Crouch, Steve and Baxter, Rob}, + title = {Software Evaluation: Criteria-Based Assessment}, + institution = {Software Sustainability Institute}, + year = {2011}, + type = {Software Evaluation Guide}, + month = nov, + url = {https://software.ac.uk/sites/default/files/SSI-SoftwareEvaluationCriteria.pdf}, +} + +@TechReport{Jackson2011b, + author = {Jackson, Mike and Crouch, Steve and Baxter, Rob}, + title = {Software Evaluation: Tutorial-Based Assessment}, + institution = {Software Sustainability Institute}, + year = {2011}, + type = {Software Evaluation Guide}, + month = nov, + url = {https://software.ac.uk/sites/default/files/SSI-SoftwareEvaluationTutorial.pdf}, +} + +@Article{Jalili2020a, + author = {Jalili, Vahid and Afgan, Enis and Gu, Qiang and Clements, Dave and Blankenberg, Daniel and Goecks, Jeremy and Taylor, James and Nekrutenko, Anton}, + title = {The {G}alaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update}, + journal = {Nucleic Acids Research}, + year = {2020}, + volume = {48}, + number = {W1}, + month = jun, + pages = {W395--W402}, + doi = {10.1093/nar/gkaa434}, + publisher = {Oxford University Press ({OUP})}, + related = {Jalili2020b}, + relatedstring = {Corrected in}, +} + +@Article{Jalili2020b, + author = {Jalili, Vahid and Afgan, Enis and Gu, Qiang and Clements, Dave and Blankenberg, Daniel and Goecks, Jeremy and Taylor, James and Nekrutenko, Anton}, + title = {The {G}alaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update}, + journal = {Nucleic Acids Research}, + year = {2020}, + volume = {48}, + number = {14}, + month = jun, + pages = {8205--8207}, + doi = {10.1093/nar/gkaa554}, + publisher = {Oxford University Press ({OUP})}, +} + +@TechReport{Jetten2021, + author = {Jetten, Mijke and Grootveld, Marjan and Mordant, Annemie and Jansen, Mascha and Bloemers, Margreet and Miedema, Margriet and van Gelder, Celia W.G.}, + title = {Professionalising data stewardship in the {N}etherlands: competences, training and education}, + institution = {National Programme Open Science}, + year = {2021}, + subtitle = {{D}utch roadmap towards national implementation of {FAIR} data stewardship}, + version = {version 1.1}, + month = feb, + doi = {10.5281/zenodo.4623713}, + publisher = {Zenodo}, +} + +@Article{Jimenez2017, + author = {Jim{\'{e}}nez, Rafael C. and Kuzak, Mateusz and Alhamdoosh, Monther and Barker, Michelle and Batut, B{\'{e}}r{\'{e}}nice and Borg, Mikael and Capella-Gutierrez, Salvador and Chue Hong, Neil and Cook, Martin and Corpas, Manuel and Flannery, Madison and Garcia, Leyla and Gelp{\'{i}}, Josep Ll. and Gladman, Simon and Goble, Carole and Gonz{\'{a}}lez Ferreiro, Montserrat and Gonzalez-Beltran, Alejandra and Griffin, Philippa C. and Gr{\"{u}}ning, Bj{\"{o}}rn and Hagberg, Jonas and Holub, Petr and Hooft, Rob and Ison, Jon and Katz, Daniel S. and Lesko{\v{s}}ek, Brane and G{\'{o}}mez, Federico L{\'{o}}pez and Oliveira, Luis J. and Mellor, David and Mosbergen, Rowland and Mulder, Nicola and Perez-Riverol, Yasset and Pergl, Robert and Pichler, Horst and Pope, Bernard and Sanz, Ferran and Schneider, Maria V. and Stodden, Victoria and Suchecki, Rados{\l}aw and Svobodov{\'{a}} Va{\v{r}}ekov{\'{a}}, Radka and Talvik, Harry-Anton and Todorov, Ilian and Treloar, Andrew and Tyagi, Sonika and van Gompel, Maarten and Vaughan, Daniel and Via, Allegra and Wang, Xiaochuan and Watson-Haigh, Nathan S. and Crouch, Steve}, + title = {Four simple recommendations to encourage best practices in research software [version 1; peer review: 3 approved]}, + journal = {F1000Research}, + year = {2017}, + volume = {6}, + pages = {876}, + month = jun, + doi = {10.12688/f1000research.11407.1}, + publisher = {F1000 Research Ltd}, +} + +@Article{Johanson2018, + author = {Johanson, Arne and Hasselbring, Wilhelm}, + title = {Software Engineering for Computational Science: Past, Present, Future}, + journal = {Computing in Science \& Engineering}, + year = {2018}, + volume = {20}, + number = {2}, + pages = {90--109}, + month = mar, + doi = {10.1109/mcse.2018.021651343}, + publisher = {Institute of Electrical and Electronics Engineers ({IEEE})}, +} + +@Article{Jones2017, + author = {Jones, W. Monty and Hope, Samantha and Adams, Brianne}, + title = {Teachers' perceptions of digital badges as recognition of professional development}, + journal = {British Journal of Educational Technology}, + year = {2017}, + volume = {49}, + number = {3}, + month = mar, + pages = {427--438}, + doi = {10.1111/bjet.12557}, + publisher = {Wiley}, +} + +@online{JOSE, + author = {{JOSE}}, + title = {The Journal of Open Source Education}, + url = {https://jose.theoj.org/}, + urldate = {2023-10-18}, +} + +@online{JOSS, + author = {{JOSS}}, + title = {The Journal of Open Source Software}, + url = {https://joss.theoj.org/}, + urldate = {2023-10-18}, +} + +@TechReport{Kampylis2015, + author = {Kampylis, Panagiotis and Punie, Yves and Devine, Jim}, + title = {Promoting Effective Digital-Age Learning}, + institution = {Joint Research Centre (European Commission)}, + year = {2015}, + type = {Science for Policy report}, + subtitle = {A {E}uropean Framework for Digitally-Competent Educational Organisations}, + number = {JRC98209, EUR 27599 EN}, + month = dec, + doi = {10.2791/54070}, + address = {Luxembourg}, + isbn = {978-92-79-54005-9}, + issn = {1831-9424}, + publisher = {Publications Office of the European Union}, +} + +@InProceedings{Kappes2015, + author = {Kappes, Sandra and Betro, Vincent C.}, + title = {Using {M}ozilla badges to certify {XSEDE} users and promote training}, + booktitle = {Proceedings of the 2015 {XSEDE} Conference on Scientific Advancements Enabled by Enhanced Cyberinfrastructure - {XSEDE} '15}, + year = {2015}, + publisher = {ACM Press}, + month = jul, + isbn = {978-1-4503-3720-5}, + doi = {10.1145/2792745.2792759}, + address = {New York, New York, USA}, + eventdate = {2015-07-26/2015-07-30}, + venue = {St. Louis, Missouri, USA}, +} + +@Misc{Katerbow2018, + author = {Katerbow, Matthias and Feulner, Georg}, + title = {Recommendations on the Development, Use and Provision of Research Software}, + year = {2018}, + howpublished = {Zenodo}, + doi = {10.5281/zenodo.1172988}, +} + +@Report{KDL, + author = {Smithies, James}, + title = {Research Software ({RS}) Careers}, + subtitle = {Generic Learnings from {King's Digital Lab}, {King's College London}}, + doi = {10.5281/zenodo.2559235}, + year = {2018}, + month = nov, + institution= {King's Digital Lab}, + type = {Report}, + version = {6.0}, + urldate = {2023-10-30}, + langid = {english}, +} + +@Article{Kim2021, + author = {Kim, Jihoon and Castelli, Darla M.}, + title = {Effects of Gamification on Behavioral Change in Education: A Meta-Analysis}, + journal = {International Journal of Environmental Research and Public Health}, + year = {2021}, + volume = {18}, + number = {7}, + month = mar, + pages = {3550}, + issn = {1660-4601}, + doi = {10.3390/ijerph18073550}, + publisher = {MDPI AG}, +} + +@TechReport{Kluzer2018, + author = {Kluzer, Stefano and Pujol Priego, Laia}, + title = {{DigComp} into action, get inspired make it happen}, + institution = {Joint Research Centre (European Commission)}, + year = {2018}, + type = {Science for Policy report}, + subtitle = {A user guide to the European Digital Competence framework}, + number = {JRC110624, EUR 29115 EN}, + month = may, + doi = {10.2760/112945}, + address = {Luxembourg}, + editor = {Carretero, Stephanie and Punie, Yves and Vuorikari, Riina and Cabrera, Marcelino and O'Keeffe, William}, + isbn = {978-92-79-79901-3}, + issn = {1831-9424}, + publisher = {Publications Office of the European Union}, +} + +@TechReport{Kluzer2019a, + author = {Kluzer, Stefano and Padroni, Rodolfo and Rizopoulos, Charalambos and Borotis, Spiros}, + title = {{DCDM} -- Digital Competence Development Methodology {v.2}}, + institution = {Digital Competences Development System}, + year = {2019}, + type = {Handbook}, + number = {Version 01}, + month = dec, + url = {http://www.dcds-project.eu/results/dcd-methodology/}, + publisher = {DCDS Project}, +} + +@TechReport{Kluzer2019b, + author = {Kluzer, Stefano and Padroni, Rodolfo}, + title = {{DCDS} Trainer Handbook ({TH})}, + institution = {Digital Competences Development System}, + year = {2019}, + type = {Handbook}, + number = {Version 03}, + month = nov, + url = {http://www.dcds-project.eu/resources/trainer-handbook/}, + publisher = {DCDS Project}, +} + +@TechReport{Kluzer2019c, + author = {Kluzer, Stefano and Padroni, Rodolfo}, + title = {{DCDS} Training Organisation Handbook ({TOH})}, + institution = {Digital Competences Development System}, + year = {2019}, + type = {Handbook}, + number = {Version 02}, + month = dec, + url = {http://www.dcds-project.eu/resources/training-organisation-handbook/}, + publisher = {DCDS Project}, +} + +@TechReport{Kluzer2020, + author = {Kluzer, Stefano and Centeno, Clara and O'Keeffe, William}, + title = {{DigComp} at Work}, + institution = {Joint Research Centre (European Commission)}, + year = {2020}, + type = {Science for Policy report}, + subtitle = {The {EU}'s digital competence framework in action on the labour market: a selection of case studies}, + number = {JRC120376, EUR 30166 EN}, + month = nov, + doi = {10.2760/17763}, + address = {Luxembourg}, + isbn = {978-92-76-22558-4}, + issn = {1831-9424}, + publisher = {Publications Office of the European Union}, +} + +@Article{KoehlerLeman2020, + author = {Koehler Leman, Julia and Weitzner, Brian D. and Renfrew, P. Douglas and Lewis, Steven M. and Moretti, Rocco and Watkins, Andrew M. and Mulligan, Vikram Khipple and Lyskov, Sergey and Adolf-Bryfogle, Jared and Labonte, Jason W. and Krys, Justyna and {RosettaCommons Consortium} and Bystroff, Christopher and Schief, William and Gront, Dominik and Schueler-Furman, Ora and Baker, David and Bradley, Philip and Dunbrack, Roland and Kortemme, Tanja and Leaver-Fay, Andrew and Strauss, Charlie E. M. and Meiler, Jens and Kuhlman, Brian and Gray, Jeffrey J. and Bonneau, Richard}, + title = {Better together: Elements of successful scientific software development in a distributed collaborative community}, + journal = {{PLOS} Computational Biology}, + year = {2020}, + volume = {16}, + number = {5}, + pages = {e1007507}, + month = may, + doi = {10.1371/journal.pcbi.1007507}, + editor = {Schneidman-Duhovny, Dina}, + publisher = {Public Library of Science ({PLoS})}, +} + +@TechReport{Konkol2021, + author = {Konkol, Markus and Jager-Ringoir, Katinka and Zurita-Milla, Ra{\'u}l}, + title = {Open Educational Resources}, + institution = {Faculty of Geo-Information Science and Earth Observation, University of Twente}, + year = {2021}, + subtitle = {Basic concepts, challenges, and business models}, + number = {Version 2.0}, + month = may, + doi = {10.5281/zenodo.4789124}, + publisher = {Zenodo}, +} + +@InProceedings{Koopman2022, + title = {{S}us{T}rainable: Promoting Sustainability as a Fundamental Driver in Software Development Training and Education}, + year = {2022}, + editor = {Koopman, Pieter and Lubbers, Mart and Fernandes, Jo{\~{a}}o Paulo}, + booktitle = {Teacher Training}, + titleaddon = {Revised lecture notes}, + publisher = {arXiv}, + month = apr, + doi = {10.48550/arXiv.2204.13993}, + eventdate = {2021-11-01/2021-11-05}, + venue = {Radboud University Nijmegen, Nijmegen, The Netherlands}, +} + +@TechReport{Krasavina2019, + author = {Krasavina, Andra and J{\=a}kobsone, M{\=a}ra and V{\=i}tola-Lapi{\c n}a, Vita}, + title = {{DCDS} Piloting and Evaluation Report}, + institution = {Digital Competences Development System}, + year = {2019}, + type = {{DCDS} Report}, + number = {Document 13 Version 2.0}, + month = oct, + url = {http://www.dcds-project.eu/resources/piloting-report/}, + publisher = {DCDS Project}, +} + +@Article{Kulikowski2012, + author = {Kulikowski, Casimir A. and Shortliffe, Edward H. and Currie, Leanne M. and Elkin, Peter L. and Hunter, Lawrence E. and Johnson, Todd R. and Kalet, Ira J. and Lenert, Leslie A. and Musen, Mark A. and Ozbolt, Judy G. and Smith, Jack W. and Tarczy-Hornoch, Peter Z. and Williamson, Jeffrey J.}, + title = {{AMIA} {B}oard white paper: definition of biomedical informatics and specification of core competencies for graduate education in the discipline}, + journal = {Journal of the American Medical Informatics Association}, + year = {2012}, + volume = {19}, + number = {6}, + month = nov, + pages = {931--938}, + doi = {10.1136/amiajnl-2012-001053}, + publisher = {Oxford University Press ({OUP})}, +} + +@Article{Kunkel2020a, + author = {Kunkel, Julian and Filinger, Weronika and Meesters, Christian and Gerbes, Anja}, + title = {The {HPC} {C}ertification {F}orum: Toward a Globally Acknowledged {HPC} Certification}, + journal = {Computing in Science \& Engineering}, + year = {2020}, + volume = {22}, + number = {4}, + pages = {110--114}, + issn = {1521-9615}, + doi = {10.1109/MCSE.2020.2996073}, +} + +@Article{Kunkel2020b, + author = {Kunkel, Julian Martin and Himstedt, Kai and Filinger, Weronika and Acquaviva, Jean-Thomas and Gerbes, Anja and Lafayette, Lev}, + title = {One Year {HPC} {C}ertification {F}orum in Retrospective}, + journal = {The Journal of Computational Science Education}, + year = {2020}, + volume = {11}, + number = {1}, + month = jan, + pages = {29--35}, + issn = {2153-4136}, + doi = {10.22369/issn.2153-4136/11/1/6}, +} + +@Article{Kunkel2020c, + author = {Kunkel, Julian and Himstedt, Kai and Filinger, Weronika and Acquaviva, Jean-Thomas and Gerbes, Anja and Lafayette, Lev}, + title = {Contributing {HPC} Skills to the {HPC} {C}ertification {F}orum}, + journal = {The Journal of Computational Science Education}, + year = {2020}, + volume = {11}, + number = {1}, + month = jan, + pages = {106--107}, + issn = {2153-4136}, + doi = {10.22369/issn.2153-4136/11/1/17}, +} + +@Article{Kunkel2020d, + author = {Kunkel, Julian and Himstedt, Kai and H\"{u}bbe, Nathanael and St\"{u}ben, Hinnerk and Schr\"{o}er, Sandra and Kuhn, Michael and Riebisch, Matthias and Olbrich, Stephan and Ludwig, Thomas and Filinger, Weronika and Acquaviva, Jean-Thomas and Gerbes, Anja and Lafayette, Lev}, + title = {Towards an {HPC} Certification Program}, + journal = {The Journal of Computational Science Education}, + year = {2019}, + volume = {10}, + number = {1}, + month = jan, + pages = {88--89}, + issn = {2153-4136}, + doi = {10.22369/issn.2153-4136/10/1/14}, +} + +@InProceedings{Laginja2022, + author = {Laginja, Iva and Robles, Pablo and Barjot, Kevin and Leboulleux, Lucie and Jensen-Clem, Rebecca and Brooks, Keira J. and Moriarty, Christopher}, + title = {Connecting the astronomical testbed community - the {CAOTIC} project: optimized teaching methods for software version control concepts}, + booktitle = {Adaptive Optics Systems {VIII}}, + year = {2022}, + editor = {Schreiber, Laura and Schmidt, Dirk and Vernet, Elise}, + volume = {12185}, + pages = {121853A}, + address = {Bellingham, Washington, USA}, + month = aug, + organization = {International Society for Optics and Photonics}, + publisher = {SPIE}, + doi = {10.1117/12.2629483}, + isbn = {9781510653528}, + issn = {1996-756X}, + eventdate = {2022-07-17/2022-07-23}, + eventitle = {{SPIE} Astronomical Telescopes + Instrumentation}, + venue = {Montr{\'e}al, Qu{\'e}bec, Canada}, +} + +@Article{Lamprecht2022a, + author = {Lamprecht, Anna-Lena and Martinez-Ortiz, Carlos and Barker, Michelle and Bartholomew, Sadie L. and Barton, Justin and Chue Hong, Neil and Cohen, Jeremy and Druskat, Stephan and Forest, Jeremy and Grad, Jean-No{\"e}l and Katz, Daniel S. and Richardson, Robin and Rosca, Robert and Schulte, Douwe and Struck, Alexander and Weinzierl, Marion}, + title = {What Do We (Not) Know About Research Software Engineering?}, + journal = {Journal of Open Research Software}, + year = {2022}, + volume = {10}, + number = {1}, + month = dec, + issn = {2049-9647}, + doi = {10.5334/jors.384}, + pages = {11}, + publisher = {Ubiquity Press, Ltd.}, +} + +@Article{Landwehr2017, + author = {Landwehr, Carl and Ludewig, Jochen and Meersman, Robert and Parnas, David Lorge and Shoval, Peretz and Wand, Yair and Weiss, David and Weyuker, Elaine}, + title = {{S}oftware {S}ystems {E}ngineering programmes a capability approach}, + journal = {Journal of Systems and Software}, + year = {2017}, + volume = {125}, + pages = {354--364}, + issn = {0164-1212}, + doi = {10.1016/j.jss.2016.12.016}, +} + +@article{Lannelongue2021, + author = {Lannelongue, Loïc and Grealey, Jason and Inouye, Michael}, + title = {Green Algorithms: Quantifying the Carbon Footprint of Computation}, + journal = {Advanced Science}, + volume = {8}, + number = {12}, + pages = {2100707}, + doi = {10.1002/advs.202100707}, + year = {2021} +} + +@article{Lannelongue2023, + title = {{GREENER} principles for environmentally sustainable computational science}, + volume = {3}, + issn = {2662-8457}, + doi = {10.1038/s43588-023-00461-y}, + pages = {514--521}, + number = {6}, + journaltitle = {Nature Computational Science}, + shortjournal = {Nat Comput Sci}, + author = {Lannelongue, Loïc and Aronson, Hans-Erik G. and Bateman, Alex and Birney, Ewan and Caplan, Talia and Juckes, Martin and {McEntyre}, Johanna and Morris, Andrew D. and Reilly, Gerry and Inouye, Michael}, + date = {2023-06-26}, + langid = {english}, +} + +@Article{Larcombe2017, + author = {Larcombe, L. and Hendricusdottir, R. and Attwood, T. 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{10.1007/s12528-019-09228-9}, + publisher = {Springer Science and Business Media {LLC}}, +} + +@Article{Mulder2018, + author = {Mulder, Nicola and Schwartz, Russell and Brazas, Michelle D. and Brooksbank, Cath and Gaeta, Bruno and Morgan, Sarah L. and Pauley, Mark A. and Rosenwald, Anne and Rustici, Gabriella and Sierk, Michael and Warnow, Tandy and Welch, Lonnie}, + title = {The development and application of bioinformatics core competencies to improve bioinformatics training and education}, + journal = {{PLOS} Computational Biology}, + year = {2018}, + editor = {Troyanskaya, Olga G.}, + volume = {14}, + number = {2}, + month = feb, + pages = {e1005772}, + doi = {10.1371/journal.pcbi.1005772}, + publisher = {Public Library of Science ({PLoS})}, +} + +@Article{Mundt2022, + author = {Mundt, Miranda R. and Beattie, Keith and Bisila, Jonathan and Ferenbaugh, Charles R. and Godoy, William F. and Gupta, Rinku and Guyer, Jonathan E. and Kiran, Miriam and Malviya-Thakur, Addi and Milewicz, Reed and Sims, Benjamin H. and Sochat, Vanessa and Teves, Joshua B.}, + title = {For the Public Good: Connecting, Retaining, and Recognizing Current and Future {RSEs} at {U.S.} National Research Laboratories and Agencies}, + journal = {Computing in Science \& Engineering}, + year = {2022}, + volume = {24}, + number = {6}, + pages = {6--13}, + month = nov, + doi = {10.1109/mcse.2023.3256759}, + publisher = {Institute of Electrical and Electronics Engineers ({IEEE})}, +} + +@article{NamingPain, + title = {Naming the Pain in Developing Scientific Software}, + author = {Wiese, Igor and Polato, Ivanilton and Pinto, Gustavo}, + year = {2020}, + month = jul, + journal = {IEEE Software}, + volume = {37}, + number = {4}, + pages = {75--82}, + issn = {1937-4194}, + doi = {10.1109/MS.2019.2899838}, +} + +@Book{NatlAcadSci2022, + author = {{National Academies of Sciences, Engineering, and Medicine}}, + title = {Transforming Trajectories for Women of Color in Tech}, + year = {2022}, + editor = {Hammonds, Evelynn and Taylor, Valerie and Hutton, Rebekah}, + publisher = {The National Academies Press}, + isbn = {978-0-309-26908-7}, + doi = {10.17226/26345}, + address = {Washington, D.C., USA}, +} + +@Online{NCCentralUniversityIBMBadges, + author = {{North Carolina Central University}}, + title = {{NCCU} {SLIS} Partners with {IBM} Skills Academy}, + url = {https://www.nccu.edu/slis/nccu-slis-partners-ibm-skills-academy}, + urldate = {2023-07-03}, +} + +@online{NFDI, +organization = {German National Research Data Infrastructure ({NFDI})}, +title = {German National Research Data Infrastructure ({NFDI})}, +url = {https://www.nfdi.de/?lang=en}, +urldate = {2023-07-14} +} + +@online{NFDI4ING, +organization = {National Research Data Infrastructure for Engineering Sciences (NFDI4Ing)}, +title={National Research Data Infrastructure for Engineering Sciences ({NFDI4Ing})}, +url={https://nfdi4ing.de/about-us/}, +urldate={2023-07-14} +} + +@inbook{Nieva2020, +author = {Nieva de la Hidalga, Abraham and Hardisty, Alex and Martin, Paul and Magagna, Barbara and Zhao, Zhiming}, +year = {2020}, +month = jul, +pages = {61--81}, +title = {The {ENVRI} Reference Model}, +booktitle = {Towards Interoperable Research Infrastructures for Environmental and Earth Sciences}, +isbn = {978-3-030-52828-7}, +doi = {10.1007/978-3-030-52829-4_4}, +} + +@Misc{NLeScienceCenterWhatIsRSE, + author = {{Netherlands eScience Center}}, + title = {What is a {R}esearch {S}oftware {E}ngineer? A definition by the {N}etherlands {eS}cience {C}enter}, + year = {2023}, + howpublished = {Zenodo}, + doi = {10.5281/zenodo.7994285}, +} + +@Article{Noor2022, + author = {Noor, Adeeb}, + title = {Improving bioinformatics software quality through incorporation of software engineering practices}, + journal = {{PeerJ} Computer Science}, + year = {2022}, + volume = {8}, + pages = {e839}, + month = jan, + doi = {10.7717/peerj-cs.839}, + publisher = {{PeerJ}}, +} + +@Article{Nordheim2021, + author = {von Nordheim, Gerret and Koppers, Lars and Boczek, Karin and Rieger, Jonas and Jentsch, Carsten and M{\"u}ller, Henrik and Rahnenf{\"u}hrer, J{\"o}rg}, + title = {Die {E}ntwicklung von {F}orschungssoftware als praktische {I}nterdisziplinarit{\"a}t}, + journal = {Medien \& Kommunikationswissenschaft}, + year = {2021}, + volume = {69}, + number = {1}, + pages = {80--96}, + doi = {10.5771/1615-634x-2021-1-80}, + publisher = {Nomos Verlag}, +} + +@Misc{NortheasternUniversityIBMBadges, + author = {{Northeastern University}}, + title = {{N}ortheastern {U}niversity and {IBM} partnership first to turn digital badges into academic credentials for learners worldwide}, + year = {2017}, + howpublished = {News@Northeastern}, + month = sep, + url = {https://news.northeastern.edu/2017/09/25/northeastern-university-and-ibm-partnership-first-to-turn-digital-badges-into-academic-credentials-for-learners-worldwide/}, + urldate = {2023-07-03}, +} + +@Article{Nowogrodzki2019, + author = {Nowogrodzki, Anna}, + title = {How to support open-source software and stay sane}, + journal = {Nature}, + year = {2019}, + volume = {571}, + number = {7763}, + pages = {133--134}, + month = jul, + doi = {10.1038/d41586-019-02046-0}, + publisher = {Springer Science and Business Media {LLC}}, +} + +@Article{OCais2020, + author = {O'Cais, Alan and Steinbach, Peter}, + title = {Expanding user communities with {HPC} {C}arpentry}, + journal = {The Journal of Computational Science Education}, + year = {2020}, + volume = {11}, + number = {1}, + month = jan, + pages = {21--25}, + issn = {2153-4136}, + doi = {10.22369/issn.2153-4136/11/1/4}, + publisher = {The Shodor Education Foundation, Inc.}, +} + +@online{OECD2023, +organization = {OECD}, +title = {Government researchers (indicator)}, +doi = {10.1787/c03b3052-en}, +urldate = {2023-05-23} +} + +@TechReport{OKeeffe2020, + author = {O'Keeffe, William}, + title = {{DigComp} at Work}, + institution = {Joint Research Centre (European Commission)}, + year = {2020}, + type = {Science for Policy report}, + subtitle = {Implementation guide}, + number = {JRC120645, EUR 30204 EN}, + month = jul, + doi = {10.2760/936769}, + address = {Luxembourg}, + isbn = {978-92-76-18581-9}, + issn = {1831-9424}, + publisher = {Publications Office of the European Union}, +} + +@Article{Oladipo2022, + author = {Oladipo, Francisca and Folorunso, Sakinat and Ogundepo, Ezekiel and Osigwe, Obinna and Akindele, Akinyinka}, + title = {Curriculum Development for {FAIR} Data Stewardship}, + journal = {Data Intelligence}, + year = {2022}, + volume = {4}, + number = {4}, + pages = {991--1012}, + doi = {10.1162/dint_a_00183}, + publisher = {MIT Press}, +} + +@Misc{Oliver2021, + author = {Oliver, Jeff and Goldman, Julie and F{\"o}rstner, Konrad}, + title = {Integration and reuse of {L}ibrary {C}arpentry content into curricula}, + year = {2021}, + month = mar, + url = {https://librarycarpentry.org/blog/2021/03/integration_and_reuse_of_lc_content_into_curricula/}, + urldate = {2023-06-27}, + publisher = {Library Carpentry}, +} + +@Online{OpenCoursesBadges, + author = {{Open Courses}}, + title = {About Open Badges}, + url = {https://opencourses.ie/about-open-badges/}, + urldate = {2023-07-03}, +} + +@TechReport{Operti2019a, + author = {Operti, Francesca and Tursi, Silvia}, + title = {Policy Influence Toolkit}, + institution = {Digital Competences Development System}, + year = {2019}, + type = {{DCDS} Report}, + number = {Document 21 Version 2}, + month = dec, + url = {http://www.dcds-project.eu/resources/dcds-policy-influence-toolkit/}, + publisher = {DCDS Project}, +} + +@TechReport{Operti2019b, + author = {Operti, Francesca}, + title = {Policy Recommendations}, + institution = {Digital Competences Development System}, + year = {2019}, + type = {{DCDS} Report}, + number = {Document 22 Version 0.3.1}, + month = dec, + url = {http://www.dcds-project.eu/resources/dcds-policy-recommendations/}, + publisher = {DCDS Project}, +} + +@InProceedings{Oprescu2022, + author = {Oprescu, Ana and Koedijk, Lukas and van Oostveen, Sander and Kok, Stephan}, + title = {Energy-driven software engineering}, + booktitle = {{S}us{T}rainable: Promoting Sustainability as a Fundamental Driver in Software Development Training and Education}, + year = {2022}, + editor = {Koopman, Pieter and Lubbers, Mart and Fernandes, Jo{\~{a}}o Paulo}, + booktitleaddon = {Revised lecture notes}, + publisher = {arXiv}, + month = apr, + pages = {27--35}, + doi = {10.48550/arXiv.2204.13993}, + eventdate = {2021-11-01/2021-11-05}, + venue = {Radboud University Nijmegen, Nijmegen, The Netherlands}, +} + +@TechReport{Orr2020a, + author = {Orr, Dominic and Pupinis, Mantas and Kirdulyt{\.e}, Greta}, + title = {Towards a {E}uropean approach to micro credentials}, + institution = {NESET}, + year = {2020}, + type = {Analytical report}, + subtitle = {A study of practices and commonalities in offering micro-credentials in {E}uropean higher education}, + number = {NC-03-20-553-EN-N}, + month = dec, + doi = {10.2766/7338}, + address = {Luxembourg}, + isbn = {978-92-76-21357-4}, + publisher = {Publications Office of the European Union}, +} + +@TechReport{Orr2020b, + author = {Orr, Dominic and Pupinis, Mantas and Kirdulyt{\.e}, Greta}, + title = {Towards a {E}uropean approach to micro credentials}, + institution = {NESET}, + year = {2020}, + type = {Executive Summary}, + subtitle = {A study of practices and commonalities in offering micro-credentials in {E}uropean higher education}, + number = {NC-03-20-554-EN-N}, + month = dec, + doi = {10.2766/392761}, + address = {Luxembourg}, + isbn = {978-92-76-21361-1}, + publisher = {Publications Office of the European Union}, + related = {Orr2020a}, + relatedstring = {Summary of}, +} + +@TechReport{OrvizFernandez2020, + author = {Orviz Fern{\'a}ndez, Pablo and David, Mario and Gomes, Jorge and Pina, Jo{\^a}o and Bernardo, Samuel and Campos Plasencia, Isabel and Molt{\'o}, Germ{\'a}n and Caballer, Miguel}, + title = {A set of Common Service Quality Assurance Baseline Criteria for Research Projects}, + institution = {EOSC Synergy}, + year = {2020}, + type = {Technical paper}, + month = apr, + doi = {10.20350/digitalCSIC/12533}, + publisher = {Digital.CSIC}, +} + +@Online{OSSFBestPracticeBadge, + author = {{Open Source Security Foundation}}, + title = {{OpenSSF} Best Practices Badge Program}, + year = {2021}, + url = {https://bestpractices.coreinfrastructure.org/en}, + urldate = {2023-07-12}, +} + +@TechReport{OSSMobilizationPlan, + author = {{The Linux Foundation} and {The Open Source Security Foundation}}, + title = {The Open Source Software Security Mobilization Plan}, + institution = {The Linux Foundation}, + year = {2022}, + month = may, + url = {https://openssf.org/oss-security-mobilization-plan/}, +} + +@InCollection{Otto2014, + author = {Otto, Nate and Hickey, Daniel T.}, + title = {Design Principles for Digital Badge Systems}, + booktitle = {New Horizons in Web Based Learning}, + year = {2014}, + editor = {Cao, Yiwei and V{\"a}ljataga, Terje and Tang, Jeff K.T. and Leung, Howard and Laanpere, Mart}, + booksubtitle = {2014 International Workshop on Social and Personal Computing for Web-Supported Learning Communities}, + volume = {8699}, + series = {Lecture Notes in Computer Science}, + publisher = {Springer International Publishing}, + isbn = {978-3-319-13296-9}, + pages = {179--184}, + doi = {10.1007/978-3-319-13296-9_20}, + address = {Cham, Switzerland}, + issn = 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related = {Vuorikari2022a}, + relatedstring = {Adapted from}, +} + +@Book{P8FutureUniversity2023c, + author = {{P8 Future University}}, + title = {Dossier Les badges num{\'e}riques ou Open Badges}, + year = {2023}, + publisher = {Universit{\'e} de Lausanne and UniDistance Suisse}, + url = {http://wp.unil.ch/digitalskills/files/2023/07/P8_Future_University_Dossier_Open_Badges.pdf}, + address = {Lausanne, Switzerland}, + month = may, +} + +@Misc{Papastamkou2019, + author = {Papastamkou, Sofia}, + title = {Welcome to {T}he {P}rogramming {H}istorian en fran{\c{c}}ais!}, + year = {2019}, + howpublished = {The Programming Historian blog}, + month = apr, + url = {https://programminghistorian.org/posts/welcome-ph-fr}, + urldate = {2023-08-23}, +} + +@Article{Park2019, + author = {Park, Sungjin and Kim, Sangkyun}, + title = {A Badge Design Framework for a Gamified Learning Environment: Cases Analysis and Literature Review for Badge Design}, + journal = {{JMIR} Serious Games}, + year = {2019}, + volume = {7}, + number = {2}, + month = may, + pages = {e14342}, + issn = {2291-9279}, + doi = {10.2196/14342}, + publisher = {JMIR Publications Inc.}, +} + +@article{Parker2022, + author = {Parker, Wendy S.}, + title = {Evidence and Knowledge from Computer Simulation}, + volume = {87}, + number = {4}, + year = {2022}, + month = aug, + journal = {Erkenntnis}, + issn = {1572-8420}, + doi = {10.1007/s10670-020-00260-1}, + pages = {1521--1538}, +} + +@Article{Patel2009, + author = {Patel, Vimla L. and Yoskowitz, Nicole A. and Arocha, Jose F. and Shortliffe, Edward H.}, + title = {Cognitive and learning sciences in biomedical and health instructional design: A review with lessons for biomedical informatics education}, + journal = {Journal of Biomedical Informatics}, + year = {2009}, + volume = {42}, + number = {1}, + month = feb, + pages = {176--197}, + doi = {10.1016/j.jbi.2008.12.002}, + publisher = {Elsevier {BV}}, +} + +@TechReport{Peer2Peer2011, + author = {{Peer 2 Peer University} and {Mozilla Foundation} and {MacArthur Foundation}}, + title = {An Open Badge System Framework}, + institution = {Mozilla Foundation}, + year = {2011}, + type = {Working Draft}, + subtitle = {A foundational piece on assessment and badges for open, informal and social learning environments}, + number = {4.0}, + month = may, + url = {https://wiki.mozilla.org/images/f/f3/OpenBadges_--_Working_Badge_Paper.pdf}, +} + +@Article{Pereira2021, + author = {Pereira, Rui and Couto, Marco and Ribeiro, Francisco and Rua, Rui and Cunha, J{\'{a}}come and Fernandes, Jo{\~{a}}o Paulo and Saraiva, Jo{\~{a}}o}, + title = {Ranking programming languages by energy efficiency}, + journal = {Science of Computer Programming}, + year = {2021}, + volume = {205}, + month = may, + pages = {102609}, + doi = {10.1016/j.scico.2021.102609}, + publisher = {Elsevier {BV}}, +} + +@Article{Pevzner2009, + author = {Pevzner, Pavel and Shamir, Ron}, + title = {Computing Has Changed Biology---Biology Education Must Catch Up}, + journal = {Science}, + year = {2009}, + volume = {325}, + number = {5940}, + month = jul, + pages = {541--542}, + doi = {10.1126/science.1173876}, + publisher = {American Association for the Advancement of Science ({AAAS})}, +} + +@Article{Pinto2017, + author = {Pinto, Gustavo and Castor, Fernando}, + title = {Energy Efficiency: A New Concern for Application Software Developers}, + journal = {Communications of the {ACM}}, + year = {2017}, + volume = {60}, + number = {12}, + month = nov, + pages = {68--75}, + issn = {1557-7317}, + doi = {10.1145/3154384}, + publisher = {Association for Computing Machinery ({ACM})}, +} + +@Article{Plomp2022, + author = {Plomp, Esther and Tsang, Emmy and Lavanchy, Paula M. Martinez}, + title = {Taking the {TU} Delft Carpentries Workshops Online}, + journal = {Journal of {eScience} Librarianship}, + year = {2022}, + volume = {11}, + number = {1}, + month = may, + issn = {2161-3974}, + doi = {10.7191/jeslib.2022.1221}, + publisher = {University of Massachusetts Medical School}, +} + +@Article{Poirier2021, + author = {Poirier, Therese I. and Weis, Logan}, + title = {Exploring pharmacy students' interest in digital badges}, + journal = {Currents in Pharmacy Teaching and Learning}, + year = {2021}, + volume = {13}, + number = {5}, + month = may, + pages = {506--511}, + doi = {10.1016/j.cptl.2021.01.004}, + publisher = {Elsevier {BV}}, +} + +@Article{Pomann2020, + author = {Pomann, Gina-Maria and Boulware, L. Ebony and Cayetano, Shari Messinger and Desai, Manisha and Enders, Felicity T. and Gallis, John A. and Gelfond, Jonathan and Grambow, Steven C. and Hanlon, Alexandra L. and Hendrix, Angelean and Kulkarni, Pandurang and Lapidus, Jodi and Lee, Hui-Jie and Mahnken, Jonathan D. and McKeel, Julie P. and Moen, Rebecca and Oster, Robert A. and Peskoe, Sarah and Samsa, Greg and Stewart, Thomas G. and Truong, Tracy and Wruck, Lisa and Thomas, Samantha M.}, + title = {Methods for training collaborative biostatisticians}, + journal = {Journal of Clinical and Translational Science}, + year = {2020}, + volume = {5}, + number = {1}, + month = aug, + pages = {e26}, + doi = {10.1017/cts.2020.518}, + publisher = {Cambridge University Press ({CUP})}, +} + +@Article{Pownall2023, + author = {Pownall, Madeleine and Azevedo, Fl{\'a}vio and K{\"o}nig, Laura M. and Slack, Hannah R. and Evans, Thomas Rhys and Flack, Zoe and Grinschgl, Sandra and Elsherif, Mahmoud M. and Gilligan-Lee, Katie A. and Oliveira, Catia M. 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Integrative Bioinformatics}, + year = {2019}, + volume = {16}, + number = {3}, + month = may, + doi = {10.1515/jib-2019-0005}, + publisher = {Walter de Gruyter {GmbH}}, +} + +@InProceedings{Queiroz2017, + author = {Queiroz, Francisco and Silva, Raniere and Miller, Jonah and {Sandor Brockhauser} and Fangohr, Hans}, + title = {Track 1 Paper: Good Usability Practices in Scientific Software Development}, + booktitle = {Proceedings of the Workshop on Sustainable Software for Science: Practice and Experiences ({WSSSPE5.1})}, + year = {2017}, + editor = {Chue Hong, Neil and Druskat, Stephan and Haines, Robert and Jay, Caroline and Katz, Daniel S. and Sufi, Shoaib}, + eventdate = {2017-09-06/2017-09-06}, + venue = {University of Manchester, Manchester, United Kingdom}, + publisher = {figshare}, + month = sep, + doi = {10.6084/m9.figshare.5331814}, +} + +@Misc{RabenseifnerCourseMPI, + author = {Rabenseifner, Rolf}, + title = {Introduction to the Message Passing Interface ({MPI})}, + year = 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Michiel and Finley, Stacey D. and Gosline, Sara J. 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H. and Carpenter, Anne E. and Fertig, Elana J.}, + title = {A field guide to cultivating computational biology}, + journal = {{PLOS} Biology}, + year = {2021}, + volume = {19}, + number = {10}, + pages = {e3001419}, + month = oct, + doi = {10.1371/journal.pbio.3001419}, + publisher = {Public Library of Science ({PLoS})}, +} + +@InProceedings{Webb2017, + author = {Webb, Mary and Bell, Tim and Davis, Niki and Katz, Yaacov J. and Reynolds, Nicholas and Chambers, Dianne P. and Sys{\l}o, Maciej M. and Fluck, Andrew and Cox, Margaret and Angeli, Charoula and Malyn-Smith, Joyce and Voogt, Joke and Zagami, Jason and Micheuz, Peter and Chtouki, Yousra and Mori, Nata{\v{s}}a}, + title = {Computer Science in the School Curriculum: Issues and Challenges}, + booktitle = {Tomorrow's Learning: Involving Everyone}, + year = {2017}, + editor = {Tatnall, Arthur and Webb, Mary}, + booksubtitle = {Learning with and about Technologies and Computing}, + volume = {515}, + series = {{IFIP} Advances in Information and Communication Technology}, + publisher = {Springer International Publishing}, + isbn = {978-3-319-74310-3}, + pages = {421--431}, + doi = {10.1007/978-3-319-74310-3_43}, + address = {Cham, Switzerland}, + issn = {1868-422X}, + lccn = {2018930742}, + eventdate = {2017-07-03/2017-07-06}, + venue = {Dublin, Ireland}, +} + +@Article{Welch2012, + author = {Welch, Lonnie R. and Schwartz, Russell and Lewitter, Fran}, + title = {A Report of the Curriculum Task Force of the {ISCB} Education Committee}, + journal = {{PLoS} Computational Biology}, + year = {2012}, + editor = {Philip E. Bourne}, + volume = {8}, + number = {6}, + month = jun, + pages = {e1002570}, + doi = {10.1371/journal.pcbi.1002570}, + publisher = {Public Library of Science ({PLoS})}, +} + +@Article{Welch2014, + author = {Welch, Lonnie and Lewitter, Fran and Schwartz, Russell and Brooksbank, Cath and Radivojac, Predrag and Gaeta, Bruno and Schneider, Maria Victoria}, + title = {Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies}, + journal = {{PLoS} Computational Biology}, + year = {2014}, + volume = {10}, + number = {3}, + month = mar, + pages = {e1003496}, + doi = {10.1371/journal.pcbi.1003496}, + publisher = {Public Library of Science ({PLoS})}, +} + +@Article{Welch2016, + author = {Welch, Lonnie and Brooksbank, Cath and Schwartz, Russell and Morgan, Sarah L. and Gaeta, Bruno and Kilpatrick, Alastair M. and Mietchen, Daniel and Moore, Benjamin L. and Mulder, Nicola and Pauley, Mark and Pearson, William and Radivojac, Predrag and Rosenberg, Naomi and Rosenwald, Anne and Rustici, Gabriella and Warnow, Tandy}, + title = {Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of {ISCB}'s Education Committee)}, + journal = {{PLOS} Computational Biology}, + year = {2016}, + volume = {12}, + number = {5}, + month = may, + pages = {e1004943}, + doi = {10.1371/journal.pcbi.1004943}, + publisher = {Public Library of Science ({PLoS})}, +} + +@TechReport{WhatResearchSoftware, + author = {{Netherlands eScience Center}}, + title = {What Is a {{Research Software Engineer}}?}, + subtitle = {A Definition by the {Netherlands eScience Center}}, + doi = {10.5281/zenodo.7994286}, + year = {2023}, + month = jun, + number = {Version 1.0}, + langid = {english}, +} + +@Article{White2022, + author = {White, Ethan and Brym, Zachary and Marx, Andrew and Riemer, Kristina and Marconi, Sergio and Harris, David and Cruz, Virnaliz and Ernest, S.}, + title = {{D}ata {C}arpentry for {B}iologists: A semester long {D}ata {C}arpentry course using ecological and other biological examples}, + journal = {Journal of Open Source Education}, + year = {2022}, + volume = {5}, + number = {50}, + month = apr, + pages = {139}, + doi = {10.21105/jose.00139}, + publisher = {The Open Journal}, +} + +@Article{Williams2016, + author = {Williams, Jason J. and Teal, Tracy K.}, + title = {A vision for collaborative training infrastructure for bioinformatics}, + journal = {Annals of the New York Academy of Sciences}, + year = {2016}, + volume = {1387}, + number = {1}, + issue = {Special Issue: Data Science, Learning, and Applications to Biomedical and Health Sciences}, + month = sep, + pages = {54--60}, + issn = {0077-8923}, + doi = {10.1111/nyas.13207}, + publisher = {Wiley}, +} + +@Article{Williams2019, + author = {Williams, Jason J. and Drew, Jennifer C. and Galindo-Gonzalez, Sebastian and Robic, Srebrenka and Dinsdale, Elizabeth and Morgan, William R. and Triplett, Eric W. and Burnette, James M. and Donovan, Samuel S. and Fowlks, Edison R. and Goodman, Anya L. and Grandgenett, Nealy F. and Goller, Carlos C. and Hauser, Charles and Jungck, John R. and Newman, Jeffrey D. and Pearson, William R. and Ryder, Elizabeth F. and Sierk, Michael and Smith, Todd M. and Tosado-Acevedo, Rafael and Tapprich, William and Tobin, Tammy C. and Toro-Mart{\'i}nez, Arl{\'i}n and Welch, Lonnie R. and Wilson, Melissa A. and Ebenbach, David and McWilliams, Mindy and Rosenwald, Anne G. and Pauley, Mark A.}, + title = {Barriers to integration of bioinformatics into undergraduate life sciences education: A national study of {US} life sciences faculty uncover significant barriers to integrating bioinformatics into undergraduate instruction}, + journal = {{PLOS} {ONE}}, + year = {2019}, + editor = {Cesario Bianchi}, + volume = {14}, + number = {11}, + month = nov, + pages = {e0224288}, + doi = {10.1371/journal.pone.0224288}, + publisher = {Public Library of Science ({PLoS})}, +} + +@Article{Wilson2006, + author = {Wilson, Greg}, + title = {Software Carpentry: Getting Scientists to Write Better Code by Making Them More Productive}, + journal = {Computing in Science \& Engineering}, + year = {2006}, + volume = {8}, + number = {6}, + month = nov, + pages = {66--69}, + doi = {10.1109/mcse.2006.122}, + publisher = {Institute of Electrical and Electronics Engineers ({IEEE})}, +} + +@misc{Wilson2012a, + author = {Wilson, Greg}, + title = {{S}loan {F}oundation Grant to {S}oftware {C}arpentry and {M}ozilla}, + howpublished = {Software Carpentry Blog}, + year = {2012}, + month = jan, + url = {https://software-carpentry.org/blog/2012/01/sloan-foundation-grant-to-software-carpentry-and-mozilla.html}, + urldate = {2023-06-19}, +} + +@misc{Wilson2012b, + author = {Wilson, Greg}, + title = {Badging}, + howpublished = {Software Carpentry Blog}, + year = {2012}, + month = jan, + url = {https://software-carpentry.org/blog/2012/01/badging.html}, + urldate = {2023-06-19}, +} + +@misc{Wilson2012c, + author = {Wilson, Greg}, + title = {Badges (Finalized)}, + howpublished = {Software Carpentry Blog}, + year = {2012}, + month = feb, + url = {https://software-carpentry.org/blog/2012/02/badges-finalized.html}, + urldate = {2023-06-19}, +} + +@misc{Wilson2013a, + author = {Wilson, Greg}, + title = {{S}loan {F}oundation Proposal Round 2}, + howpublished = {Software Carpentry Blog}, + year = {2013}, + month = jul, + url = {https://software-carpentry.org/blog/2013/07/sloan-proposal-round-2.html}, + urldate = {2023-06-19}, +} + +@misc{Wilson2014a, + author = {Wilson, Greg}, + title = {Translating {S}oftware {C}arpentry into {S}panish}, + howpublished = {Software Carpentry Blog}, + year = {2014}, + month = jun, + url = {https://software-carpentry.org/blog/2014/06/translating-software-carpentry-into-spanish.html}, + urldate = {2023-06-19}, +} + +@misc{Wilson2014b, + author = {Wilson, Greg}, + title = {Translating {S}oftware {C}arpentry into {K}orean}, + howpublished = {Software Carpentry Blog}, + year = {2014}, + month = nov, + url = {https://software-carpentry.org/blog/2014/11/korean-translation.html}, + urldate = {2023-06-19}, +} + +@Article{Wilson2014c, + author = {Wilson, Greg and Aruliah, D. A. and Brown, C. Titus and Chue Hong, Neil P. and Davis, Matt and Guy, Richard T. and Haddock, Steven H. D. and Huff, Kathryn D. and Mitchell, Ian M. and Plumbley, Mark D. and Waugh, Ben and White, Ethan P. and Wilson, Paul}, + title = {Best Practices for Scientific Computing}, + journal = {{PLoS} Biology}, + year = {2014}, + editor = {Eisen, Jonathan A.}, + volume = {12}, + number = {1}, + month = jan, + pages = {e1001745}, + doi = {10.1371/journal.pbio.1001745}, + publisher = {Public Library of Science ({PLoS})}, +} + +@Article{Wilson2016a, + author = {Wilson, Greg}, + title = {{S}oftware {C}arpentry: lessons learned [version 2; peer review: 3 approved]}, + journal = {F1000Research}, + year = {2016}, + volume = {3}, + number = {62}, + month = jan, + doi = {10.12688/f1000research.3-62.v2}, + publisher = {F1000 Research Ltd}, +} + +@Article{Wilson2017a, + author = {Wilson, Greg and Bryan, Jennifer and Cranston, Karen and Kitzes, Justin and Nederbragt, Lex and Teal, Tracy K.}, + title = {Good enough practices in scientific computing}, + journal = {{PLOS} Computational Biology}, + year = {2017}, + volume = {13}, + number = {6}, + pages = {e1005510}, + month = jun, + doi = {10.1371/journal.pcbi.1005510}, + editor = {Ouellette, Francis}, + publisher = {Public Library of Science ({PLoS})}, +} + +@Book{Wilson2019a, + author = {Wilson, Greg}, + title = {Teaching Tech Together}, + year = {2019}, + subtitle = {How to Make Your Lessons Work and Build a Teaching Community around Them}, + publisher = {CRC Press}, + isbn = {9780429330704}, + url = {https://www.routledge.com/Teaching-Tech-Together-How-to-Make-Your-Lessons-Work-and-Build-a-Teaching/Wilson/p/book/9780367352974}, + lccn = {2019030230}, +} + +@Online{Wilson2019b, + author = {Wilson, Greg}, + title = {Teaching Tech Together}, + year = {2019}, + url = {https://teachtogether.tech/en/index.html}, + subtitle = {How to Make Your Lessons Work and Build a Teaching Community around Them}, + urldate = {2023-07-12}, +} + +@Online{Wilson2019c, + author = {Wilson, Greg}, + title = {Ense{\~n}ar tecnolog{\'i}a en comunidad}, + year = {2019}, + url = {https://teachtogether.tech/es/index.html}, + subtitle = {C{\'o}mo crear y dar lecciones que funcionen y construir una comunidad docente a su alrededor}, + urldate = {2023-07-12}, +} + +@Article{WilsonSayres2018, + author = {Wilson Sayres, Melissa A. and Hauser, Charles and Sierk, Michael and Robic, Srebrenka and Rosenwald, Anne G. and Smith, Todd M. and Triplett, Eric W. and Williams, Jason J. and Dinsdale, Elizabeth and Morgan, William R. and Burnette, III, James M. and Donovan, Samuel S. and Drew, Jennifer C. and Elgin, Sarah C. R. and Fowlks, Edison R. and Galindo-Gonzalez, Sebastian and Goodman, Anya L. and Grandgenett, Nealy F. and Goller, Carlos C. and Jungck, John R. and Newman, Jeffrey D. and Pearson, William and Ryder, Elizabeth F. and Tosado-Acevedo, Rafael and Tapprich, William and Tobin, Tammy C. and Toro-Mart{\'i}nez, Arl{\'i}n and Welch, Lonnie R. and Wright, Robin and Barone, Lindsay and Ebenbach, David and McWilliams, Mindy and Olney, Kimberly C. and Pauley, Mark A.}, + title = {Bioinformatics core competencies for undergraduate life sciences education}, + journal = {{PLOS} {ONE}}, + year = {2018}, + editor = {Dalby, Andrew R.}, + volume = {13}, + number = {6}, + month = jun, + pages = {e0196878}, + doi = {10.1371/journal.pone.0196878}, + publisher = {Public Library of Science ({PLoS})}, +} + +@article{winsberg_sanctioning_1999, + title = {Sanctioning Models: The Epistemology of Simulation}, + volume = {12}, + issn = {1474-0664, 0269-8897}, + doi = {10.1017/S0269889700003422}, + shorttitle = {Sanctioning Models}, + pages = {275--292}, + number = {2}, + journaltitle = {Science in Context}, + author = {Winsberg, Eric}, + date = {1999-07}, +} + +@InProceedings{Winter2021, + author = {Winter, Emily and Thomas, Lisa and Blair, Lynne}, + title = {`It's a Bit Weird, but it's {OK}'? How Female Computer Science Students Navigate being a Minority}, + booktitle = {Proceedings of the 26\textsuperscript{th} {ACM} Conference on Innovation and Technology in Computer Science Education}, + year = {2021}, + volume = {1}, + publisher = {ACM}, + month = jun, + isbn = {978-1-4503-8214-4}, + pages = {436--442}, + doi = {10.1145/3430665.3456329}, + address = {New York, New York, USA}, + eventdate = {2021-06-26/2021-07-01}, + venue = {Virtual Event}, +} + +@TechReport{Woodley2021, + author = {Woodley, Lou and Pratt, Katie and Sandstr{\"o}m, Malin and Wood-Charlson, Elisha and Davison, Jennifer and Leidolf, Andreas}, + title = {The {CSCCE} Skills Wheel}, + institution = {Center for Scientific Collaboration and Community Engagement}, + year = {2021}, + type = {Guidelines}, + subtitle = {Five core competencies and 45 skills to describe the role of the community engagement manager in {STEM}}, + month = jan, + doi = {10.5281/zenodo.4437294}, + publisher = {Zenodo}, +} + +@Article{Wuttke2022, + author = {Wuttke, Joachim and Cottrell, Stephen and Gonzalez, Miguel A. and Kaestner, Anders and Markvardsen, Anders and Rod, Thomas H. and Rozyczko, Piotr and Vardanyan, Gagik}, + title = {Guidelines for collaborative development of sustainable data treatment software}, + journal = {Journal of Neutron Research}, + year = {2022}, + volume = {24}, + number = {1}, + pages = {33--72}, + month = mar, + doi = {10.3233/jnr-220002}, + publisher = {{IOS} Press}, +} + +@Article{Yurkovich2017, + author = {Yurkovich, James T. and Yurkovich, Benjamin J. and Dr{\"a}ger, Andreas and Palsson, Bernhard O. and King, Zachary A.}, + title = {A {P}adawan Programmer's Guide to Developing Software Libraries}, + journal = {Cell Systems}, + year = {2017}, + volume = {5}, + number = {5}, + pages = {431--437}, + month = nov, + doi = {10.1016/j.cels.2017.08.003}, + publisher = {Elsevier {BV}}, +} + +@Article{Zahan2023, + author = {Zahan, Nusrat and Kanakiya, Parth and Hambleton, Brian and Shohan, Shohanuzzaman and Williams, Laurie}, + title = {{OpenSSF} Scorecard: On the Path Toward Ecosystem-Wide Automated Security Metrics}, + journal = {IEEE Security \& Privacy}, + year = {2023}, + pages = {2--14}, + doi = {10.1109/MSEC.2023.3279773}, +} + +@Article{Zhou2019, + author = {Zhou, Li and Chen, Liwen and Fan, Qinman and Ji, Yueli}, + title = {Students' Perception of Using Digital Badges in Blended Learning Classrooms}, + journal = {Sustainability}, + year = {2019}, + volume = {11}, + number = {7}, + month = apr, + pages = {2151}, + doi = {10.3390/su11072151}, + publisher = {MDPI AG}, +} + +@TechReport{Zignani2020, + author = {Zignani, Tiana and Massara, Flavia and Doncheva, Aneta and Tarandova, Spaska and {DAISSy Research Group} and Holma, Baiba and Pakalna, Daina}, + title = {Librarianship in {E}urope -- Mapping Professional Needs}, + institution = {Biblio Project Consortium}, + year = {2020}, + type = {Report}, + number = {Version 1.1}, + month = aug, + url = {https://all-digital.org/wp-content/uploads/2020/12/BIBLIO_WP2_Mapping-Professional-Needs_Report.pdf}, + publisher = {ALL DIGITAL AISBL}, +} + +@Book{Zobel2004, + author = {Zobel, Justin}, + title = {Writing for Computer Science}, + year = {2004}, + publisher = {Springer}, + isbn = {978-0-85729-422-7}, + doi = {10.1007/978-0-85729-422-7}, + address = {London, United Kingdom}, + lccn = {2004042550}, +} + +@online{jones_codemeta_2017, + title = {{CodeMeta}: An Exchange Schema for Software Metadata}, + author = {Jones, Matthew B. and Boettiger, Carl and Mayes, Abby Cabunoc and Arfon Smith and Slaughter, Peter and Niemeyer, Kyle and Gil, Yolanda and Fenner, Martin and Nowak, Krzysztof and Hahnel, Mark and Coy, Luke and Allen, Alice and Crosas, Merc{\`e} and Sands, Ashley and Hong, Neil Chue and Cruse, Patricia and Katz, Daniel S. and Goble, Carole and Mecum, Bryce and Gonzalez-Beltran, Alejandra and Ross, Noam}, + year = {2017}, + doi = {10.5063/schema/codemeta-2.0} +} + +@misc{alves_elixir_2021, + title = {{ELIXIR} {Software} {Management} {Plan} for {Life} {Sciences}}, + doi = {10.37044/osf.io/k8znb}, + urldate = {2022-06-23}, + publisher = {BioHackrXiv}, + author = {Alves, Renato and Bampalikis, Dimitrios and Castro, Leyla Jael and Fern{\'a}ndez, Jos{\'e} M. and Harrow, Jennifer and Kuzak, Mateusz and Mart{\'i}n del Pico, Eva and Psomopoulos, Fotis and Via, Allegra}, + month = oct, + year = {2021}, +} + +@techreport{martinez_ortiz_practical_2022, + title = {Practical guide to {Software} {Management} {Plans}}, + urldate = {2023-04-06}, + institution = {Zenodo}, + author = {Martinez-Ortiz, Carlos and Martinez Lavanchy, Paula and Sesink, Laurents and Olivier, Brett G. and Meakin, James and de Jong, Maaike and Cruz, Maria}, + month = oct, + year = {2022}, + doi = {10.5281/zenodo.7248877}, +} + +@techreport{castro_research_sw_metadata_2023, + type = {Charta}, + title = {``{Research} {Software} {Metadata}'' - {Working} {Group} {Charter} ({NFDI} section-metadata)}, + language = {en}, + urldate = {2023-11-05}, + author = {Castro, Leyla Jael and Ferenz, Stephan and Fuhrmans, Marc and G{\"o}pfert, Jan and Iglezakis, Dorothea and Karras, Oliver and Struck, Alexander}, + month = oct, + year = {2023}, + doi = {10.5281/zenodo.10036379}, +} + +@inproceedings{giraldo_metadata_2023, + title = {A metadata schema for machine-actionable {S}oftware {M}anagement {P}lans}, + doi = {10.4126/FRL01-006444988}, + publisher = {PUBLISSO-FRL}, + author = {Giraldo, Olga and Geist, Lukas and Qui{\~n}ones, Nelson and Solanki, Dhwani and Alves, Renato and Bampalikis, Dimitrios and Fern{\'a}ndez Gonz{\'a}lez, Jos{\'e} M. and Martin Del Pico, Eva and Psomopoulos, Fotis E. and Via, Allegra and Rebholz-Schuhmann, Dietrich and Castro, Leyla Jael}, + year = {2023}, + month = jun, + booktitle = {3\textsuperscript{rd} International Workshop on Metadata and Research (objects) Management for Linked Open Science ({DaMaLOS} 2023)}, + eventdate = {2023-05-29}, + venue = {Hersonissos, Greece}, +} + +@article{druskat_hermes_2022, + title = {Software Publications with Rich Metadata: State of the Art, Automated Workflows and {{HERMES}} Concept}, + shorttitle = {Software Publications with Rich Metadata}, + author = {Druskat, Stephan and Bertuch, Oliver and Juckeland, Guido and Knodel, Oliver and Schlauch, Tobias}, + year = {2022}, + month = jan, + journal = {arXiv}, + doi = {10.48550/arXiv.2201.09015}, +} + +@article{druskat_cff_2021, + title = {Citation {{File Format}}}, + author = {Druskat, Stephan and Spaaks, Jurriaan H. and Chue Hong, Neil and Haines, Robert and Baker, James and Bliven, Spencer and Willighagen, Egon and {P\'erez-Su\'arez, David} and Konovalov, Olexandr}, + year = {2021}, + month = aug, + journal = {{Zenodo}}, + doi = {10.5281/zenodo.1003149}, + copyright = {Creative Commons Attribution 4.0 International, Open Access}, +} + +@book{turing_way_2022, + title = {{T}he {T}uring {W}ay: A Handbook for Reproducible, Ethical and Collaborative Research}, + author = {{The Turing Way Community}}, + year = {2022}, + month = jul, + doi = {10.5281/zenodo.3233853}, + publisher = {Zenodo}, + urldate = {2023-06-07}, +} + +@article{smith_SoftwareCitationPrinciples2016, + title = {Software Citation Principles}, + author = {Smith, Arfon M. and Katz, Daniel S. and Niemeyer, Kyle E. and {FORCE11 Software Citation Working Group}}, + year = {2016}, + journal = {PeerJ Computer Science}, + volume = {2}, + number = {e86}, + issn = {2376-5992}, + doi = {10.7717/peerj-cs.86} +} + +@Misc{zuCastell2024, + author = {zu Castell, Wolfgang and Dransch, Doris and Juckeland, Guido and Meistring, Marcel and Fritzsch, Bernadette and Gey, Ronny and H{\"o}pfner, Britta and K{\"o}hler, Martin and Mee{\ss}en, Christian and Mehrtens, Hela and M{\"u}hlbauer, Felix and Schindler, Sirko and Schnicke, Thomas and Bertelmann, Roland}, + title = {Towards a Quality Indicator for Research Data publications and Research Software publications -- A vision from the {H}elmholtz {A}ssociation}, + year = {2024}, + howpublished = {arXiv}, + month = jan, + eprint = {2401.08804}, + archiveprefix = {arXiv}, + primaryclass = {cs.DL}, +} + +@report{hettrick_survey_2022, + author = {Hettrick, Simon and + Bast, Radovan and + Crouch, Steve and + Wyatt, Claire and + Philippe, Olivier and + Botzki, Alex and + Carver, Jeffrey and + Cosden, Ian and + D'Andrea, Florencia and + Dasgupta, Abhishek and + Godoy, William and + Gonzalez-Beltran, Alejandra and + Hamster, Ulf and + Henwood, Scott and + Holmvall, Patric and + Janosch, Stephan and + Lestang, Thibault and + May, Nick and + Philips, Johan and + Poonawala-Lohani, Nooriyah and + Richmond, Paul and + Sinha, Manodeep and + Thiery, Florian and + Werkhoven, Ben and + Zhang, Qian}, + title = {International RSE Survey 2022}, + month = aug, + year = 2022, + publisher = {Zenodo}, + version = {v0.9.3}, + doi = {10.5281/zenodo.7015772}, + url = {https://doi.org/10.5281/zenodo.7015772} + } + +@Online{vihps, + title = {Virtual Institute - High Productivity Supercomputing}, + url = {https://vi-hps.org/}, + urldate = {2024-05-06}, +} + +@Online{techniciancommitment, + title = {The Technician Commitment}, + url = {https://www.techniciancommitment.org.uk/}, + urldate = {2024-07-31}, +} + +@Online{ukri_rtp, + title = {Investing in Research Teams}, + url = {https://www.ukri.org/what-we-do/developing-people-and-skills/bbsrc/investing-in-research-teams/technicians-and-technology-and-skills-specialists/}, + urldate = {2024-07-31}, +} + + +@Inbook{Weinzierl2021, +author="Weinzierl, Tobias", +title="The Pillars of Science", +bookTitle="Principles of Parallel Scientific Computing: A First Guide to Numerical Concepts and Programming Methods", +year="2021", +publisher="Springer International Publishing", +address="Cham", +pages="3--9", +isbn="978-3-030-76194-3", +doi="10.1007/978-3-030-76194-3_1", +} + +@Misc{Lamprecht2024-giradar, + author = {Anna-Lena Lamprecht}, + title = {{T}hema im {F}okus: {F}orschungssoftware und {R}esearch {S}oftware {E}ngineering ({RSE})}, + year = {2024}, + volume = {351}, + howpublished = {GI-Radar}, + url = {https://gi-radar.de/351-research-software/}, + month = feb +} + diff --git a/002/competencies.md b/002/competencies.md new file mode 100644 index 0000000..e30c9f1 --- /dev/null +++ b/002/competencies.md @@ -0,0 +1,1775 @@ +--- +title: "Foundational Competencies and Responsibilities of a Research Software Engineer" +geometry: "top=0.5cm,right=2.5cm,bottom=2.5cm,left=2.5cm" # Only for the title page, see include-before for the rest. +author: + - Florian Goth | Corresponding author + - Renato Alves + - Matthias Braun + - Leyla Jael Castro + - Gerasimos Chourdakis + - Simon Christ + - Jeremy Cohen + - Stephan Druskat + - Fredo Erxleben + - Jean-Noël Grad + - Magnus Hagdorn + - Toby Hodges + - Guido Juckeland + - Dominic Kempf + - Anna-Lena Lamprecht + - Jan Linxweiler + - Frank Löffler + - Michele Martone + - Moritz Schwarzmeier + - Heidi Seibold + - Jan Philipp Thiele + - Harald von Waldow + - Samantha Wittke + +output: + pdf_document: + citation_package: biblatex + toc: true + number_sections: true +secnumdepth: 3 +biblatexoptions: [alldates=iso] +bibliography: bibliography.bib +header-includes: + - \input{preamble.sty} + - \usepackage{pdflscape} + - \usepackage{multirow} + - \usepackage{array} + - \usepackage{longtable} + - \usepackage[inkscapepath=svg-inkscape]{svg} + - \pdfsuppresswarningpagegroup=1 + - \newcommand{\blandscape}{\begin{landscape}} + - \newcommand{\elandscape}{\end{landscape}} + - \newcommand{\fonticon}[2]{\includesvg[height=1.5ex]{{../fonts/#1}}\nobreakspace{}#2} + - 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\newglossaryentry{DIST}{name={\DIST},type={skills},description={Building distributable software}} + - \newglossaryentry{SWLC}{name={\SWLC},type={skills},description={Adapting to the software life cycle}} + - \newglossaryentry{SWREPOS}{name={\SWREPOS},type={skills},description={Use software repositories}} + - \newglossaryentry{MOD}{name={\MOD},type={skills},description={Software behaviour awareness and analysis}} + - \newglossaryentry{NEW}{name={\NEW},type={skills},description={Conducting and leading research}} + - \newglossaryentry{RC}{name={\RC},type={skills},description={Understanding the research cycle}} + - \newglossaryentry{SRU}{name={\SRU},type={skills},description={Software re-use}} + - \newglossaryentry{SP}{name={\SP},type={skills},description={Software publication and citation}} + - \newglossaryentry{DOMREP}{name={\DOMREP},type={skills},description={Using domain repositories/directories}} + - \newglossaryentry{TEAM}{name={\TEAM},type={skills},description={Working in a team}} + - \newglossaryentry{TEACH}{name={\TEACH},type={skills},description={Teaching}} + - \newglossaryentry{PM}{name={\PM},type={skills},description={Project management}} + - \newglossaryentry{USERS}{name={\USERS},type={skills},description={Interaction with users and other stakeholders}} +include-before: + - \newpage + - \newgeometry{top=2.5cm,right=2.5cm,bottom=2.5cm,left=2.5cm} +include-after: + - \printglossary + - \printglossary[type=skills] + - \printglossary[type=\acronymtype] +xnos-cleveref: True +xnos-capitalise: True +toc-baselinestretch: 0.85 +keywords: + - research software engineering + - RSE + - competencies + - curriculum design + - teaching +acknowledgements-before: "" +acknowledgements-after: " +We appreciate the comments and suggestions from Yves Vincent Grossmann, +Wilhelm Hasselbring, and Bernhard Rumpe. +" +abstract: " +The term Research Software Engineer, or RSE, +emerged a little over 10 years ago as a way to represent +individuals working in the research community but focusing on software development. +The term has been widely adopted and there are a number of high-level definitions of what an RSE is. +However, the roles of RSEs vary depending on the institutional context they work in. +At one end of the spectrum, RSE roles may look similar to a traditional research role. +At the other extreme, they resemble that of a software engineer in industry. +Most RSE roles inhabit the space between these two extremes. Therefore, providing a straightforward, +comprehensive definition of what an RSE does +and what experience, skills and competencies are required to become one is challenging. +In this community paper we define the broad notion of what an RSE is, explore the different types of work they undertake, and +define a list of foundational competencies as well as values that outline the general profile of an RSE. +Further research and training can build upon this foundation of skills +and focus on various aspects in greater detail. +We expect that graduates and practitioners will have a larger +and more diverse set of skills than outlined here. +On this basis, we elaborate on the progression of these skills along different +dimensions. We look at specific types of RSE roles, propose recommendations for organisations, and give examples of future specialisations. +An appendix details how existing curricula fit into this framework. +" +--- + +# Introduction {#sec:introduction} + +Computers and software have played a key role in the research life cycle for many +decades. +They are now vital elements of the research process across almost all domains. +They enable researchers to collect and process ever-increasing amounts of data, +simulate a wide range of physical phenomena across previously unexplored scales of the universe, +and discover previously inconceivably complex structures in nature and societies via \ac{ML}. +This prevalence of computation and digitally-aided data analysis in research means that +digital skills are now required by researchers at all +career levels, and in fields significantly beyond those that would previously +have been expected. +Research software is now used and developed not only in \ac{STEM} domains, +but also in other fields, like medicine and the humanities. + +Researchers often lack the skills to use specialised software +for their research, let alone write it [@NamingPain]. If they come from a non-technical domain, they may +also struggle to know what to ask when trying to request help from and interact with +more experienced colleagues. A gap still exists in +academic education, as many curricula do not sufficiently prepare students +in this regard. This situation is exemplified by the extracurricular \ac{MIT} class +"The Missing Semester of Your CS Education" [@MIT], which aims to increase +"computing ecosystem literacy" even among students of Computer Science at \ac{MIT}. + +Researchers investing increasing amounts of their time developing their \ac{SE} +skills to support their research work can find themselves with little time to do the research +itself. +This, in turn, presents career development challenges since the experience required to gain +and progress in research and academic roles is traditionally assessed through metrics that +do not directly include software outputs. +A recent shift towards the establishment of the distinct role of a +_"Research Software Engineer"_ [@WhatResearchSoftware] +(RSE, a term that was coined in the \ac{UK} a little over 10 years ago [@Hettrick2016]), +now provides a base on which sustainable career opportunities can be (and are being) built, +allowing for better training of researchers and more effective support for the development of high +quality research software. +There is still a long way to go, but positive change is well underway. + +RSEs may work within one of the increasing number of research software engineering teams that +have been set up at universities and research +organisations over the past decade, or they may be embedded within a research +team. They may have a job title that officially recognises them as an RSE, or +they may have a standard research or technical job title such as Research +Assistant, Research Fellow, or Software Engineer. Regardless of their job title, +RSEs share a set of core skills that are required to design and develop research software, understand +the research environment, and ensure that they produce sustainable, maintainable +code that supports reproducible research outputs, following the \ac{FAIR} principles [@FAIR4RS]. + +This community paper defines a set of core values and foundational competencies, +which an RSE should acquire during training and formal education. +These skills are formulated independently of a specific research domain +and current technical tools used to support the application of the skills. +By defining these competencies, +we provide a guiding framework to facilitate +the training and continuous professional development of RSEs, +thus helping to provide a positive impact on +research outputs and, ultimately, society as a whole. +These competencies draw upon skills from traditional SE practice, +established research culture, and the commitment to being part of a team. +However, we see this set of skills as a foundation to build upon. +We envision that through specialised training, the set of skills +of graduate RSEs and domain researchers will grow. +This is underlined by a growing interest to perform RSE research, +i.e. research into methods and tools more catered to the unique +challenges that research software provides. + + +While this community paper is based on workshop discussions that were attended +largely by RSEs (deRSE23 in Paderborn, un-deRSE23 in +Jena, and deRSE24 in Würzburg, all in Germany), +we believe that the competencies formulated here can offer far-reaching +impact beyond the domain of RSE into adjacent aspects of research and, indeed, the wider research community. +This is especially important given that much research involves some amount of +data management, processing and visualisation, or the creation of tools for these tasks, +and funding bodies and computing infrastructure providers will sometimes prioritise projects that generate archived, +annotated, re-usable, and potentially remotely executable data. +In particular, funding agencies and research managers will find the discussion in this paper +valuable in order to discover where RSEs see their place in the existing landscape of scientific domains +and how to support the work of RSEs at different positions and career levels. + +The outline of the paper is as follows. +We start with a non-exhaustive overview of existing initiatives in @sec:related-work. +@sec:values elaborates on the values that +provide the guiding principles for the work of an RSE. +@sec:required-generic-skills defines a set of core skills based on these values. +We categorise these skills into three pillars, namely +"software/technical", "research", and "communication" skills, +reflecting the hybrid nature of an RSE. +To justify the selection of these skills, +we also list some current tasks +and discuss the skills used therein. +As with any general skill set, not all RSEs will need +to use all the skills highlighted to the same level of expertise. +Therefore, @sec:how-much-to-know examines how much a person +needs to know depending on their education or career level +or on the type of projects they would like to be involved with. +In the same section, we provide an overview of what skills and limitations +an RSE in different team structures typically has, and we give +recommendations for organisations that need to support RSEs. +@sec:rse-specialisations provides a list of RSE specialisations +and discusses the level of skill needed to work in each of them, +before we conclude the paper with details of future work in @sec:future-work +and conclusions in @sec:conclusion. +Finally, @sec:appendix provides an example curriculum in @subsec:examplemaster, +a story-like description of a fictional RSE career progression in @subsec:examplecareer, +and a list of existing skills and certifications in related fields, in @subsec:existingframeworks. + +## Terminology + +### The term Research Software Engineer + +Research Software Engineering can be considered an interface discipline, + linking traditional Software Engineering with Research itself [@Lamprecht2024-giradar]. +Due to this nature there is a plethora of different variations of RSE depending on the particular Research domain they are working in. +Therefore the broad notion of Research Software Engineers is better thought of as a collection of sub-communities. +The term Research Software Engineer is made more difficult to grasp + since an internationally recognised definition is still missing. +While there is consensus about the general notion that an RSE is a person with one leg in their research domain and the other in software development, + this spans a whole spectrum depending on which one is more emphasised. +There is also the question of what level of professionalism concerning both non-SE research and SE is expected. +A more inclusive definition allows more people to self-identify as RSEs, + thereby also fostering an inclusive community of people working in digital science (see also @sec:values on the values of an RSE). +RSEs fall therefore somewhere on the spectrum between a researcher at one end and a software engineer at the other. +Common to all of them is, that they need to be able to work in the research environment the software is used in, ideally at eye-level with native researchers, but at least as close as possible. +RSEs often need to deal with non-technical complexities that are characteristic for research environments: + organisational, motivational, with respect to the size of projects, independence and heterogeneous goals of stakeholders, boundary conditions for funding and future funding, to name just a few. +Summarising, RSEs have skills and experience in three important areas: in the research area(s) their software is used in, in software engineering topics, as well as in interdisciplinary communication. + +### Further definitions + +Depending on the national research +environments and processes that readers are familiar with, the notion of the terms *software* and *research* might differ. +Therefore, to avoid ambiguities, we define these as follows: + +**Software**: Source code, documentation, tests, executables +and all other artefacts that are created during the development process +that are necessary to understand its purpose. + +**Research software**: Foundational algorithms, the software itself, +as well as scripts and computational workflows that were created +during the research process or for a research purpose, across all domains of research. +This definition is broader than in [@FAIR4RS] and is the outcome of a recent +discussion in [@Gruenpeter2021]. + +**Research software engineers**: People who +create or improve research software and/or the structures that the software interacts with +in the computational environment of a research domain. +They are highly skilled team members who may also choose to conduct their own research as +part of their role. +However, we also recognise that many RSEs have chosen specifically to focus on a technical +role as an alternative to a traditional research role because they enjoy and wish to focus +on the development of research software. + +**Researchers**: +People who are using the services provided by Research Software Engineers. +This, on purpose, is a very broad definition and was chosen for a better reading. + +# Related work {#sec:related-work} + +Various initiatives are working to support technical professionals develop their computational skills. +Particularly related to this work are initiatives that aim to define sets of such skills +and to guide the community with certification programs and training resources. + +#### RSE Competencies Toolkit + +The RSE Competencies Toolkit [@RSECompetenciesToolkit2023] is a community project +that developed out of a hack day activity at the 2023 edition of the annual +Software Sustainability Institute Collaborations Workshop [@SSICW23]. The +toolkit provides a web application that aims to support technical professionals +in understanding how to develop their skills. It enables them to build a profile +of their competencies within the system, while it also provides a set of training +resources that are linked to a competency framework. + +#### HPC Certification Forum + +The \ac{HPC} Certification Forum [@HPCCF] is working towards providing a certification +process for \ac{HPC} skills. +As part of this process, the group is developing a Competence Standard [@HPCCFCompetencies] +and an associated skill tree that provides a classification of \ac{HPC} competencies. +This work aims to develop a standardised representation of relevant \ac{HPC} knowledge +and skills which can, in turn, lead to structured and recognised sets of skills +that can underpin the certification process. + +#### EMBL-EBI Competency Hub + +The \ac{EMBL-EBI} Competency Hub [@CompetencyHub] provides a bioinformatics/computational +biology-focused example of a competency portal. In addition to collecting +information on a range of competencies that can be browsed within the +web-based tool, it also provides career profiles for roles +within the domains that \ac{EMBL-EBI} focuses on. The hub provides +access to a variety of training resources that are linked to the specific +competencies that they relate to. This enables learners to more easily +find the right training materials in order to support their career +development journey, helping them to identify what they might want to +learn and in what order. + +#### Training-focused initiatives + +Further initiatives implicitly define sets of competencies by providing (open) +teaching material for selected skills. This is a non-exhaustive list of related +initiatives, which will be discussed in more detail in a separate publication. +In some cases, the activities extend beyond training, but they do not focus +on defining frameworks of competencies. + +One prominent example is the Carpentries [@Carpentries], a non-profit entity that supports +a range of open source training materials and international communities +of volunteer instructors and helpers who run courses around these materials. +A similar framework is provided by CodeRefinery [@CodeRefinery], currently +funded by the Nordic e-Infrastructure, +as well as SURESOFT [@SURESOFTLink; @SURESOFT2022], a project at Technical University (TU) Braunschweig and Friedrich-Alexander-University (FAU) Erlangen-Nürnberg, funded by the \ac{DFG} and targeting more advanced \ac{SE} topics such as +software design principles, \glspl{design-pattern}, refactoring, \ac{CI} and \ac{TDD}. + +There are also several initiatives focused on training \acrshort{HPC}-oriented RSEs, +such as the \acrfull{PRACE} [@PRACE] +(with material aggregated on various websites, e.g., on EuroCC Training [@EuroCCTraining]), +\ac{UNIVERSE-HPC} [@UNIVERSEHPC] (a project funded under the \acrshort{UK}'s +ExCALIBUR research programme [@EXCALIBUR]), and the \ac{ENCCS} [@ENCCS], +which offers a collection of lessons for \ac{HPC} skills [@ENCCSLessons]. + +Initiatives focused on Germany include EduTrain [@EDUTRAIN] (a section of the \acrfull{NFDI} [@NFDI]), +the \acrfull{HIFIS} [@HIFIS], and the already mentioned SURESOFT [@SURESOFTLink]. + +# Values {#sec:values} + +It is important that the activities of an RSE are guided by ethical values. +In addition to the values for good scientific practice [@dfg_gsp], RSEs also adhere to +the \ac{SE} Code of Ethics [@Gotterbarn1999]. +Central to that code is the RSE's obligation to +In addition to the values for good scientific practice +commit to the health, safety and welfare of the public and act in the interest of society, their employer and their clients. +Further values loosely based on that code include the obligations + ++ to commit to objectivity and fact-based, honest research conclusions, ++ to promote openness and accountability in the research process, ++ to take great care to develop software that adheres to current best practices, ++ to judge independently and maintain professional integrity, ++ to treat colleagues and collaborators with respect and work towards a fair and inclusive environment, and ++ to promote these values whenever possible and make sure that they are passed on to new practitioners. + +The deployment of computer-based modelling and simulation has dramatically changed the practice of science in a large number of fields. +It has enabled the hitherto impossible study of new classes of problems, +often replacing traditional experimentation and observation. +It can also serve to integrate a communal body of knowledge [@Parker2022]. +Humphreys [@humphreys_extending_2004] regards this development as "more important than the invention of the calculus in the 1660s, an event that remained unparalleled for almost 300 years". +The epistemological status of computer modelling and simulation is still the subject of debate, +which ranges from the postulate of a new process of knowledge creation that has its own, unique, epistemology [@winsberg_sanctioning_1999] +to the perception that from a philosophy of science perspective, there is nothing really new [@frigg_philosophy_2009]. +In any case, it is clear that a number of decisions in the construction of a simulation-model +will have a significant impact on the adequacy for purpose [@bokulich_data_2021] of the model. +These decisions include the selection of the salient characteristics of the system to be modelled, +the choice of the mathematical representation of the processes to be represented, +the choice of numerical methods and other algorithms +and even including the design of the user-interface. + +The relationship between initial state, inputs and final state of a computer simulation is "epistemically opaque" [@humphreys_extending_2004], +in that not every step of the process is directly observable. +The current trend of an increasing application of computationally irreducible systems, such as those based on artificial neural networks, +further exacerbates this inherent limitation of explainability. +An RSE usually takes a pivotal role in assessing this adequacy for purpose of a model +as well as in characterising and communicating the domain of its legitimate application +and its limits of interpretability. +This role, together with the enormous reliance on modelling and simulation of scientific results, +as well as real-world decision-making, +places a large responsibility on the RSE. +It is important that RSEs are aware of this responsibility and continuously improve their capabilities to live up to it. + +Research software is also well on its way to being ever-present in data-driven research, in all research fields. +This can probably be most prominently seen by considering software used to analyse data, e.g. within experimental research. +It is not unusual for RSEs to support those more research data oriented efforts as well. +Here, specifically, they closely interact with research data management professionals +and practices by designing research software +that is better able to adhere to the \ac{FAIR} principles for research data, +but also to follow similar rules for research software (FAIR4RS [@FAIR4RS]). +As such, they are then familiar with special requirements stemming from the field itself, e.g., in medical research, and with privacy related issues especially for personal data, e.g., for conducting surveys. + +RSEs often assume a multifaceted role at the junction of research, \ac{SE} and data management. +They work with a varying and diverse set of colleagues that might include other developers, +support unit staff and academics of different fields and all career stages. +This situation yields a specific set of challenges RSEs should be aware of +to consciously make ethically sound judgement calls. +We list some example areas that highlight present-day challenges. + +## Current challenges + +### Handling of data and personal data + +A lot of RSE work involves the manipulation or creation of data processing tools. +We highlight that professional conduct requires these creations to be reliable and to maintain data integrity. +In particular, the way that personal data is handled can have far-reaching implications for society. +Independent of the encoding into the respective national law in an RSE's jurisdiction, +the right to information privacy is internationally recognised as a fundamental human right, +e.g., in the European Convention on Human Rights [@CouncilOfEurope-ETS005-2021; @Hirvela2022]. +RSEs need to be aware of this topic's importance +and deal with tensions that might arise with researchers' desire for trouble-free sharing of data, thereby expecting openness about the research process, +versus the integrity expectations of the society towards \ac{IT} systems. +Handling personal data also has ramifications for information security considerations during the software development process. +Data protection is a complex topic, so RSEs should be aware that they may need to consult external expertise, for example when dealing with +special topics such as cryptography or re-identification attacks [@Henriksen2016]. + + +### Mentoring and diversity {#sec:mentoring-and-diversity} + +RSEs are often experienced professionals who work closely with and provide technical training and guidance to early career researchers. +Similarly to academic supervisors, they bear a certain responsibility to guide and advise less-experienced colleagues +with respect to career development and the achievement of academic goals. +This can take the form of supervising a student or mentoring a fellow RSE. +The RSE needs to be aware of the biases arising from the sociological imbalances in research and academia. +According to the \ac{UNESCO} Science Report [@Schneegans2021] women account for 33.3% of all researchers. +60.2% of researchers come from high-income countries which account for 17.5% of the global population in 2018. +Furthermore, the socioeconomic background of academics is not representative of the general population, for example in the US a tenure-track academic is 25 times more likely to have a parent with a PhD [@Morgan2022]. +Thereby, to promote their values of an honest, open, and inclusive research space, they should be aware of +the diversity problems and help to mitigate them whenever they have the chance to do so. + +### Shaping digital science + +Through writing research software, RSEs have a pivotal position in the process of scientific production. +Their choices might determine whether the respective research is reproducible or not, +whether the results can be re-used, whether future research can build on existing tools or has to start from scratch. +Builders of larger research-infrastructure projects determine to some extent the possibilities and limitations of future research +and therefore need to be able to make a value-based judgement on topics +such as open science, path dependence, and vendor lock-in. + + +### Addressing environmental sustainability within planetary limits + +The last two decades saw transistor technology approach the limits of attainable miniaturisation, +and maximum chip clock frequency begin to plateau [@Sutter2005]. +Nevertheless, a misleading belief in limitless growth of computing capabilities +(storage, computing power, transfer speed) is still widespread within popular perception. +A practical consequence of this is an ever-growing demand for resources to cover +the expanding need of storage and processing, with no clear deceleration in +sight (e.g. the IEA estimates a doubling in data centres energy consumption from +2024 to 2026 [@IEA2024]). At the same time, current science is well aware of + +several planetary boundaries being exceeded due to human activities [@Richardson2023]. +Data processing, storage and transfer account for a non-negligible fraction [@IEA2024]. +Demands to move resource consumption to a sustainable rate are well justified and supported by science [@Sills2019]. + +RSEs have the opportunity to contribute to this effort by, for example, +choosing computationally adequate approaches (e.g. recognising where a +proven statistical method may suffice in place of a power-hungry AI model, +or configuring a test pipeline to minimise redundancy), and embracing data +frugality measures (e.g. recognising sufficient resolution when sampling data +for processing or storage). If past computational solutions were frugal because +of technological limits, in future they should tend to that by virtue of an +awareness of what may be adequate. The \ac{GREENER} principles [@Lannelongue2023] suggest how +these concerns can be addressed and how research computing can become more environmentally +sustainable. + +### Emerging challenges + +RSEs often operate at the cutting edge of technological development +and therefore might have to deal with technologies of which the dangers and drawbacks are still poorly understood. +A current example is the rush for the application of \acp{LLM}, +where RSEs working in these fields should stay up-to-date and be able to help researchers assess topics +such as training-data bias, \ac{LLM} "hallucinations" or malicious use, with the greater goal of +making these powerful tools work for the welfare of society. + +# Foundational RSE competencies {#sec:required-generic-skills} + +The role of an RSE lies somewhere on the spectrum between that of a researcher +(the "R") and a software engineer (the "SE") and, therefore, requires +competencies in both fields. RSEs typically have a background in research or software engineering, +but they definitely have obtained broader knowledge in both fields. +Even when working as the only RSE on a task or project, they typically apply +their knowledge and experience as part of larger teams of researchers and +technical professionals, which allows them to cultivate this hybrid nature. +There are many ways to categorise the competencies of an RSE. We chose to +distribute these competencies over three pillars to reflect the fact +that RSEs are both competent researchers (the research skills, +@sec:research-skills) and software engineers (the software/technical skills, +@sec:software-skills). The third pillar (communication skills, +@sec:communication-skills) forms the bridge between the former two +categories, with a particular focus on the software and +research cycle and the scientific process. These competencies are relevant in a +broad setting and form the foundation for specific specialisations. +These competencies have been chosen in order to make RSEs contribute to an open and inclusive research +environment, with tools that respect their professional values. + +These skills and competencies come into play in various forms: The +RSEs themselves need to acquire and develop them as their career progresses +(**Career level**). However, some knowledge of software and data processing is +required at all academic levels and for all positions +(**Academic Progression**). The relative importance of the skills +and competencies also depends on the size of the RSE team +(**Project team size**). Finally, different sets of skills are emphasised in +the different RSE specialisations (**RSE specialisations**). + + +During the Paderborn workshop (deRSE23) we asked learners and novice RSEs what they would +like to have learnt. The top five items mentioned were: testing, contributing to +large projects, when or why to keep repositories private, high-quality software development, and +finding a community. Those topics comprise combinations of the skills and +competencies defined below. We will elaborate these in +@sec:tasks-and-responsibilities. + +## Software/Technical skills {#sec:software-skills} + +\newcommand{\skillsection}[1]{\hypertarget{skills-#1}{% +\subsubsection{\glsentrydesc{#1} (\texorpdfstring{\glsentrytext{#1}}{#1})}\label{skills-#1}}} + +Besides skilled researchers, RSEs are also competent software engineers. +As such, they ideally can solve complex software engineering problems and design software as a user-oriented, future-proof product. +The technical skills required by an RSE overlap to a large extent with + the common fundamental software engineering skills (see, e.g., @Landwehr2017), + but put greater emphasis on aspects related to achieving good scientific practice and to serving special needs of research software. +In addition, a lot of RSEs are either self- or peer taught in these skills (see, e.g., figure 14 in @Barker2023). +These skills include requirements analysis, design, construction, testing, program analysis, and maintenance of software. +On the other hand, RSEs also know how to make research software adhere to the \ac{FAIR} principles [@FAIR4RS], + and how to achieve different levels of research software reusability (see, e.g., @ChueHong2014), + while they have deeper understanding of the scientific context around the research software projects they work on. +To reflect this, the technical skills listed below complement competencies regarding the standard life cycle of software development (as summarised in \autoref{subsec:technical-general}) with RSE-specific focus skills. + +\subsubsection{Classical software engineering skills}\label{subsec:technical-general} + +To summarise the vast range of the skills a software engineer is typically equipped with, +we refer to the Guide to the Software Engineering Body of Knowledge (@swebok_2014). +Because research software engineering is an interface discipline, +RSEs are often stronger in topics more commonly +encountered in research software contexts (e.g., mathematical and engineering foundations) +than in other areas (e.g., software engineering economics). +However, they bring a solid level of competence in all software engineering topics. +Therefore, RSEs can set and analyse software requirements in the context of +open-ended, question-driven research. They can design software so that it can sustainably grow, often +in an environment of rapid turnover of contributors. They are competent in implementing +solutions themselves in a wide range of technologies fit for different scientific applications. +They can formulate and implement various types of tests, they can independently maintain software +and automate operations of the integration and release process. They can +provide working, scalable, and future-proof solutions in a professional context and with common +project and software management techniques, adapted to the needs of the research environment. +Finally, as people who have often gained significant research experience +in a particular discipline, they combine the necessary foundations from their domain with software +engineering skills to develop complex software. + + +\skillsection{SWLC} + +The traditional software development life cycle defines the stages that form the process of building a piece of software. +Initial development generally involves an analytic process where requirements and ideas are gathered and analysed (requirements engineering), +followed by formulating a plan to fulfil them (design) that is finally turned into running code (implementation). +This is accompanied by different measures of quality control (e.g., reviews, testing), validating and verifying +that things work as expected and that they continue to do so when development progresses further. Depending on the software project, this can mean a simple "Think-before-you-do", or more elaborate and formal processes. +Often the development cycles are executed iteratively and incrementally. +The life cycle further includes periods of deployment, maintenance and further development (software evolution), +as well as software retirement. +To assess the current state and needs of the software, +the RSE should be familiar with different maturity metrics, +e.g. the DLR application classes [@Schlauch2018b], the research software maturity model [@Deekshitha2024] or technology readiness levels (TRLs). +Additionally, the research software life cycle extends the traditional life cycle +with \gls{software-publication}. The RSE should be aware of this life cycle +and be able to predict and cater to the changing needs of a software project as it moves through the stages. + + + +\skillsection{DOCBB} + +The RSE should be able to create building blocks from source code that are +reusable. This ranges from simple libraries of functions up to complex +architectures consisting of multiple software packages. An important part of +enabling code reusability is the provision of sufficient information in the +form of comments within code, documentation or other means. This is vital to +ensure that developers and maintainers understand what a piece of software aims +to do and how to enable others to use the provided functionality. +This is primarily achieved through a "clean" implementation and enhanced by +documentation. Documentation ranges from commenting code blocks to using +documentation (building) tools. +It should be written with consideration for the different audiences who may need it +depending on their goals and expertise, +for example by following the Diátaxis framework [@Procida_Diataxis_documentation_framework]. + + +\skillsection{DIST} + +The RSE should be able to distribute their code on their domain/language +specific distribution platforms. This almost always encompasses +handling/documenting dependencies with other packages/libraries. It sometimes +requires knowledge of using build +or package management systems to enable interoperability with other projects. +In terms of usability and needs of the user community the RSE should be able +to decide whether a library or a framework is the right type of program +to build and distribute. + + + +\skillsection{SWREPOS} + +The RSE should be able to identify and use fitting public platforms (so-called software repositories or "repos") +to share the artefacts they have created and invite the public to scrutinise them in public reviews. +These software repositories usually provide facilities for software development, which +differentiate them from the domain repositories described later. + + + +\skillsection{MOD} + +We define this as a certain quality of analytical thinking that enables an RSE to +form a mental model of a piece of software in a specific environment (program comprehension). +Using that, an RSE should be able to make predictions about a software's behaviour. +This is a required skill for common tasks such as debugging, profiling, optimising, designing good +tests, or predicting user interaction. +Many tools exist to help with understanding and evaluating existing code, +especially from a structural point of view. +An RSE should understand their output and its implications. +An important facet of this capability relates to information security. +RSEs need to consider the safety and integrity of personal data and other sensitive information +and make sure that they do not negatively impact the integrity of their +institution's network and computing infrastructure. + +## Research skills {#sec:research-skills} + + +\skillsection{NEW} + +RSEs are curious and able to conduct research, both on research software engineering, +and on their research-wise "home domain" (see also @subsec:examplemaster). +Senior RSEs are also able to lead research, and many RSEs have a doctorate [@hettrick_survey_2022]. +Since RSEs often operate in different research fields, they also gain their reputation from their effectiveness in interacting with researchers from the same or other domains. Therefore, some curiosity together with a broad overview of the +research field is required, as this enables the RSE to learn new methods and algorithms directly from domain peers. +Similarly, a broad overview of the field of SE research +and the growing field of RSE research enables the RSE to learn, apply, and teach +new methods and tools for improving the way they develop software. +This curiosity, together with the ability to convert it into new ideas, is also reflected when an RSE is actively +trying out new tools or discovering related literature from adjacent domains. Lifelong learning is then no longer just a phrase but +becomes a motivation to work. + + +\skillsection{RC} + +One of the key skills that RSEs have is their understanding of how research +works. +They embrace being part of a larger community which, +despite friendly competition, shares the common goal of gaining knowledge +to disseminate it. +Thereby they know that they are part of a bigger undertaking +that involves many other parties in and outside their domain, +and also that their software can be utilised at different stages +of the research cycle by different people. +They may be asked to contribute to the ethical and regulatory evaluation of a project +to ensure integrity of the research performed therein. +Like other researchers, RSEs are open to discussions and arguments beyond +their own expertise and appreciate the underlying principles of +good research, including publications, reviews and reproducibility. + + +\skillsection{SRU} + +The re-use of existing assets such as libraries and pieces of code +to improve efficiency and quality +belongs to the fundamentals of software construction [@swebok_2014]. +To discover software, RSEs rely on domain-specific knowledge and +domain repositories, as well as research skills, discovering related +software via software citations and metadata. +To evaluate whether the artefacts to be re-used suit their needs, +RSEs often need to consider the scientific context of their origin. +For example, a paper that references the code under consideration +might be crucial to validate its fitness for purpose or lack of suitability. +Code that incorporates research-domain specific knowledge +needs to be understood at a very detailed level +and its re-use documented to meet standards of good research practice. +Not only the technical compatibility needs to be understood and documented +(programming languages, system interoperability), but also the underlying +models and computational methods need to fit the purpose; this question +often requires wider research skills and deeper understanding of the +research domain at hand. + + +\skillsection{SP} + +Another part of \ac{FAIR} software is concerned with publishing new and derived works +and making them available for re-use by the research community and the general public. +RSEs need to have a basic understanding of common software licence types, including +proprietary and open source licences and how "copyleft" and "permissive" open +source licences differ. They should also understand compatibility between +different licences, and the ramifications for re-using and composing programs. +Beyond that, RSEs will need to properly execute the technicalities of software publishing. +These include the application of licences and copyright statements, +understanding and assigning software authorship, crediting contributors, +maintaining FAIR software metadata and publishing software artefacts. +Finally, RSEs will need to understand the principles of software citation [@smith_SoftwareCitationPrinciples2016]. +This concerns both the potential for reuse of their own work, +which demands the provision of complete and correct up-to-date citation metadata for their software, +as well as their own citation obligations deriving from building on previous work in the form of dependencies. + + +\skillsection{DOMREP} + +Almost all research software is developed within a specific scientific domain. +Some software may be able to cross boundaries, but the majority will have a +home domain, with which it needs to be able to interact. +The RSE then needs to be aware of any domain specific repositories that will contain +data sets, catalogues, and other domain specific artefacts, in addition to software. +The RSE also needs to be aware of how their software can interact with the existing +domain-specific data repositories. +Finally, they need to be able to assess and use software repositories - +domain-specific or generic - for publishing software with the relevant metadata. + +## Communication skills {#sec:communication-skills} + +RSEs do not work in isolation. +They are embedded in a research group or work within a team of RSEs supporting particular research projects. +RSEs often need to interact with and facilitate communication among colleagues, clients and contractors +with a very broad spectrum of background-knowledge, specialisation, expectations, and experience whilst keeping diversity issues in mind (@sec:mentoring-and-diversity). +Communication skills are therefore crucially important. +Team skills are also mentioned in common guides for \ac{SE} such as the software engineering body of knowledge [@swebok_2014]. +However, the interpersonal and organisational skills and the capacity for adaption required to work in a research setting +warrants a much stronger emphasis on this field of competence. + + +\skillsection{TEAM} + +Being able to work, and effectively communicate in teams is essential for RSEs. +For example, RSEs need to be able to explain particular implementation choices made and may even need to defend them. +Within a team of RSEs, code reviews improve knowledge transfer and increase team cohesion. +The team might change on a project-to-project basis and might be comprised of colleagues with very different backgrounds +including, for example, \ac{IT} staff, domain scientists and technicians working alongside software engineers. +The shared values come into play and each RSE needs to ensure that these values are lived by and passed on to others. +Senior RSEs may lead a team of RSEs. + + +\skillsection{TEACH} + +RSEs have many opportunities to teach. +These range from inducting new colleagues to teaching digital skills either through short courses, +for example from The Carpentries [@Carpentries], or entire lecture series. +RSEs may also act as mentors and consultants. +Code review also includes aspects of the teaching skill. + + +\skillsection{PM} + +The RSE should have knowledge of project management processes. At some +institutes, project management tools and approaches differ between individual research groups, +but it is useful if an RSE understands general structures of a \gls{PM} scheme, or can bring in new ideas for improvement. +Project management in research software engineering poses specific challenges (see \gls{USERS}) that might require the capacity +to flexibly adapt to changing conditions and deviate from common project management methods. +Additionally, the RSE should know that SE offers various methods and approaches +specifically tailored to management of software projects and products. + + +\skillsection{USERS} + +Since research software is often developed as part of the research process itself, +its requirements and specifications might change with the progression of research. +Stakeholders of research software often change across different research projects +or even within the course of one project. +Roles in connection with research software are often in flux and diffuse. +For example, a single person might be user, developer and project manager at the same time. +Often this means it is necessary for an RSE to think "outside their comfort zone", +but at the same time to be able to convey their knowledge and experience to experts +of other fields or persons at different hierarchy levels in a way they can understand more easily. +These conditions pose specific challenges for requirements analysis, project management, training and support. + +## RSE tasks and responsibilities {#sec:tasks-and-responsibilities} + +These skills, while already numerous are also generic on purpose. They span a +multidimensional space in which the day-to-day tasks and responsibilities of an +RSE can be found. +We describe here some examples of the competencies applied in combination to +the set of current common tasks and challenges for RSEs identified during the +deRSE23 Paderborn workshop. + +The most obvious task of an RSE is to develop software that is used in research. +This broad topic requires all the \ac{SE} skills. Of course, these are the +competencies that are the most fluid since they have to adapt to frequent +technological advancements. Additionally, proper \ac{SE} skills often require +knowledge of \gls{TEAM}, and \gls{PM}. Today, this means effective use of +\acp{IDE}, \gls{static-analysis} tools, \glspl{design-pattern} and documentation +(for oneself and others). + +The RSE needs to be able to formulate and discuss structural +and behavioural aspects of software on a more general level than +through the code itself and often even before a first line of code is written. +A set of tools and diagrams for effective and standardised communication +about software on a meta level is provided by the \acp{UML}. +As a modelling tool, it is directly related to \gls{MOD}. +Additionally, it can be applied in various stages of the \gls{SWLC}, +especially in the early stages, as a first documentation of the planned +modular structure to facilitate +\gls{DOCBB}, \gls{USERS}, \gls{PM} and \gls{TEAM}. + +The RSE needs to be able to choose appropriate algorithms and techniques +(\gls{MOD} and \gls{NEW}). Apart from the technical feasibility, this choice is +also informed by the values outlined in @sec:values. For example, the +RSE needs to be able to estimate resource usage (processing, memory and storage +consumption, e.g. [@Lannelongue2021]). Resource usage has not only a direct financial price tag but also +environmental costs via associated energy consumption. + +Software development also includes testing. This task is a manifestation of the +\ac{SE} competencies of \gls{DOCBB} and \gls{MOD} since a model of the software +is required in order to write good tests that facilitate understanding and +documentation. Today this encompasses the knowledge of testing frameworks as +well as \ac{CICD} practices. In addition to being +tested, software should also provide reproducible outputs. Projects like ReproHack +[@ReproHack] can greatly help in fostering that competency. + +Apart from testing, there are many code analysis tools to monitor and improve the quality of code. +An RSE should be familiar with the tools available for their specific environment +and how to include some of them into a \ac{CICD} pipeline. +Typically, this includes linters and similar static tools as well as +dynamic tools like profilers and code coverage analysis. +The development of these tools is very dynamic and environment specific. +A good introduction can be found in [@swebok_2014] and an online resource is [@vihps]. +As these tools help with behavioural and structural analysis and therefore +modularisation these tools enable \gls{MOD} as well as \gls{DOCBB}. + +Part of the \ac{FAIR} principles is to make software findable and reusable. The +RSE needs to be able to decide when and why to keep a repository private. +This decision requires knowledge in \gls{RC}, \gls{USERS}, \gls{TEAM}, and sometimes \gls{SP}. +Furthermore, knowledge of the practices and contractual regulations of the RSE's institution is also required. + +The RSE also needs to understand metadata for research data and research software. +There are ongoing efforts on metadata for research software such as CodeMeta +[@jones_codemeta_2017] and the \ac{NFDI} working group +[@castro_research_sw_metadata_2023] on the subject. These are complemented by +the development of new tools and methods for providing and working with software +metadata, such as the Citation File Format project [@druskat_cff_2021] and +HERMES [@druskat_hermes_2022]. Other efforts focus on Software Management Plans +(e.g., [@alves_elixir_2021; @martinez_ortiz_practical_2022]) which could be +helpful for RSEs at early stages (i.e., with not much experience of project +management). They give quick hints on what to look for regarding basic +management for research software (including information on, e.g., licenses, +releases, publication, citation, archiving) together with some ongoing work on +corresponding metadata [@giraldo_metadata_2023]. +Metadata can also be used +actively during and within a research project, to inform the decision-making +processes [@Bird2016]. + +Most RSEs will contribute to other projects, some of which will be large. This +is a topic that requires competency in \gls{SWREPOS}, \gls{SRU}, and \gls{SP} in +order to understand the ramifications of sharing, and in \gls{DOCBB}, since the +contributed code has to be understood by others. Interacting with project +members depends on the \gls{TEAM} skill. Today, this frequently involves the effective use +of collaborative platforms like \gls{GitHub}/\gls{GitLab}, honouring a +project's code of conduct, and some knowledge of popular open source software licences, +e.g. the \ac{GPL}. + +RSEs are embedded in communities. There are two different aspects to finding +these communities: First, we have the aspect of community building for a +research project. Since this deals with software that is supposed to be used in +research this requires knowledge of \gls{RC}, \gls{USERS}, and also \gls{NEW}, +in order to effectively interact with domain scientists. Today, an example is a +presence on social media. The other \gls{TEAM}-related aspect is the embedding +of recently-trained RSEs into the Research Software Engineering community, +sharing the same set of values and competencies. +We envision newcomers to the RSE field becoming part of a strong network of +RSEs, tool-related communities, and the classical domain communities, +making them more effective at supporting research. These networks are a lifelong +manifestation where RSEs work to provide an inclusive environment for their +peers and provide opportunities for lifelong learning. + +RSEs are also mentoring colleagues (see also @sec:mentoring-and-diversity). +This necessitates giving good advice that +fits to a project's stage in its life cycle, thereby requiring knowledge of +(\gls{SWLC}), and its context in its research domain and thus (\gls{RC}). +Research software can often start out as a tool to answer a personal research +question, becoming more important when other researchers start to rely on it. +At the other end of the scale, research software can sometimes underpin key +processes that deal with critical questions such as +weather forecasting or medical diagnosis. A classification of software is commonly used +to formalise the process of giving good advice [@Wang2012; @Schlauch2018b] where research software can move from one class to another +during its life cycle. [@Schlauch2018b] classifies applications based on their scope +and criticality and provides \ac{SE} recommendations. The RSE needs to be able to +identify the application class they are dealing with and apply the respective +RSE practices. + +Often RSEs, especially in RSE groups, will develop applications +and services with different variants for different research purposes and groups. +Additionally, many research groups develop their own codes for specific +research purposes, e.g. simulation codes or specialised data analysis pipelines. +A lot of their development of new features is project-based, +often through PhD projects. Work can sometimes result in code that diverges from +the main project into a separate variant with re-integration planned as a final step. +To reduce the chance of variant source code diverging significantly and producing +a large integration overhead, \gls{PM} skills and methods are needed. +More specifically, software product line management methods have been +developed for this exact problem and purpose. + + +# How much do different people need to know? {#sec:how-much-to-know} + +Now that we have the different competencies, we can explore various dimensions of these competencies, +depending on their circumstances. A strong beneficiary of specialised RSEs can also be newly formed RSE centres at research institutions. + +## Career level + +At different career levels, differing skills are required. +To elaborate on that, we have prepared the following table with three levels of experience in mind. + +- Junior RSE: These are people who are in the earlier stages of their RSE career journey, but they should ideally have research experience of their own as well as the skills to contribute reliable and well-structured code to software projects. +- Senior RSE: They have gained experience, both concerning their software skills as well as in their research collaborations in potentially many different fields. They can set the standards in a software project. +- Principal RSE: Their actual job description varies a lot. These may be RSE team leaders based in a professional services type role, or they may be professors or research group leaders based in a more academic-focused role. They are often the people responsible for bringing in the funding that supports new and sustains existing projects. Generally speaking, they do not need to be actively involved in the day-to-day technical tasks, but they should be able to guide projects from both a technical and a research perspective while providing an inclusive working space. + +@tbl:comp-lvls-techn, @tbl:comp-lvls-res, and @tbl:comp-lvls-comm elaborate on the required facets of the competencies in different roles. +A story-like example of an individual through the hierarchies can be found in @subsec:examplecareer . + +\blandscape +\small +\renewcommand*{\arraystretch}{1.4} + +| Competency | Junior RSE | Senior RSE | Principal RSE | +| --- | ---------- | ---------- | ---------- | +| \gls{SWLC} | Should be aware of the software life cycle. | Should know where in the life cycle their project is and which decisions are likely to lead to technical debt. | Should know how to manage and steer development/project resources accordingly. Should also have an understanding of the potential consequences of key project management decisions. | +| \gls{DOCBB} | Should be able to write reusable building blocks. | Same as junior, but the quality should set the standard for the project, while following current best practices. | Should know the current best practices and point their team members and collaborators to the right resources. | +| \gls{DIST} | Should be able to use package distribution platforms. | Same as junior, but should also be familiar with current best practices for building and deploying packages. | Should ensure that their project is available via an up-to-date and secure distribution platform. | +| \gls{SWREPOS} | Should seamlessly interact with the repository of their project. | Should be well-versed in the intricacies and best practices around working with a repository, and probably interact with repositories of multiple projects. | Should promote the use of repositories and be able to convey best practices of sharing and reviewing to junior and senior RSEs. | +| \gls{MOD} | Should have a basic grasp of the part of the software they are responsible for in order to use basic tools such as a debugger. | Should understand the characteristics of large parts of the codebase considering a variety of the metrics. | Should have a detailed understanding of the software project as well as its aims and potential for impact, in order to effectively steer it. | + +Table: Levels of technical skills expected per RSE career stage. {#tbl:comp-lvls-techn} + +\newpage + +| Competency | Junior RSE | Senior RSE | Principal RSE | +| --- | ---------- | ---------- | ---------- | +| \gls{NEW} | Should have some curiosity to fit into research teams. | Same as junior, but they should proactively propose directions in individual aspects of the project. | Should have research insights and a broad view of the research field to steer the project. | +| \gls{RC} | Should be aware of the research life cycle. | Should know the position of the project in the research life cycle. | Should know what is necessary for the project to fit into its position in the research life cycle. | +| \gls{SRU} | Should be aware of software reusability tools. | Should be able to search with software reusability tools. | Should be able to effectively search with \gls{SRU} tools and to evaluate and perform the integration of a library into the project. | +| \gls{SP} | Should be aware of available opportunities to publish software and understand the need to consider issues of intellectual property. | Should be able to correctly publish software in simple cases and to identify cases where professional legal advice is needed. | Same as senior, plus the ability to take the future publication of software into account when initiating and guiding larger software collaboration projects. | +| \gls{DOMREP} | Should be able to interact with the domain repository. | Same as junior RSE. | Same as junior, and should know about how it fits into workflows surrounding these domain repositories. | + +Table: Levels of research skills expected per RSE career stage. {#tbl:comp-lvls-res} + +| Competency | Junior RSE | Senior RSE | Principal RSE | +| --- | ---------- | ---------- | ---------- | +| \gls{TEAM} | Should be able to work in the team in order to effectively fulfil the given tasks. Should be able to learn from code review. | Should be able to break down tasks into more easily digestible sub-tasks and review or guide work undertaken by less-experienced team members. | Should be able to lead the team and set the respective direction. | +| \gls{TEACH} | Should be able to perform simple peer-to-peer on-boarding tasks. | Should be able to explain logical components and the general architecture to other RSEs. | Should be able to effectively communicate about all high-level parts of the project. | +| \gls{PM} | Should be aware of the employed \gls{PM} method. | Should be able to use and adapt the employed \gls{PM} method. | Should be able to design and adapt the employed \gls{PM} method. | +| \gls{USERS} | Should be able to communicate with both users and SEs on the project, on topics of the research and SE. | Same as junior RSE, and be able to interpret the feedback. | Same as senior, and should also be able to effectively take feedback into account when steering the project. | + +Table: Levels of communication skills expected per RSE career stage. {#tbl:comp-lvls-comm} + +\elandscape + +## Helpful RSE skills for researchers in an academic career + +In the previous section, +we looked at the competency levels needed for RSE specialists. +However, many of these competencies are important for researchers in academia as well. +Naturally, the 'R' competencies apply, +and research in general is increasingly team based. +Additionally, many researchers in fields from classical examples like +numerical mathematics or theoretical physics +to newer disciplines like digital humanities +will spend time in their research on writing and developing software. +Therefore, RSE focused training, e.g., in a master's programme, +is also beneficial for students in these fields +resulting in a broader audience. +This also means that students as well as researchers need to be given time to acquire those skills, e.g., to be able to attend training in RSE-relevant topics as part of their regular work or study. + +This section outlines how the RSE competencies could be reflected at all academic levels. +It is important to note that this section does not reflect the current state of academic training and research institutions. +Instead, it summarises the discussions with and between workshop participants at different levels of academic progression on what they would have liked to learn at an earlier stage or know before starting their current position. +While individuals already work at implementing some of these changes and teaching these skills, it has not yet reached a systemic level. + +The text is organised along the academic progression path (bachelor's degree, master's degree, PhD, Postdoc, \ac{PI}/Professor). +Since each level is based on the previous levels, we presume that the skills and competencies at each level also encompass those of the previous levels. +Due to the broad need throughout academic specialisations, +the described levels serve as a baseline +and certain fields will require higher \ac{SE} skill levels +as development is a large part of their actual research. + +#### Bachelor's level + +Students at the undergraduate level mostly consume science/knowledge. +During their studies, they should also learn about the existence of digital tools and structures. +Undergraduate students should be aware that RSEs exist and that software has different quality aspects (\gls{DOCBB}). +They should be aware of domain specific tools (\gls{DIST}, \gls{SRU}) and where to find them (\gls{SWREPOS}, \gls{DOMREP}). +At this level, it may be sufficient to consider software as black boxes (\gls{USERS}) although some training in data presentation would be very helpful and a good way to find out about programming (\gls{MOD}, \gls{NEW}). +They should have an awareness of software licences and whom to ask regarding licensing issues (\gls{SP}). +They will be taught about the research cycle (\gls{RC}) and that researchers often work in groups (\gls{TEAM}). +During practicals, they will have an opportunity for peer learning (\gls{TEACH}). + +#### Master's level + +A student at a master's level can participate in science and should therefore be able to use "some" digital structures. +A master's student needs to be aware of relevant tools and data sets for their domain, where to find them and how to use them (\gls{DIST}, \gls{SWREPOS}, \gls{DOMREP}). +They should be able to process and present their data (\gls{MOD}). +They need to understand how their research depends on software (\gls{SWLC}). +Working on their master's thesis allows them to understand the research cycle (\gls{RC}), practice project management (\gls{PM}) and collaborate with other members of their research group (\gls{TEAM}). + +#### PhD + +PhD students perform independent research under guidance. +They need to know relevant tools and structures. +They should know where to find information about tools and where to find help using them (\gls{DOCBB}, \gls{SWREPOS}). +They should be able to use the tools (\gls{DIST}) and identify and report bugs (\gls{MOD}). +They need to be aware that the user's perspective is different from the developer's perspective in order to be able to write good bug reports (\gls{USERS}). +They might produce new software (\gls{MOD}, \gls{SRU}), in which case they need to understand how to licence their code for publication (\gls{SP}). +PhD students need to be curious to be able to conduct their research. +In order to be able to explore new tools (\gls{NEW}) they must be able to evaluate research software (\gls{SWLC}). +They need to be able to interact with services (\gls{RC}) and domain specific repositories (\gls{DOMREP}). +They should be able to supervise a student (\gls{TEACH}). + +#### Postdoc + +Postdocs are independent researchers. +Their role is similar to that of a PhD student, with a deepened focus on their research career. +However, they are proficient users of all relevant tools, which makes them active contributors to their domain of research. +They need to be aware of more advanced topics regarding intellectual property rights, such as patents (\gls{SP}). + +#### PI/Professor + +They are experts in their field and should be able to give proper guidance to their students on which digital tools are currently relevant. +They should be aware of the skills of an RSE and when they might need one in their group. +They should encourage their students to use relevant tools (\gls{DIST}). +They need to be able to judge the suitability of the software (\gls{SWLC}) and follow the interactions between relevant projects (\gls{SWREPOS}). +They should be able to advise their students on the legal aspects of software production and distribution (\gls{SP}). +They should be able to contribute meaningfully to the steering decisions of the software in their field (\gls{USERS}). +They are able to guide students and prepare and deliver a full lecture course (\gls{TEACH}). +They need to manage and lead their research group (\gls{PM}, \gls{TEAM}). + +## Project team structures + +In @tbl:teams-se, @tbl:teams-res, and @tbl:teams-comm, we look at individual or team competencies and approaches to them, +considering how these differ depending on whether an RSE is working alone on a software project, +or whether they are working as part of a team of RSEs. +We extend this to consider how things differ when an RSE or a group +of RSEs is based locally within a research team or department, +or when they are based in a dedicated, centralised RSE team. +We also look at organisational aspects in the context of each of the considered +competencies, since there are a variety of ways that organisations can contribute +to and support them, complementing those proposed by [@Katerbow2018]. Some of them are brought to life in the example career path of @subsec:examplemaster. +We first summarise the meaning of each of the columns in the tables: + +- **Competency:** The code assigned to the competency being considered, as defined in @sec:required-generic-skills, e.g. \gls{TEAM}. +- **Individual RSE (Locally-based):** A single person working on some +research software - often an RSE with focus on their own research. Often time-constrained, + may be self-taught. +- **Individual RSE (RSE team-based):** A single person working on research + software - generally a professional RSE assigned to support another team's software on their own, + who however is connected to an RSE team. +- **Group of RSEs (Locally-based):** A group within + a research group or team, working together on software to support + or undertake a single research goal/project. + Similarly to the individual RSE, they are often research-focused with RSE skills, + often self-taught. +- **Group of RSEs (RSE team-based):** An RSE team + working together on research software projects for a research group. +- **Organisation-level RSE support:** Describes how the defined competencies are recognised + and represented at an organisational level and what the organisation can + do to support the RSEs in the context of the different team structures. + These can be read as policy/action recommendations. + +These tables take the perspective of the expected skill set of each RSE or team +of RSEs, similarly to personas in a user experience analysis. +The current situation may differ. + +\blandscape +\small +\renewcommand*{\arraystretch}{1.4} +\begin{longtable}{|p{1.8cm}|p{3.5cm}|p{3.5cm}|p{3.5cm}|p{3.5cm}|p{4.5cm}|} + \caption{Levels of software eng. skills expected per team structure.}\label{tbl:teams-se}\\ + \hline + \multirow{2}{*}{Competency} & \multicolumn{2}{c|}{Working as an individual RSE} + & \multicolumn{2}{c|}{Working with a group of RSEs} & \multirow{2}{*}{Organisation-level support} \\ + \cline{2-5} + & Locally-based & RSE-Team based & Locally-based & RSE-Team based &\\\hline + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + \gls{DOCBB}& + Focuses on supporting research. May not be very familiar with code quality and + structure. Follows basic best practice guides.& + Puts greater focus on reusability, documentation, and knowledge of best practices, + but potentially lacks domain knowledge.& + Has more opportunities to discuss and share ideas, but team members may be + less aware of key practices.& + Has stronger ingrained focus on team-based \gls{PM} and development + methodologies, resulting in higher quality, more reusable code.& + Should offer training and other resources in core topics to support individual RSEs. + Should have research software guidance/policies that provide advice.\\ + \hline + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + \gls{DIST}& + Does not emphasise code reusability and sharing/distribution.& + Puts greater focus on reusability/sharing, but likely not as part of the project aims.& + May want to develop reusable, shareable outputs for a specific case. Needs clear guidelines.& + Focuses on quality and best practices. Reusability/packaging driven by project needs and spec.& + Should provide policies on reusability/sharing. May be driven by requirements/policies, e.g., of institution or funding agency. + \\\hline + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + \gls{SWLC}& + Manages the complete life cycle, \glspl{bus-factor} equal to 1.& + The team supports parts of the software life cycle, but with low bus factor.& + The team infrastructure and tooling supports the life cycle and sustainability.& + The bus factor may still be low in parts of the code. + Need to think about coherent life cycle management across the team - generally + a key area of expertise for an RSE team.& + Should support with training. Organisation may also provide site + licences for, e.g., management tools. + \\\hline + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + \gls{SWREPOS}& + Uses repositories for code management and demonstrating outputs, + e.g., for supporting academic credit, but may be missing skills.& + As locally-based, but professional RSEs are generally very experienced + with use of repositories and their many features.& + Uses repositories to collaborate inside the team. + Can benefit from short courses on effective use.& + Uses repositories extensively for project + management, issue tracking, etc. in addition to code itself. + May train others.& + Should offer enterprise repository set ups, + site licences etc. Also provide training + for this vital research software development tooling. + \\\hline + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + \gls{MOD}& + Needs full awareness of entire codebase to extend/maintain. + If project taken on from another developer, + there may be challenges in transferring the mental model.& + As local, but more aware of need for future transition to other + RSE(s), likely provides docs, issues, and other + support from central services to support this. May only need to know + parts of the code.& + Internal team training ensures ability to build necessary + mental model of codebase and to document it via text or tools for + sustainability.& + As local team, but likely more aware of tooling and practices + in place within RSE team. Distributing work makes it only necessary + for each developer to understand code related to their assigned tasks.& + Should provide training and retain experience via + coordinating and provide support for mentoring/community activities. + Establishing RSE departments with specialists for certain aspects of software + will improve overall turnaround times. + \\\hline + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +\end{longtable} + +\begin{longtable}{|p{1.8cm}|p{3.5cm}|p{3.5cm}|p{3.5cm}|p{3.5cm}|p{4.5cm}|} + \caption{Levels of research skills expected per team structure.}\label{tbl:teams-res}\\ + \hline + \multirow{2}{*}{Competency} & \multicolumn{2}{c|}{Working as an individual RSE} + & \multicolumn{2}{c|}{Working with a group of RSEs} & \multirow{2}{*}{Organisation-level support} \\ + \cline{2-5} + & Locally-based & RSE-Team based & Locally-based & RSE-Team based &\\\hline + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + \gls{NEW}& + May struggle to learn new methods and skills due to split research focus + between research goal and software project.& + Gets support from the RSE team to explore new methods and skills, + make relevant contacts and learn more about the domain.& + Has increased interest in learning new methods and skills, + but still prioritises domain research.& + As team-based individual& + Should reach out to relevant local groups to facilitate training + and sharing of know-how on new technical processes and tooling. + \\\hline + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + \gls{RC}& + Is familiar with the \gls{RC} in their domain, + especially when embedded in a research team.& + Is familiar with the \gls{RC}, + although they may not have domain knowledge, which a group can provide.& + Is familiar with the \gls{RC} and can share knowledge within the team.& + One or more members of the team are strongly aware of the + \gls{RC}.& + Should provide extensive infrastructure to manage + the \gls{RC}, supporting researchers/RSEs. + \\\hline + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + \gls{SRU}& + Has limited awareness of existing solutions and limited support regarding \gls{SRU}.& + Is familiar with software sharing and can discover tools and platforms.& + As locally-based individual, but being part of a team can help to address this.& + As team-based individual& + Should run local environments to host software, catalogue software, + and/or provide institution-level access to platforms that support this. + \\\hline + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + \gls{SP}& + Has limited knowledge and motivation regarding \gls{SP}.& + Applies practices, workflows, and policies established in the RSE team.& + As locally-based RSE& + As team-based RSE& + Should raise awareness about software as a publishable scientific output, provide recommendations and checklists to support software publications, and have legal experts in place to offer advice on complex cases. + \\\hline + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + \gls{DOMREP}& + Domain researchers working on software are likely to be more familiar + with the domain-specific solutions.& + RSEs may need guidance from domain researchers around domain-specific + repositories if they have a background in a different domain.& + As locally-based individual& + As team-based individual& + Should host domain-specific repositories for areas that the organisation works + extensively in, but this is likely to be handled at a research group level. + \\\hline + \end{longtable} + +\newpage + +\begin{longtable}{|p{1.8cm}|p{3.5cm}|p{3.5cm}|p{3.5cm}|p{3.5cm}|p{4.5cm}|} + \caption{Levels of communication skills expected per team structure.}\label{tbl:teams-comm}\\ + \hline + \multirow{2}{*}{Competency} & \multicolumn{2}{c|}{Working as an individual RSE} + & \multicolumn{2}{c|}{Working with a group of RSEs} & \multirow{2}{*}{Organisation-level support} \\ + \cline{2-5} + & Locally-based & RSE-Team based & Locally-based & RSE-Team based &\\\hline + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + \gls{USERS}& + May have additional skills to safeguard potential future development + and maintenance of the software for external users. Resourcing for future maintenance may be a challenge.& + Has additional skills or can access support to safeguard potential + future development and maintenance of the software for external users.& + Needs to safeguard future development and maintenance of the software for + external users, but may not have the skills or resources to support this.& + Applies best practices to prepare the code for external users, + while the team provides infrastructure and/or specialised RSEs for user support.& + Should have institutions that are able to offer support with outreach and publicising outputs. + \\\hline + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + \gls{TEACH}& + May be independently involved in training activities.& + May be able to support researchers with core technical skills.& + Shares knowledge and skills within the group (peer support).& + Supports teaching more widely, either through organised courses + or ad hoc activities such as ``code clinics''.& + Should have programs for a diverse range of teaching/training activities, + such as an RSE curriculum, as described in~\autoref{subsec:examplemaster}. + \\\hline + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + \gls{PM}& + Is organised enough to be able to transfer the codebase to future RSEs.& + Follows the project management approach set by the team, or can suggest such \gls{PM} approaches.& + Has additional \gls{PM} challenges, but may not have awareness of or experience with key \gls{PM} skills, + which can be acquired with low-key courses.& + Team provides well-structured approaches and tooling to support management of projects.& + Should offer training to support management of projects. + May offer organisation-level tooling. + \\\hline + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + \gls{TEAM}& + When not developing code for themselves, they must be able to work effectively with researchers they are potentially developing code for.& + Must be able to work effectively with their home RSE team, as well as + with researchers they are potentially developing code for.& + Must have strong team skills and knowledge + to support team-based software development.& + Must be able to work and collaborate effectively in an interdisciplinary team, + use required tools and processes, infrastructure, etc.& + Should offer support with team work and promote interdisciplinary interaction. Should facilitate team-building initiatives, + also on a social level. + \\\hline +\end{longtable} +\elandscape + +In the tables above, we have looked at how different competencies can be related +to and handled by researchers and RSEs working in different environments within +an organisation and how the organisations themselves can contribute. +We recognise that this is a challenging area to gain a detailed view of +and that this is still a significant generalisation. +We talk about the "Research Software Engineer" as a single entity but as the field expands, +we expect to see more roles and job titles emerging around the RSE concept, +many of which fit under the wider umbrella of research technology professionals (RTPs) [@ukri_rtp] [@techniciancommitment]. +Examples are different RSE-like computational roles of +the \ac{EMBL-EBI} BioExcel competency framework [@BIOEXCEL] (also @subsec:emblbio), +as is a range of different roles from King's Digital Lab at King's College London [@KDL]. + +# RSE specialisations {#sec:rse-specialisations} + +What we have defined above are intended to be base skills that an RSE irrespective of domain, position, and experience should know about. +There is a large variety of RSEs. They specialise in different areas, +some of which we want to present below. Many of the specialisations may overlap, +so the same RSE might for example work on data management and open science. +We categorise them into those that can be viewed as a specialisation within RSE-specific topics, +while other RSEs might expand their skill set and profession to areas that are not typical for an RSE. + + +## Specialisations within the core RSE competencies + +#### Open science RSE +Open science and FAIRness of data and software are increasingly important topics in research, +as exemplified by the demand of an increasing amount of research funding agencies requiring openness. +Hence, an open science RSE is required to have a deeper knowledge of (\gls{RC}) and how to distribute software publicly (\gls{SRU}, \gls{SP}). +Open Science RSEs can help researchers navigate the technical questions that come up +when practising Open Science, such as "How do I make my code presentable?", +"How do I make my code citable?", +"What do I need to do to make my software \ac{FAIR}?", or +"How do I sustainably work with an (international) team on a large code base?". +Like the Data-focused RSE, they have a deep understanding of \ac{RDM} topics. + +#### Project/community manager RSEs + +When research software projects become larger, they need someone who manages +processes and people. +In practice, this concerns change management for code and documentation +and community work to safeguard usability and adaptability, +but also handling project governance and scalable decision-making processes. +This gap can be filled by people who invest in the (\gls{PM}), (\gls{USERS}), and (\gls{TEAM}) skills, as exemplified in @subsec:examplecareer. +Building a community around a research project is an +important building block for sustainable software [@Segal2009], so these RSEs play +an important role, even if they do not necessarily touch much of the code themselves. + +#### Teaching RSEs +RSEs interested in developing their (\gls{TEACH}) skill can focus on teaching the next generation of researchers and/or RSEs and will play +a vital role in improving the quality of research software. +They need to have a good understanding of all RSE competencies relevant to their domain and +additionally should have teaching experience and training in didactics and pedagogy. + + +#### User interface/user experience designers for research software +Scientific software is a complex product that often needs to be refined in order to be usable even by other scientists. +To facilitate this, there are people required that specialise in the (\gls{DOCBB}) and probably the (\gls{DIST}) competency +with a focus on making end-user facing software really reusable and hence \ac{FAIR}. +This task is supported by strong (\gls{MOD}) skills to reason about the behaviour of potential users of the software. + +## Specialisations outside the core RSE competencies + + + + +#### \${DOMAIN}-RSE +While software is the common focus of all RSEs, +there will be RSEs that have additionally specialised in the intricacies of one particular research domain, +such as medical RSEs, digital humanities RSEs, or physics RSEs. +This can often serve as a base domain for RSE specialisation as in @subsec:examplemaster. + +#### Data-focused RSE +Data-focused RSEs work at the flourishing intersection between data science and RSE. +They are additionally skilled in cleaning data and/or running data analyses and can help researchers +in setting up their analysis pipeline and/or \ac{RDM} solutions. +When the field requires research on sensitive data or information, e.g., patient information in medicine, +this RSE should have knowledge about secure transfer methods and/or ways to anonymise the data. +As part of \ac{RDM}, this RSE profile is able to support all stages of the research data life cycle [@Nieva2020], with synchronous data management processes. +Those processes implement established best practices for planning and documenting of data acquisition in a \ac{DMP}, as well as for management, +storage, and preservation of data, and publication and sharing of data in repositories according to the \ac{FAIR} principles [@FAIR]. + + + + +#### Research infrastructure RSE +This RSE has a special interest in \glspl{SysOp} and system administration and sets up \ac{IT} infrastructures for and with researchers. +Therefore, this specialisation on the one hand requires a deep knowledge of physical computer and network hardware and +on the other hand knowledge about setup and configuration of particular server software, +e.g., setup of virtual machines on hypervisors or the planning and setup of compute server clusters for special purposes, e.g., \ac{ML}. +As an interface between the researchers and the infrastructure, they take care of user management, access permissions, and configuration of required services. + +#### HPC-RSE + +RSEs with a focus on \ac{HPC} have specialist knowledge +about programming models that can be used to efficiently undertake large-scale +computations on parallel computing clusters. They may have knowledge of (automatic) +code optimisation tools and methods and will understand how to write code that is +optimised for different types of computing platforms, leveraging various efficiency +related features of the target hardware. They are familiar with \acrshort{HPC}-specific +package managers and can build dependencies from sources. They also understand the process of +interacting with job scheduling systems that are often used on \ac{HPC} clusters to +manage the queuing and running of computational tasks. \acrshort{HPC}-focused RSEs may be +involved with managing \ac{HPC} infrastructure at the hardware or software level (or +both) and understand how to calculate the environmental impact of large-scale +computations. Their knowledge of how to run \ac{HPC} jobs and write successful \ac{HPC} +access proposals can be vitally important to researchers wanting to make use of +\ac{HPC} infrastructure. + + + +#### ML-RSE +The development of research software based on \ac{ML} requires additional specialised theoretical background and experienced handling of appropriate software in order to produce meaningful results. +This involves knowledge about data analysis and feature engineering, metrics that are involved in \ac{ML}, \ac{ML} algorithm selection and cross validation, and knowledge in mathematical optimisation methods and statistics. +Here, we use \ac{ML} in a broad sense of machine-based learning including deep learning, reinforcement learning, neuro-symbolic learning and similar. + +ML-RSEs analyse and check the suitability of an algorithm. They check if it +fulfils the needs of a certain task and they play a central role in deciding on +and selecting \ac{ML} libraries for a given task. +The increasing usage of \ac{ML} in numerous scientific areas with social impact involves an emphasised awareness and consideration of possible influences and biases. +At the intersection of data science [@SSIDataScience] and data-focused RSEs, +the complex way of solving problems utilising \ac{ML} calls for this separate specialisation. + +#### Legacy RSEs +Research software may have evolved over generations of researchers without change management or governance processes, while software "ecosystems" (e.g., programming languages, frameworks, operating systems) constantly evolve. +This may lead to the emergence of legacy code that is still actively used. +To safeguard continued usability and adoption, +these RSEs have experience in working with +code written in language standards and on software stacks considered deprecated by their communities. +Adaption of existing, large-scale codebases to evolving dependencies (\gls{DIST}) or changing hardware (\ac{HPC}; see the HPC-RSE specialisation) +may require mastery in refactoring techniques and in the usage of specialised code transformation tools. + +#### Web-development RSE +This RSE is skilled in the development of web applications and/or mobile apps. +They have expertise in one or more of frontend development, backend development +and the design or implementation of APIs, for example to support research data portals or big research projects. +Since a lot of web services for research may be accessible to a large audience or even to the public, +this RSE is also familiar with aspects relating to cybersecurity, usability and accessibility. +Not only do they need to balance these concerns while adhering to their values from @sec:values, +but they also need to efficiently communicate the decisions made to stakeholders. + +#### Legal-RSE +RSEs are often the go-to person for questions about software licensing, in particular when mixing software components that use different licences. +But with the rising requirements from legislation, +we foresee the need for RSEs that still have a background in RSE but extend it with a knowledge of legal processes that cover corner cases and go beyond applying Best Practice guides. +These requirements may arise in the area of publication of research software, +as this also requires knowledge about particular laws or regulatory frameworks concerning data protection, +like the \ac{GDPR} within the \ac{EU} [@GDPR]. +Another area are legal aspects of cybersecurity and export control in science and research (see [@ExportControl] for Germany). +Legal-RSEs focus on facilitating the achievement of technically feasible solutions, while adhering to regulatory mandates. +They are able to communicate and collaborate effectively with lawyers. + + + +# Future work {#sec:future-work} + +This list and description of competencies is a first step to finding common ground + around which to structure curricula, institutions, and teachers in this framework. +Applications of these competencies in an individual's career can be found in @subsec:examplemaster. +An omission that we found and that we would like to highlight in order to spark a community discussion is + that RSEs that choose explicitly a science-supporting role outside of research will not be eligible for funding + under the statutes of many funding organisations that require at least a PhD. + +To alleviate this and to give RSEs in leadership positions a means to become eligible for funding themselves, + since completion of scientific training is often a requirement [@DFG_50_01], + we see two possible parts of a solution. +One is to allow for doctorates primarily based on software contributions to the scientific community. +Secondly, we propose the introduction of new, standardised certificates like those in @subsec:examplecareer, + and to officially accept them as PhD-equivalent concerning eligibility to be a \ac{PI}. +Beyond this discussion, a diverse set of publications on the topic RSE teaching is already in the making. + +Within this set, we will work next on how to institutionalise education. +In that publication, we will detail how we organise our institutions + and what qualifications our teachers need to have in order to effectively communicate our values. +We will put forward ideas on how to build up bachelor's and master's programmes, + of which a glimpse can already be found in @subsec:examplemaster. +We will show how we intend to provide the necessary continuous education for RSEs after graduation, + and we will connect that with the integration of RSEs into a mesh of community networks aimed at supporting research, + while providing them with an inclusive social network that further facilitates lifelong learning. +That publication will again intentionally be free of regional specifics, + to also serve as a blueprint that other national RSE societies can build upon. + +Online resources for courses are another important building block. +This is the general intention of the learn-and-teach project [@learnandteach]. +Surveying and curating of existing resources is not carried out as a traditional publication, +but it is made available as a continuously-evolving online resource at [@learnandteach]. + +And finally, we plan to formulate a call to action, + building on the previously mentioned publication on the necessary institutions, + that spells out everything that is required to best support the continuous need for young RSEs to support digital science specifically in Germany. + +# Conclusion {#sec:conclusion} + +This paper started from a community workshop at deRSE23 in Paderborn +where people working in RSE related fields got together to figure out +structures and ideas for educating newcomers to this field. +One outcome of this diverse gathering is that RSEs from differing fields gather +around similar core concepts, At the same time they share a vision of how to +renew scientific research practice making extensive use of digital tools. +In this publication, we have tried to formalise these concepts. +We have formulated a set of values that guide our actions in society, +manifestly making RSEs part of the scientific community that shares the ideals of good scientific practice. +At the same time, +being close to software engineers, we cherish that we have to take responsibility for our tools. +We listed core competencies that have been intentionally formulated +abstractly without referencing any particular information-processing device. +As expected, we have drawn equally upon notions from \ac{SE} and other research fields, +but found that we likewise require teamwork capabilities. +We detailed these competencies in various dimensions and found that +a different amount is required in different positions and scientific domains. +Using this, we proposed recommendations for organisations to foster the development of these competencies. + +The gathered values and competencies form a common denominator that unifies RSEs + and enables them to identify with this domain, + in the knowledge that it is already or will soon become critically important for many areas of science. +These competencies at the intersection of research and SE, +coupled with a firm belief in team processes, make RSEs sought after on the job market +and their values make them responsible members of a digital society. +The result is a qualification profile which is highly attractive for young people. + +At an institutional level, research performing organisations have a growing +interest in fostering RSE training to support the use of \ac{FAIR} data and \ac{FAIR} software in the academic world, +a direction determined by new incentives created by scientific journals and librarians. +How we update existing institutions and set up new ones +that provide this education will be the topic of a follow-up paper. + +# Contribution details {-} + +Heidi Seibold came up with the original idea for the deRSE23 workshop in Paderborn. +Heidi Seibold, Jeremy Cohen, Florian Goth, Renato Alves, Jan Philipp Thiele, and Samantha Wittke organised the deRSE23 workshop. +We thank all the participants of this community workshop! +Toby Hodges conceptualised and organised the un-deRSE23 workshop together with Jan Philipp Thiele and Florian Goth. +We also thank all the participants of this follow-up community workshop! +Jeremy Cohen, Gerasimos Chourdakis, Magnus Hagdorn, Jean-Noël Grad, Jan Philipp Thiele, and Matthias Braun organised the deRSE24 workshop in Würzburg. +We are also grateful to the participants of this third community workshop! +Heidi Seibold, Jeremy Cohen, Florian Goth, Renato Alves, Jan Philipp Thiele, +Jan Linxweiler, Jean-Noël Grad, and Samantha Wittke contributed the initial draft. +Florian Goth supervised the project and did the project administration. +Jean-Noël Grad designed and implemented the software tooling for the collaborative writing of this manuscript on GitHub. +Everybody contributed to the final review and editing. + + +The CRediT system [@Brand2015] is far too generic to adequately describe the contributions of everybody in various workshops, spread over a two year period. +While everybody contributed to the discussion formulating and refining the ideas, and to collaboratively writing and/or reviewing and editing the entirety the script, some parts merit special mention. +Renato Alves quickly jumped in to host the first deRSE23 workshop to take over from a sick organiser. +Matthias Braun contributed early versions of the specialisations and also contributed to the survey. +Leyla Jael Castro contributed to the initial draft of the example career path, and provided helpful insights in discussions on metadata. +Gerasimos Chourdakis' contributions to the paper are numerous (extensively editing large parts of the initial draft), but he especially wrote first drafts for clarifying +the relationship of the RSE competencies to the SE competencies. He also designed the "Learning and teaching RSE" website [@learnandteach]. +Simon Christ helped with typesetting and contributed the competencies' symbols and the spell-checker script. +Jeremy Cohen drafted the initial introduction and contributed the tables for RSEs in centralised RSE departments. +Stephan Druskat contributed parts on proper software citation and publication and sharpened various RSE specialisations. +Fredo Erxleben contributed to early discussions of the paper and added the contributions by the Helmholtz Association. +Jean-Noël Grad contributed initial drafts for the ELIXIR framework and the section on the work of the HPC certification forum +as well as numerous other contributions to the BibTeX infrastructure and the GitHub actions. +Magnus Hagdorn drafted and supervised the ethics and values section for an RSE and made sure that these values are reflected in the competencies of RSEs. +Toby Hodges contributed parts on the Carpentries, and helped steer the curriculum discussion. +Guido Juckeland contributed experiences from his first RSE course for students. +Dominic Kempf drafted the first version of the example curriculum. +Anna-Lena Lamprecht helped with proper wording, especially with awareness about established SE terminology, that was misused earlier. +Jan Linxweiler drafted various RSE specialisations and made sure that clean coding techniques got their due recognition. +Frank Löffler rewrote numerous parts to be actually legible, and helped with preparation for the final steps of a de-RSE position paper. +Michele Martone wrote the first draft of the environmental sustainability section. +Moritz Schwarzmeier drafted the categorisation of the specialisations. +Heidi Seibold contributed the idea and started everything. +Jan Philipp Thiele drafted initial parts of the technical pillar of the RSE competencies, and represented the project on numerous discussions. +Harald von Waldow contributed to initial drafts of the Masters program and contributed his knowledge to the explainability of computer simulations. +Samantha Wittke contributed the parts on CodeRefinery and how to reach out to new RSEs. +Florian Goth has the pleasure of being grateful to all collaborators in this project for contributing their time and knowledge into this project! + + +\appendix + + +# Appendix {#sec:appendix} + +## An example master's programme for research software engineering {#subsec:examplemaster} + +The target audience for such a master's programme are students holding a bachelor's degree from +a domain science, which we will call "home domain" in the following. There is explicitly +no restriction on the candidates' home domain: it may be from the \ac{STEM} disciplines, life +sciences, humanities or social sciences, and it can also change later in their career. +Candidates with a bachelor's degree in computer science are also +explicitly included, although we acknowledge that their master's programme should include adaptations +to make their interaction effective with other domain scientists. +In order to give the future RSE the necessary breadth, we expect this to be a four-semester curriculum. + +The curriculum is formed from a combination of modules, +some of which are core modules teaching essential skills that must be completed by all students. +Other modules introduce more specialised concepts and skills. +During the master's programme, students should pick an RSE specialisation from the list in this paper +and attend these additional modules to deepen their knowledge in that field. + +Core modules are of course drawn from the three pillars of the RSE and can be categorised accordingly. + +- Software/Technical skills: + - Foundational module: Here we have an introduction to programming: Emphasising use cases over programming paradigms, students learn at least two languages: a language that facilitates prototyping and data processing (e.g., \gls{Python} or \gls{R}) and a language for designing complex, performance-critical systems (e.g., \gls{C}/\gls{Cpp}). This exposes them to computers in a hands-on fashion and is the foundation for (\gls{DOCBB}, \gls{DIST}). + - Computing environment module: Programming languages are not enough to work in a landscape of many interconnected software components; hence we require something like software craftsmanship, where tools such as the Unix shell, version control systems, build systems, documentation generators, package distribution platforms, and software discovery systems are taught to strengthen skills in (\gls{DIST}, \gls{DOCBB}, \gls{SWREPOS}, \gls{SRU}). + - Software engineering module: Here we develop foundational software engineering competencies (basic knowledge and skill regarding requirements engineering, software architecture and design, implementation, quality assurance, software evolution), again emphasising and strengthening (\gls{DOCBB}, \gls{DIST}) on a more abstract level. + +- Research skills: + - Optional domain mastery module: Additional minor research courses, but students with a home-domain already have the research part well-covered. Courses here should be allowed to fall in any research field, and those outside of the own home-domain should be especially encouraged. + - Research tools module: Here we teach tools used to distribute and publish software, as well as introducing students to domain specific data repositories, thereby gaining foundational knowledge in (\gls{SRU}, \gls{SP}, \gls{DOMREP}). + - Meta-research module: Here we teach people how research works. The research life cycle is introduced, as well as the data life cycle and the software life cycle are abstractly introduced. + +- Communication skills: + - Project management methods: Here we teach project management methods that are useful in science, such as agile ones (\gls{PM}). + - Communication skills module: Here we have courses focusing on interdisciplinary communication, interacting across cultures, communication in hierarchies, supporting end users effectively. These are all facets of the (\gls{USERS}) skill. + - Teaching module: This module covers topics to effectively design courses and teaching material for the various digital tools, thereby strengthening the (\gls{TEACH}) skill. + +Given that RSE work also involves a lot of craftsmanship skills, +hands-on practice is an integral part of the curriculum. +At least two lab projects are required within the mandatory curriculum. +These should be executed as a team and involve a question from a domain science. +We recommend covering both the candidate's home domain as well as a different one. +Ideally, projects stem from collaborations with scientists within the institution and RSE +students take the role of a consultant. This setup strengthens the (\gls{TEAM}, \gls{TEACH}, \gls{USERS}) skill +and encourages also the (\gls{MOD}) skill through interaction. + +To emphasise the exposure to domains outside their bachelor's degree domain, +we recommend that RSEs also support their non-home-domain project with introductory +courses from this discipline. +This schools their ability to quickly adapt their vocabulary and thinking to other disciplines and is an aspect of (\gls{MOD}). + +To align with the specialisations listed in this paper, example optional modules include topics on +\ac{HPC} engineering/parallel programming, numerical mathematics/scientific computing, web technologies, +data stewardship, AI models/statistics, and community management/training. + +The programme is finalised with a master's thesis which should be dual-supervised by an +RSE supervisor from an actual project, and a domain supervisor. +The thesis should answer a relevant research question from the domain using computational methods, strengthening (\gls{NEW}). +Software development is required, and the code is part of the gradable deliverables. +The RSE supervisor ensures and grades the software craftsmanship aspects of the project. +This setup ensures that we are grading the effectiveness of applying RSE skills in an actual research environment. + +## An example of a possible career path {#subsec:examplecareer} +#### Setting the stage + +Meet Kay, Kim's [@Anzt2021] younger sister who currently studies researchology in a bachelor's programme in the established domain of researchonomy at University of Orithena (UofO). +We will follow Kay’s fictional career to illustrate how education, job-experience and a career in academic institutions could lead to become a successful RSE. +In Kay’s world, some of the measures proposed in this paper have already been implemented. + +#### Bachelor's degree + +Through a program like Software Carpentry [@CarpentriesSoftware] or The Missing Semester [@Athalye2023], +Kay learns about using computational tools to support the sophisticated statistical analysis typical for researchology. +She uses those tools to create and automate the steps of processing data and producing outcomes for her bachelor's thesis +(generating plots with matplotlib and even CI for automatic building) +and takes pride in a fully open and reproducible bachelor's thesis enabling her to graduate with honours from the faculty of researchonomy. + +#### Master's degree + +Kay ponders whether to continue with computational researchology, which her bachelor's supervisor is responsible for, +or enrol in a domain-agnostic RSE master's programme. +Researchers in computational researchology need to acquire a large part of the general RSE know-how presented +in this paper and specialise in Quantum-Accelerated Bayesian Optimisation methods. +However, Kay decides to go for the more generic route of a dedicated RSE programme because she wants to continue in academia, +but does not like the idea of becoming stuck with one research topic. +She also experienced the immediate satisfaction gained by helping colleagues from her research group with tricky technical problems, +which makes her happier than the subdued sense of achievement from having a research paper accepted long after she had written it. +For her, coding and sharing knowledge in the form of software is of similar importance to writing a paper focused mostly on the obtained results. + +The domain-agnostic RSE Master programme consists of a core of RSE topics with various electives for specialisation, some of them domain-specific (e.g., chemistry) or topic-specific (e.g., cloud computing for research). +Kay chooses digital archaeology and develops a pipeline for reconstructing 3D models from ground penetrating radar data, to simplify the process for archaeologists (reproducibility, big data, \ac{ML}). +The project management skills that are being taught as part of the core RSE curriculum really help her to not get lost in this project. +Apart from working with the researchers in her archaeology group, +she has to work with members of the central RSE department to help her with the pipelines. +She also has to liaise with the central \ac{IT} department to organise storage for the large data sets. +Towards the end of the programme, she visits her first RSE conference where she sees a lot of notions (\gls{SWLC}, \gls{RC}) in action +that so far have been abstract in her master's degree. + +The exposure to the wider RSE community inspires her to invest additional time into her thesis to publish +her software project under a licence approved by the Open Source Initiative and to write an accompanying article in the open source journal JOSS [@JOSS]. +Inspired by the discussion with reviewers of her JOSS paper, +and the citation metadata file that JOSS created automatically for her when her paper is published, +Kay starts to think more about making her software FAIR. +She reads up on the topic in a guide suggested to her, the Turing Way [@turing_way_2022], +and creates metadata files that provide the citation metadata and general description for her software. +She adds the files to her source code repository, +and also adds an automated \gls{CI}/\gls{CD} pipeline that updates metadata and creates a new publication record in the Zenodo repository for each new release. +Kay has now completed the RSE programme and has reached Junior RSE level. + +#### Junior RSE + +Kay finds a position in the central RSE department at her university with a competitive \ac{IT} salary. +Although the contract is temporary, there is a good chance that it will lead to a permanent position. +The university makes an effort to enable that since it is a member of "The Technician Commitment"[@techniciancommitment], an initiative to ensure recognition and career development of technicians, who face similar challenges to RSEs. +Kay completes the Software Carpentry Instructor training and teaches basic research computing, +while advising fellow students of her department on better programming (\gls{DOCBB} and \gls{MOD} skill). +She also runs a seminar in the RSE Master's programme. She publishes a condensed version of that in JOSE[@JOSE]. +During her teaching duties, she becomes aware of a new project in her department that requires a community manager RSE, +and she gladly signs up to focus more on her communication skills. +After three years, she takes an exciting opportunity to work in another university. + +#### Senior RSE + +The new position involves taking responsibility for the RSE related aspects of a large inter-organisational project. +With her new responsibilities comes a shift in the importance of various aspects of her work. +Having this position in an inter-organisational project places far more emphasis on communication and organisation skills. +She is spending time teaching people (\gls{TEACH} skill) to onboard them into the project. +There is a lot of interaction with different stakeholders in the project like funders and user groups (\gls{USERS} skill). +To oversee the project, she uses an amalgamation of both agile and traditional project-management concepts and methods which she acquires on-the-job (\gls{PM} skills). +Her work so far has already been heavy on (\gls{TEAM}) skills, but now also the leadership aspect comes into play. + +#### RSE-focused principal investigator + +The job experience as a leading RSE for a large project was the last requirement necessary to be awarded the title of a "Certified Research Software Professional" (CRSP) +from an institutionalised centre of RSE education. +The certificate confirms her track record of valuable software contributions +and of teaching and mentoring people, +as well as her capability to enable, foster and contribute to high-quality research in a leading position. +It is recognised by various funding agencies, such as the DFG, and hence enables RSEs to act as a \ac{PI} for RSE-focused grant applications. It is also recognised by many prestigious universities and opens many career options that are also typical for PhDs. +Kay can now write her own grant proposals to effectively fund work of moving research software projects from prototypes to infrastructure. + +## Existing frameworks {#subsec:existingframeworks} + +### HPC skills and certification + +As an area that generally requires a range of advanced skills, +\ac{HPC} is one field where there is ongoing work +to identify relevant sets of skills for \ac{HPC} practitioners and potential paths +to develop these skills. The \acrshort{HPC} Certification Forum [@HPCCFCompetencies] has +developed a competence standard for \ac{HPC} that defines a range of skills and +how they are related in the context of a skill tree [@Kunkel2020a; @Kunkel2020b]. +This competence standard is currently being built upon by the CASTIEL 2 [@CASTIEL2] project +in collaboration with initiatives funded by the \ac{EuroHPC-JU} to create a framework for \ac{HPC} certification [@EuroHPCJU2023]. +While this framework focuses mostly on skills specific to \ac{HPC}, there are a couple of similarities +to the framework proposed in this paper. The "SD: Software Development" skill set +is very similar to the \ac{SE} skills discussed in @sec:required-generic-skills, +describing a wide range of such skills. +This skill set contains +Programming Best Practices (SD2), Software Configuration Management (SD3), Software Quality (SD5), +Software Design and Software Architecture (SD6), and explicit mention of documentation (SD7, see our \gls{DOCBB}). +Besides the Software Concepts for \ac{HPC} (SD1), which mainly concerns \acrshort{HPC}-focused RSEs, +most of the skills contained in the SD2-SD7 categories apply to all RSEs. +A significant difference compared to the framework proposed in this paper is +the absence of skills related to research or communication. +Noteworthy is already now the level of detail in their skill tree which is more similar to @subsec:examplemaster. + +Also looking at pathways and how different skills are related, +the \ac{UNIVERSE-HPC} project [@UNIVERSEHPC], funded under the \acrshort{UK}'s ExCALIBUR +research programme [@EXCALIBUR], is looking to understand and develop +training pathways to support the development of specialist skills in the \ac{HPC} +and exascale domains. The project is gathering open source training materials +to develop curricula that support the training pathways that are underpinned +by high-quality training materials. + +### Bioinformatics skills and certification {#subsec:emblbio} + +Bioinformatics is another field that actively works on developing skill trees. +The Bioinformatics Core Competencies [@Mulder2018; @Welch2016; @Welch2014], +the BioExcel competency framework [@Matser2016], +the PerMedCoE competency framework [@Lloret-Llinares2021], +the Research Data Management and Data Stewardship competence framework [@Demchenko2021] +and the ELIXIR Data Stewardship Competency Framework for Life Sciences [@Scholtens2019] +are examples of grassroots efforts aiming at defining the set of skills +of various bioinformatics specialities, +one of them as a taxonomy [@Mulder2018]. +These frameworks eventually converged into the \ac{EMBL-EBI} Competency Hub +[@CompetencyHub; @Lloret-Llinares2022], +where typical RSE and bioinformatician profiles at different levels +of seniority can be queried +(e.g., Junior RSE[^JuniorRSE], +Senior Computational Chemist[^SeniorCC]) +and compared against one another +(e.g., Junior vs. Senior RSE[^Comp]). + +Competencies can be divided into more fine-grained building blocks: +knowledge, skills and abilities (KSAs). They can be organised in a taxonomy, +and are also transferable, i.e. a KSA can be a prerequisite to multiple competencies. +The Mastery Rubric for Bioinformatics [@Tractenberg2019] and the ELIXIR +Data Stewardship Competency Framework for Life Sciences [@Scholtens2019] +are examples of KSA frameworks for bioinformatics curricula. + +The Curriculum Task Force of the \ac{ISCB} curates a database of degrees and certificates +in bioinformatics [@BioinformaticsCertification; @Mulder2018]. +The database includes bachelor's and master's degree programs and specialisations, +PhD programs, and certificates from graduate schools. + +BioExcel has research competencies that combine some of our research competencies and some notions from the communication skills. +Their computing competencies roughly map to our software skills. +Here, we find competencies such as "package and distribute software", which maps to our (\gls{DIST}) competencies, +and "comply with licensing policy", which would in our framework be part of (\gls{SP}) in the research competencies. +In addition, they have a dedicated parallel computing competency section, +thereby shifting the emphasis of the knowledge of their computational tools towards the \acrshort{HPC}-RSE specialisation in our framework. +Career profiles, such as the computational chemist, bring additional domain specific knowledge; +we would classify those as a mixture of \${DOMAIN}-RSE and \acrshort{HPC}-RSE. +It is noteworthy, however, that the BioExcel framework puts very little emphasis on communication skills, which are often involved in RSE-related tasks. + +[^JuniorRSE]: [https://competency.ebi.ac.uk/framework/bioexcel/3.0/profile/view/10115/alex-2](https://competency.ebi.ac.uk/framework/bioexcel/3.0/profile/view/10115/alex-2) +[^SeniorCC]: [https://competency.ebi.ac.uk/framework/bioexcel/3.0/profile/view/10121/kim-0](https://competency.ebi.ac.uk/framework/bioexcel/3.0/profile/view/10121/kim-0) +[^Comp]: [https://competency.ebi.ac.uk/framework/bioexcel/3.0/profiles/compare/10115/10117](https://competency.ebi.ac.uk/framework/bioexcel/3.0/profiles/compare/10115/10117) diff --git a/002/contributors.yml b/002/contributors.yml new file mode 100644 index 0000000..35c0bbe --- /dev/null +++ b/002/contributors.yml @@ -0,0 +1,263 @@ +authors: + + - author: "Heidi Seibold" + firstName: Heidi + lastName: Seibold + initials: HS + affiliations: + - IGDORE Munich, Germany + orcid: 0000-0002-8960-9642 + email: heidi@seibold.co + + - author: "Florian Goth" + firstName: Florian + lastName: Goth + initials: FG + affiliations: + - Institute for Theoretical Physics and Astrophysics, University of Würzburg, Germany + orcid: 0000-0003-2707-4790 + email: florian.goth@uni-wuerzburg.de + acknowledgements: | + FG acknowledges funding from the Deutsche Forschungsgemeinschaft + (DFG, German Research Foundation) through the SFB 1170 “Tocotronics”, + project Z03 - project number \geprislink{258499086}. + + - author: "Jan Linxweiler" + firstName: Jan + lastName: Linxweiler + initials: JL + affiliations: + - Technische Universität Braunschweig, Germany + orcid: 0000-0002-2755-5087 + email: j.linxweiler@tu-braunschweig.de + + - author: "Jan Philipp Thiele" + firstName: Jan Philipp + lastName: Thiele + initials: JPT + affiliations: + - Weierstrass Institute, Berlin, Germany + - Leibniz University Hannover, Institute of Applied Mathematics, Scientific Computing, Hannover, Germany + orcid: 0000-0002-8901-6660 + email: thiele@wias-berlin.de + + - author: "Jeremy Cohen" + firstName: Jeremy + lastName: Cohen + initials: JC + affiliations: + - Imperial College London, London, UK + orcid: 0000-0003-4312-2537 + email: jeremy.cohen@imperial.ac.uk + acknowledgements: | + JC acknowledges support from the UK Engineering and Physical Sciences + Research Council (UKRI-EPSRC) under grants EP/R025460/1, EP/W035731/1 and + EP/Y530608/1. + + - author: "Renato Alves" + firstName: Renato + lastName: Alves + initials: RA + affiliations: + - European Molecular Biology Laboratory, Heidelberg, Germany + orcid: 0000-0002-7212-0234 + email: renato.alves@embl.de + + - author: "Samantha Wittke" + firstName: Samantha + lastName: Wittke + initials: SW + affiliations: + - CSC – IT Center for Science, Espoo, Finland + orcid: 0000-0002-9625-7235 + email: samantha.wittke@csc.fi + + - author: "Jean-Noël Grad" + firstName: Jean-Noël + lastName: Grad + initials: JNG + affiliations: + - Institute for Computational Physics, University of Stuttgart, Germany + orcid: 0000-0002-5821-4912 + email: jgrad@icp.uni-stuttgart.de + acknowledgements: | + JNG acknowledges funding from the Deutsche Forschungsgemeinschaft + (DFG, German Research Foundation) - project number \geprislink{391126171} + (PI: Holm) and from the European Union – this work has received funding + from the European High Performance Computing Joint Undertaking (JU) and + countries participating in the project under grant agreement + No [101093169](https://doi.org/10.3030/101093169). + + - author: "Fredo Erxleben" + firstName: Fredo + lastName: Erxleben + initials: FE + affiliations: + - Helmholtz-Zentrum Dresden-Rossendorf, Germany + orcid: 0000-0001-7233-3005 + email: f.erxleben@hzdr.de + + - author: "Magnus Hagdorn" + firstName: Magnus + lastName: Hagdorn + initials: MH + affiliations: + - Geschäftsbereich IT, Charité Universitätsmedizin Berlin, Germany + orcid: 0000-0002-5076-4864 + email: magnus.hagdorn@charite.de + + - author: "Moritz Schwarzmeier" + firstName: Moritz + lastName: Schwarzmeier + initials: MS + affiliations: + - Mathematical Modeling and Analysis, TU Darmstadt, Germany + orcid: 0000-0001-8992-6245 + email: moritz.schwarzmeier@tu-darmstadt.de + acknowledgements: | + MS would like to thank Hessian Ministry of Higher Education, Research, Science and the Arts + and the Federal Government and the Heads of Government of the Länder, + as well as the Joint Science Conference (GWK), for their + funding and support within the framework of the NFDI4Ing consortium. + Part of this work was funded by the German Research Foundation (DFG) - project number + \geprislink{442146713}. + Part of this work was funded by the Hessian Ministry of Higher Education, + Research, Science and the Arts - cluster project Clean Circles. + + - author: "Matthias Braun" + firstName: Matthias + lastName: Braun + initials: MB + affiliations: + - Cluster of Excellence IntCDC, University of Stuttgart, Germany + orcid: 0000-0001-8591-3690 + email: matthias.braun@intcdc.uni-stuttgart.de + acknowledgements: | + MB acknowledges support by the Deutsche Forschungsgemeinschaft + (DFG, German Research Foundation) under Germany's Excellence Strategy – + EXC 2120/1 – \geprislink{390831618}. + + - author: "Harald von Waldow" + firstName: Harald + lastName: von Waldow + initials: HvW + affiliations: + - Johann Heinrich von Thünen Institute, Centre for Information Management, Germany + orcid: 0000-0003-4800-2833 + email: harald.vonwaldow@thuenen.de + + - author: "Simon Christ" + firstName: Simon + lastName: Christ + initials: SC + affiliations: + - Leibniz University Hannover, Department of Cell Biology and Biophysics, Computational Biology, Germany + orcid: 0000-0002-5866-1472 + email: christ@cell.uni-hannover.de + + - author: "Gerasimos Chourdakis" + firstName: Gerasimos + lastName: Chourdakis + initials: GC + affiliations: + - School of Computation, Information and Technology, Technical University of Munich, Garching, Germany + - Institute for Parallel and Distributed Systems, University of Stuttgart, Stuttgart, Germany + orcid: 0000-0002-3977-1385 + email: gerasimos.chourdakis@tum.de + + - author: "Dominic Kempf" + firstName: Dominic + lastName: Kempf + initials: DK + affiliations: + - Heidelberg University, Scientific Software Center, Germany + orcid: 0000-0002-6140-2332 + email: dominic.kempf@iwr.uni-heidelberg.de + acknowledgements: | + DK acknowledges support from the Scientific Software Center which is funded as part + of the Excellence Strategy of the German Federal and State Governments. + + - author: "Anna-Lena Lamprecht" + firstName: Anna-Lena + lastName: Lamprecht + initials: ALL + affiliations: + - Institute of Computer Science, University of Potsdam, Germany + orcid: 0000-0003-1953-5606 + email: anna-lena.lamprecht@uni-potsdam.de + + - author: "Toby Hodges" + firstName: Toby + lastName: Hodges + initials: TH + affiliations: + - The Carpentries, USA + orcid: 0000-0003-1766-456X + email: tobyhodges@carpentries.org + + - author: "Leyla Jael Castro" + firstName: Leyla Jael + lastName: Castro + initials: LJC + affiliations: + - ZB MED Information Centre for Life Sciences, Cologne, Germany + orcid: 0000-0003-3986-0510 + email: ljgarcia@zbmed.de + acknowledgements: | + LJC acknowledges support from the NFDI4DS consortium funded by the German + Research Foundation (DFG) - project number \geprislink{460234259}. + + - author: "Guido Juckeland" + firstName: Guido + lastName: Juckeland + initials: GJ + affiliations: + - Helmholtz-Zentrum Dresden-Rossendorf, Germany + orcid: 0000-0002-9935-4428 + email: g.juckeland@hzdr.de + + - author: "Stephan Druskat" + firstName: Stephan + lastName: Druskat + initials: SD + affiliations: + - German Aerospace Center (DLR), Institute for Software Technology, Berlin, Germany + - Humboldt-Universität zu Berlin, Department of Computer Science, Berlin, Germany + orcid: 0000-0003-4925-7248 + email: stephan.druskat@dlr.de + + - author: "Frank Löffler" + firstName: Frank + lastName: Löffler + initials: FL + affiliations: + - Michael Stifel Center Jena \& Friedrich Schiller University Jena, Germany + orcid: 0000-0001-6643-6323 + email: frank.loeffler@uni-jena.de + + - author: "Michele Martone" + firstName: Michele + lastName: Martone + initials: MM + affiliations: + - Leibniz Supercomputing Centre, Garching, Germany + orcid: 0000-0003-3239-8554 + email: michele.martone@lrz.de + acknowledgements: | + MM acknowledges funding from the SiVeGCS Project. + +# please use the following author template (all fields are optional): + +# - author: "F. D. C. Willard, Jr." +# firstName: F. D. C. +# lastName: Willard +# suffixName: Jr. +# initials: FDCW +# affiliations: +# - University of Arcadia +# - Michigan State University, East Lansing, Michigan, USA +# orcid: 0000-0000-0000-0000 +# email: willard@u-arcadia.edu +# acknowledgements: | +# FDCW acknowledges support from the University of Arcadia +# under grants UofA/A1234/5 and UofA/A1234/6. diff --git a/002/filter.py b/002/filter.py new file mode 100644 index 0000000..a7527ad --- /dev/null +++ b/002/filter.py @@ -0,0 +1,118 @@ +""" +Edit a Markdown file based on an external metadata file. +Replace each author in the YAML header file by a LaTeX string +with full author information (name, affiliation(s), ORCID iD). +Add funding acknowledgements at the bottom of the manuscript. +""" + +import yaml +import argparse + +parser = argparse.ArgumentParser(description=__doc__) +parser.add_argument("--input", type=str, required=True, + help="input Markdown file") +parser.add_argument("--output", type=str, required=False, + help="output Markdown file") +parser.add_argument("--contributors", type=str, required=False, + default="contributors.yml", + help="contributors YAML file") + + +def get_contributors_metadata(content): + entries = yaml.safe_load(content)["authors"] + dictionary = {entry["author"]: entry for entry in entries} + assert len(entries) == len(dictionary), "duplicate keys found in YAML file" + return dictionary + + +def get_manuscript_metadata(markdown): + markdown = markdown.lstrip() + assert markdown.startswith("---") + markdown = markdown.split("\n", 1)[1] + markdown = markdown.lstrip() + metadata, body = markdown.split("\n---", 1) + body = body.split("\n", 1)[1] + return yaml.safe_load(metadata), body + + +def get_author_thanks(metadata): + retval = {} + for line in metadata["author"]: + author, *thanks = [x.strip() for x in line.split("|")] + retval[author] = thanks + return retval + + +def process_markdown(metadata, body, contributors): + authors_tex = [] + authors_xmp = [] + affiliations = {} + acknowledgements = ["# Acknowledgements {- #sec:acknowledgements}"] + bookkeeping_initials = {} + author_thanks = get_author_thanks(metadata) + if "acknowledgements-before" in metadata: + acknowledgements.append(metadata["acknowledgements-before"]) + del metadata["acknowledgements-before"] + # parse metadata + for fullname, annotations in author_thanks.items(): + author_metadata = contributors[fullname] + authors_xmp.append(fullname) + author_tex = fullname + if "orcid" in author_metadata: + author_tex += f"\\texorpdfstring{{\\thinspace\\orcidlink{{{author_metadata['orcid']}}}}}{{}}" + author_affil = [] + if annotations: + author_affil.append("") + for thanks in annotations: + author_tex += f"\\texorpdfstring{{\\thanks{{{thanks}}}}}{{}}" + for affiliation in author_metadata.get("affiliations", []): + if affiliation not in affiliations: + affiliations[affiliation] = f"{len(affiliations) + 1}" + author_affil.append(affiliations[affiliation]) + authors_tex.append(f"\\author[{','.join(author_affil)}]{{{author_tex}}}") + initials = author_metadata["initials"] + assert initials not in bookkeeping_initials, f"initials '{initials}' collide with '{fullname}' and '{bookkeeping_initials[initials]}'" + bookkeeping_initials[initials] = fullname + if "acknowledgements" in author_metadata: + message = author_metadata["acknowledgements"] + assert initials in message, f"'{initials}' doesn't appear in the acknowledgements of '{fullname}'" + acknowledgements.append(message) + affiliations_tex = [f"\\affil[{key}]{{{affil}}}" for affil, key in affiliations.items()] + if "acknowledgements-after" in metadata: + acknowledgements.append(metadata["acknowledgements-after"]) + del metadata["acknowledgements-after"] + # update Markdown metadata + del metadata["author"] + metadata["authorxmp"] = authors_xmp + metadata["header-includes"].extend(authors_tex) + metadata["header-includes"].extend(affiliations_tex) + # rewrite Markdown file + markdown = [] + markdown.append("---") + markdown.append(yaml.dump(metadata, allow_unicode=True)) + markdown.append("---") + token_appendix = "\n\\appendix\n" + if token_appendix in body: + body = body.replace(token_appendix, "\n\n" + "\n".join(acknowledgements) + "\n\n" + token_appendix, 1) + markdown.append(body) + else: + markdown.append(body) + markdown.append("") + markdown.extend(acknowledgements) + return "\n".join(markdown) + + +if __name__ == "__main__": + args = parser.parse_args() + with open(args.contributors) as f: + contributors = get_contributors_metadata(f.read()) + with open(args.input) as f: + metadata, body = get_manuscript_metadata(f.read()) + for key in get_author_thanks(metadata).keys(): + assert key in contributors, f"author '{key}' in {args.input} not found in {args.contributors}" + markdown = process_markdown(metadata, body, contributors) + if args.output: + with open(args.output, "w") as f: + f.write(markdown) + else: + print(markdown) diff --git a/002/fonts/arrows-spin.svg b/002/fonts/arrows-spin.svg new file mode 100644 index 0000000..e88dded --- /dev/null +++ b/002/fonts/arrows-spin.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/002/fonts/boxes-packing.svg b/002/fonts/boxes-packing.svg new file mode 100644 index 0000000..428d2de --- /dev/null +++ b/002/fonts/boxes-packing.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/002/fonts/chalkboard-user.svg b/002/fonts/chalkboard-user.svg new file mode 100644 index 0000000..516f2ed --- /dev/null +++ b/002/fonts/chalkboard-user.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/002/fonts/clipboard-list.svg b/002/fonts/clipboard-list.svg new file mode 100644 index 0000000..48c81ec --- /dev/null +++ b/002/fonts/clipboard-list.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/002/fonts/code-pull-request.svg b/002/fonts/code-pull-request.svg new file mode 100644 index 0000000..875e299 --- /dev/null +++ b/002/fonts/code-pull-request.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/002/fonts/comments.svg b/002/fonts/comments.svg new file mode 100644 index 0000000..6936141 --- /dev/null +++ b/002/fonts/comments.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/002/fonts/folder.svg b/002/fonts/folder.svg new file mode 100644 index 0000000..53c4a49 --- /dev/null +++ b/002/fonts/folder.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/002/fonts/graduation-cap.svg b/002/fonts/graduation-cap.svg new file mode 100644 index 0000000..6d34bbd --- /dev/null +++ b/002/fonts/graduation-cap.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/002/fonts/laptop-code.svg b/002/fonts/laptop-code.svg new file mode 100644 index 0000000..9278a70 --- /dev/null +++ b/002/fonts/laptop-code.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/002/fonts/lightbulb.svg b/002/fonts/lightbulb.svg new file mode 100644 index 0000000..696fa4e --- /dev/null +++ b/002/fonts/lightbulb.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/002/fonts/newspaper.svg b/002/fonts/newspaper.svg new file mode 100644 index 0000000..15886c4 --- /dev/null +++ b/002/fonts/newspaper.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/002/fonts/recycle.svg b/002/fonts/recycle.svg new file mode 100644 index 0000000..6a955f2 --- /dev/null +++ b/002/fonts/recycle.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/002/fonts/sitemap.svg b/002/fonts/sitemap.svg new file mode 100644 index 0000000..1173229 --- /dev/null +++ b/002/fonts/sitemap.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/002/fonts/user-group.svg b/002/fonts/user-group.svg new file mode 100644 index 0000000..fc06cfb --- /dev/null +++ b/002/fonts/user-group.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/002/glossary.tex b/002/glossary.tex new file mode 100644 index 0000000..52cb58b --- /dev/null +++ b/002/glossary.tex @@ -0,0 +1,66 @@ +%%%%%%%%%%%% +% glossary % +%%%%%%%%%%%% + +% programming languages +\newglossaryentry{Fortran}{name={Fortran},description={general-purpose compiled programming language}} +\newglossaryentry{Cpp}{name={C++},description={general-purpose compiled programming language}} +\newglossaryentry{C}{name={C},description={general-purpose compiled programming language}} +\newglossaryentry{R}{name={R},description={general-purpose scripting language}} +\newglossaryentry{Python}{name={Python},description={general-purpose scripting language}} + +% platforms, services, companies +\newglossaryentry{GitHub}{name={GitHub},description={online software repository hosting and collaboration platform}} +\newglossaryentry{GitLab}{name={GitLab},description={online software repository hosting and collaboration platform}} + +% software engineering +\newglossaryentry{design-pattern}{name={design pattern},description={general and reusable solution to solve a \ac{SE} problem (often a best practice, or a ``recipe'')}} +\newglossaryentry{static-analysis}{name={static analysis},description={automated procedure to detect software bugs in source code without executing the code}} +\newglossaryentry{bus-factor}{name={bus factor},description={vulnerability of a project to losing key and irreplaceable team members - a bus factor of 1 means that a single such team member vanishing would already stall the project's advancement.}} + +% other +\newglossaryentry{SysOp}{name={SysOp},description={system administrator in charge of a computing infrastructure}} +\newglossaryentry{DevOps}{name={DevOps},description={set of practices and tools for code development and computing infrastructure maintenance}} +\newglossaryentry{software-publication}{name={software publication},description={the practice of long-term archiving software artifacts with software metadata under a permanent identifier}} + +%%%%%%%%%%%% +% acronyms % +%%%%%%%%%%%% + +% organisations and institutions +\newacronym{EMBL-EBI}{EMBL-EBI}{European Molecular Biology Laboratory - European Bioinformatics Institute} +\newacronym{EuroHPC-JU}{EuroHPC JU}{European High-Performance Computing Joint Undertaking} +\newacronym{UNESCO}{UNESCO}{United Nations Educational, Scientific and Cultural Organization} +\newacronym{MIT}{MIT}{Massachusetts Institute of Technology} +\newacronym{ISCB}{ISCB}{International Society for Computational Biology} +\newacronym{ENCCS}{ENCCS}{EuroCC National Competence Center Sweden} +\newacronym{PRACE}{PRACE}{Partnership for Advanced Computing in Europe} +\newacronym[first={German Research Foundation (DFG, Deutsche Forschungsgemeinschaft)}]{DFG}{DFG}{German Research Foundation (Deutsche Forschungsgemeinschaft)} +\newacronym[first={National Research Data Infrastructure (NFDI, Nationale Forschungsdateninfrastruktur)}]{NFDI}{NFDI}{National Research Data Infrastructure (Nationale Forschungsdateninfrastruktur)} +\newacronym{UNIVERSE-HPC}{UNIVERSE-HPC}{Understanding and Nurturing an Integrated Vision for Education in RSE and \glsentrytext{HPC}} + +% other acronyms +\newacronym[plural=IDEs,firstplural=integrated development environments (IDE)]{IDE}{IDE}{integrated development environment} +\newacronym[plural=KPIs,firstplural=key performance indicators (KPIs)]{KPI}{KPI}{key performance indicator} +\newacronym[plural=LLMs,firstplural={large language models (LLMs)}]{LLM}{LLM}{large language model} +\newacronym{UML}{UML}{Unified Modelling Language} +\newacronym{HPC}{HPC}{High-Performance Computing} +\newacronym{HTC}{HTC}{High-Throughput Computing} +\newacronym{STEM}{STEM}{science, technology, engineering and mathematics} +\newacronym{SE}{SE}{software engineering} +\newacronym{FAIR}{FAIR}{Findability, Accessibility, Interoperability and Reusability} +\newacronym{IT}{IT}{information technology} +\newacronym{ML}{ML}{machine learning} +\newacronym{GPL}{GPL}{General Public License} +\newacronym{CI}{CI}{continuous integration} +\newacronym{CD}{CD}{continuous delivery} +\newacronym{CICD}{CI/CD}{continuous integration and continuous delivery} +\newacronym{RDM}{RDM}{research data management} +\newacronym{GDPR}{GDPR}{General Data Protection Regulation} +\newacronym{PI}{PI}{Principal Investigator} +\newacronym{TDD}{TDD}{test-driven development} +\newacronym{HIFIS}{HIFIS}{Helmholtz Federated IT Services} +\newacronym{DMP}{DMP}{data management plan} +\newacronym{EU}{EU}{European Union} +\newacronym{UK}{UK}{United Kingdom} +\newacronym{GREENER}{GREENER}{Governance, Responsibility, Estimation, Energy and embodied impacts, New collaborations, Education and Research} diff --git a/002/preamble.sty b/002/preamble.sty new file mode 100644 index 0000000..60336e1 --- /dev/null +++ b/002/preamble.sty @@ -0,0 +1,6 @@ +\usepackage{hyperref} +\usepackage{libertine} +\usepackage{orcidlink} +\usepackage[blocks]{authblk} +\renewcommand\Affilfont{\small} +\newcommand{\geprislink}[1]{\href{https://gepris.dfg.de/gepris/projekt/#1?language=en}{#1}} diff --git a/002/requirements.txt b/002/requirements.txt new file mode 100644 index 0000000..9fb6ae0 --- /dev/null +++ b/002/requirements.txt @@ -0,0 +1,5 @@ +pandoc-fignos +pandoc-eqnos +pandoc-tablenos +pandoc-secnos +PyYAML diff --git a/002/template.py b/002/template.py new file mode 100644 index 0000000..716a424 --- /dev/null +++ b/002/template.py @@ -0,0 +1,100 @@ +""" +Customize the default pandoc template used to generate PDF files. +""" + +import re +import argparse + +parser = argparse.ArgumentParser() +parser.add_argument("file", type=str, help="pandoc template file") +args = parser.parse_args() + +def substitute(content, old_text, new_text): + assert old_text in content + assert content.count(old_text) == 1 + return content.replace(old_text, new_text) + +with open(args.file) as f: + content = f.read() + +# generate XMP data and make document PDF-A compliant +content = re.sub("\n *pdfcreator=\{[^\{\}]+\},?", "\n$if(pdfa-true)$\n$else$\g<0>\n$endif$\n", content) +content = substitute(content, r"\begin{document}", r""" +$if(pdfa-true)$ +\begin{filecontents*}{\jobname.xmpdata} +\Author{$for(authorxmp)$$authorxmp$$sep$\sep $endfor$} +$if(title-meta)$ +\Title{$title-meta$} +$endif$ +$if(lang)$ +\Language{$lang$} +$else$ +\Language{English} +$endif$ +$if(subject)$ +\Subject{$subject$} +$endif$ +$if(keywords)$ +\Keywords{$for(keywords)$$keywords$$sep$\sep $endfor$} +$endif$ +$if(datexmp)$ +\Date{$datexmp$} +$endif$ +\PublicationType{journal} +\end{filecontents*} + +% PDF/A compliance with pdfx, must be loaded last (loads hyperref and xcolor) +\usepackage[a-3u]{pdfx} +$endif$ + +\begin{document}""") + +# include packages that must be included before hyperref +content = substitute(content, +r"""\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}""", +r"""\usepackage[bottom]{footmisc} +\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}""") + +# generate the abstract and keywords list +content = substitute(content, r"""$if(abstract)$ +\begin{abstract} +$abstract$ +\end{abstract} +$endif$""", +r"""$if(abstract)$ +\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center} +$elseif(keywords)$ +\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center} +$endif$ +$if(abstract)$ +\textbf{Abstract}: {$abstract$} +$endif$ + +$if(keywords)$ +\textbf{Keywords}: {$for(keywords)$$keywords$$sep$, $endfor$} +$endif$ +$if(abstract)$ +\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center} +$elseif(keywords)$ +\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center} +$endif$""" +) + +content = substitute(content, +r"\printbibliography$if(biblio-title)$[title=$biblio-title$]$endif$", +r"\printbibliography[heading=bibintoc$if(biblio-title)$,title=$biblio-title$$endif$]" +) + +content = substitute(content, +r""" +\tableofcontents +""", +r""" +$if(toc-baselinestretch)$\renewcommand{\baselinestretch}{$toc-baselinestretch$}\normalsize$endif$ +\tableofcontents +$if(toc-baselinestretch)$\renewcommand{\baselinestretch}{1.0}\normalsize$endif$ +""" +) + +with open(args.file, "w") as f: + f.write(content)