Open Source meets Open Science

Software Heritage Archive | STL | 09/12/2025 Open Source meets Open Science By Morane Gruenpeter (Director of Scholarly Ecosystem) Goals ★Introduction: why are we here? ★What is Open Source? ★What is Open Science? ★Good practices for software curation ★Conclusion Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #2/70 s © Inria / Photo M. Magnin Morane Gruenpeter Currently, Director of Scholarly Ecosystem @Software Heritage, Fondation Inria ●2008-2011 B.A in Musique (Harpist) @Rubin Academy ●2012-2015 Licence (B.SC) in Computer Science @CNAM ●2015-2017 Master (M.SC) in Software Engineering (STL) @UPMC ●2017 Internship Software Heritage (SWH) as a Software engineer ●2018-2019 European project EU2020 CROSSMINER ●2020-2022 European project Horizon EU FAIRsFAIR ●2022-2025 European project FAIR-IMPACT ●2022-2025 European project FAIRCORE4EOSC ●2024-2026 CHIST-ERA project SoFAIR ●2025-2027 Sloan funded project OSPO-RADAR Experience ●Software engineering and metadata specialist (Semantic Web) ●Project Manager & product owner ○the deposit component, metadata workflow ○the Software Stories ●Engagement & Operations activities setting up ERP / CRM (communication, community & partnerships) Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #3/70 https://forge.softwareheritage.org/P169 Problem-solving with a strategic plan Build the semantic web of FOSS and promote Software Heritage in citation and metadata workflows 🧭 Why STL? 🧭 Why R&D track? 🧭 Why this internship in 2017? 🧭 Why 9 years, in 4 different roles? Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #4/70 Turn to your neighbor ★Why are you here? ★What is your favorite part in STL / software engineering? Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #5/70 Concepts: establishing shared understanding ❏Digital Commons Share digital ressource ❏FOSS/FLOSS Free Libre Open Source Software ❏Copyleft vs. Non-copyleft Licenses for Open Source / Free software ❏OSPO Open Source Programme Office ❏Forge A platform for collaboration on software development ❏Git a free and open source distributed version control system, widely used ❏MVP Minimum Viable Product ❏PID Persistent Identifier ❏RSE Research Software Engineer ❏SWH Software Heritage: the universal source code archive ❏SWHID SoftWare Hash Identifier ❏CodeMeta Vocabulary for describing Research Software Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #6/70 Goals ★Introduction: why are we here? ★What is Open Source? ★What is Open Science? ★Good practices for software curation ★Conclusion Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #7/70 What is software? Software as a concept ●project or entity ●the community around the project ●the software idea / algorithms / solutions Not a digital artifact Software artifacts ●Executables ○For multiple environments ●Source code A very large collection of digital artifacts Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #8/70 The Knowledge is in the Source Code “Programs must be written for people to read, and only incidentally for machines to execute.” Harold Abelson, 1985 Structure and Interpretation of Computer Programs (1st ed.), “Source code provides a view into the mind of the designer.” Len Shustek, 2006 Computer History Museum https://en.wikipedia.org/wiki/The_Human_Condition_%28 Magritte%29 René Magritte, 1933, The Human Condition https://en.wikipedia.org/wiki/Binary_file Is this for humans? Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #9/70 Version control system (VCS) history •records changes made to a (set of) source code file (s) •allows to operate on versions: diff/merge/fork/recover etc. •essential tool for software development Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #16/70 git status git add [file] git diff [file] git diff --staged [file] git checkout -- [file] git commit - The commit must have a message! Git day to day: find a cheat sheet and use it! https://sst.jguni.in/understanding-git-a-beginners-guide-t o-version-control-for-devops/index.html Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #17/70 https://stackademic.com/blog/git-workflow-best-practices-for-a-smooth-and-efficient-development-process https://gist.github.com/thakichowdhury/b4ac923f2c451bed9716bf01d2b78c48#submitting-a-feature-bugfix Git workflow: learn a team language Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #18/70 https://chris.beams.io/git-commit Code commits is a story Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #19/70 Do you put your code on a Forge? Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #20/70 Are you curating your code and your profile? https://docs.github.com/fr/account-and-profile/setting-up-and-managing-your-github-profile/customizing-your-profile/about-your-profile Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #21/70 Source code is fragile! Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #22/70 Source code can be destroyed 1.4 million projects Source: TechCrunch Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #23/70 Archiving the web - using the wayback machine Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #24/70 Collect, preserve and share all software source code Preserving our heritage, enabling better software and better science for all Snapshot:Dec. 4th 2025 https://archive.softwareheritage.org/ Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #25/70 Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #32/70 Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #33/70 Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #34/70 Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #35/70 Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #36/70 Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #37/70 Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #38/70 Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #39/70 Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #40/70 The complete workflow Full development history permanently archived in a uniform data model Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #41/70 Software is a pillar of Open Science Research Software ➔created ○during the research process ○for a research purpose Software in research ➔used for research FAIR4RS output: Gruenpeter et al. Defining Research Software: a controversial discussion (Version 1). Zenodo. https://doi.org/10.5281/zenodo.5504016 Software has multiple facets: -a tool -a research outcome or result -the object of research https://doi.org/10.1038/d41586-025-03196-0 Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #48/70 Guy Courbebaisse, Bernd Flemisch, Kay Graf, Uwe Konrad, Jason Maassen, & Raphael Ritz. (2023). Research Software Lifecycle. Zenodo. https://doi.org/10.5281/zenodo.8324828 The Research Software lifecycle Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #49/70 What’s the the Software Collapse? Konrad Hinsen. Dealing With Software Collapse. Computing in Science and Engineering, 2019, 21 (3), pp.104-108. ⟨10.1109/MCSE.2019.2900945⟩. ⟨hal-02117588⟩ Research Software is a thin layer on top of the global software stack https://xkcd.com/2347/ 🧭 The software stack: More than Research Can be preserved in a: - Scholarly Infrastructure - Universal Source Code Archive Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #50/70 What is at stake? Archive ➔make sure we can access to retrieve the software (reproducibility) Reference ➔make sure we can identify the software artifacts (reproducibility) Cite (for credit) = Recognition for Researchers ➔make it rewarding to create software by giving credit to authors (evaluation!) Describe ➔make it easy to discover the software projects (visibility) Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #51/70 The Open Source Stakeholders in Academia A few personas Sofia: Academic OSPO Manager Christine: Academic Library Director Leo: Infrastructure Technical Manager Jitin: Researcher Mostafa: Lead of Research Unit Elena: Research Funder Liam: Publisher (C. Dillon, 2025) Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #52/70 The Scholarly Ecosystem: Complex and fragmented SIRS report Short term recommendations • Strengthening interactions between • Aggregators, publishers , scholarly repositories, and SWH • Metadata standards & tools • Generalizing the use of PIDs (extrinsic & intrinsic) => SWHID SIRS report: European Commission, Directorate-General for Research and Innovation, Scholarly infrastructures for research software : report from the EOSC Executive Board Working Group (WG) Architecture Task Force (TF) SIRS, Publications Office, 2020, https://data.europa.eu/doi/10.2777/28598 ISO/IEC 18670:2025 Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #53/70 The project has three main objectives: 1. Developing a Software Assets Dashboard service: simplified workflows for OSPOs 2. Adapt the CodeMeta standard to address the specific requirements of OSPOs 3. Create a dedicated Open Science helpdesk, supporting OSPO adoption and effective use of the portal. 💡 What: A layer on top the universal archive OSPO-RADAR Elias Chbeir source Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #54/70 Minimum Viable Product: features and workflows overviews The MVP delivers the minimal end-to-end path, including: • Secure account/role management; •Collection population • Batch import • Signal sw repo (by Researcher without account - using magic links) • Search/add •Management: Internal view/filter/curate; • A public front-shop that can be injected in institutional website through an API. 💡A SW Assets Dashboard MVP Definition of MVP: the minimum viable product is that version of a new product which allows a team to collect the maximum amount of validated learning about customers with the least effort. Eric Ries https://www.startuplessonslearned.com/2009/08/minimum-viable-product-guide.html Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #55/70 “If I had asked people what they wanted, they would have said faster horses.” Henry Ford Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #56/70 Goals ★Introduction: why are we here? ★What is Open Source? ★What is Open Science? ★Good practices for software curation ★Conclusion Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #57/70 Save any your code now! https://save.softwareheritage.org/ Save code now Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #64/70 Reference and even cite software in Software Heritage Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #65/70 ★🏆Master your craft ★📑 Describe your code with metadata README, LICENSE, AUTHORS, codemeta.json ★🏛 Archive your code! https://save.softwareheritage.org/ ★🔗 Reference your code ★󰳐 🔍Cite your code - and get long lasting recognition Wrap up Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #66/70 Thank you for your attention [email protected] https://www.softwareheritage.org/ Time for your questions… Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #67/70 Links to be shared with your users: 🔑 Guidelines for researchers: https://www.softwareheritage.org/howto-archive-and-reference-your-code/ 🏷 Describe a software (intrinsic metadata made easy) : https://codemeta.github.io/codemeta-generator/ ❓ The FAQ: https://www.softwareheritage.org/faq/ 🗺 The SWH guided tour: https://archive.softwareheritage.org/?guided_tour=0&guided_tour_next=https://a rchive.softwareheritage.org/ 🎯 "Open Science tutorial: source code deposit" (how to build services upon SWH): https://youtube.com/playlist?list=PLD2VqrZz2-u3bOWtoCoBIh5Flt6iYXsq3 👋 “Book” a SWH ambassador: https://www.softwareheritage.org/ambassadors/ Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #68/70 🧲 Let’s keep in touch https://twitter.com/SWHeritage https://twitter.com/rdicosmo https://twitter.com/moraneottilia https://www.linkedin.com/company/swheritage/ https://sympa.inria.fr/sympa/info/swh-science https://www.softwareheritage.org/newsletter/ https://www.softwareheritage.org/blog Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #69/70 🧰 Implementing new services at the library: the SWH documentation treasure island The Web API: https://archive.softwareheritage.org/api/ API terms of use: https://www.softwareheritage.org/legal/api-terms-of-use/ API endpoints: https://archive.softwareheritage.org/api/1/ The technical roadmap: https://docs.softwareheritage.org/devel/roadmap/roadmap-2023.html#road map-current SWH legacy software services: https://www.softwareheritage.org/swhap/ Software Heritage@STL M1 | M.Gruenpeter | Open Science x Open Source | 09/12/2025 | CC-BY 4.0 | #70/70