Making Code FAIR: Connecting Software with Publications

As researchers produce valuable software and datasets, appropriate publishing is becoming increasingly important to prevent software and data artifacts from being lost in personal repositories and instead make them citable and accessible in the long-term.

Because of this, there’s a noticeable shift in scholarly publishing. Publishers see software code as vital to research and are working to make it easier to find and keep safe. Linking software to publications ensures availability and enables citation and reuse by enforcing proper documentation and archiving. This trend in publishing was initially described in the Scholarly Infrastructures for Research Software report (EU Commission, 2020).

Dagstuhl manages its own storage for software artifacts, publishing them separately with individual metadata and DOIs. This approach ensures the code is accessible and discoverable, aligning with the broader goal of preserving research software. The Dagstuhl team—Saadet Bozaci, Michael Wagner, and Michael Didas—played a key role in making it happen. The European Commission’s FAIRCORE4EOSC project is funding this effort.

FAIR Supplementary Materials: A Publishers Perspective

Since April 2023, Dagstuhl Publishing has been working on an improved submission process and has expanded both its submission system DSUB and its publication server DROPS to support supplementary material (especially research software) associated with scholarly articles (either contributions to journals or conference proceedings). The updated workflow supports authors, editors, and publishers in preparing related materials for the article and is:

•  Integrated: Easily attach research software to author's paper.
•  Standardized: Metadata follows FAIR principles.
•  Preserved: Archiving with Software Heritage ensures long-term access.

Both DROPS and DSUB are an integral part of Dagstuhl’s mission to support transparency and reproducibility in computer science research. By providing these services, Dagstuhl Publishing ensures the long-term preservation of valuable digital artefacts while promoting Open Science and FAIR practices. 

In the extended workflow for submitting peer-reviewed, camera-ready articles, authors must include related supplementary materials, such as research software. If the software is not yet archived on Software Heritage, authors are encouraged to request archiving. To ensure proper citation, authors should provide the software’s URL and descriptive metadata (CodeMeta standard), including the SWHID. The system provides support with pre-filled metadata forms. Metadata, if already available, is automatically read from the hosting platform, such as GitHub, or other sources, such as citation.cff files, and presented to the author in the form for revision and approval. 

Authors have the option to synchronize contributor details with the published article. The publisher integrates this metadata into the scholarly article during publication preparation for accurate referencing and citation. The publishing team verifies the metadata for completeness and accuracy. This curation process ensures critical metadata, like affiliations and funding details, are accurate and current. The publishing team checks for metadata inconsistencies. If missing, authors are asked to provide the missing information.

Authors can review and make any final adjustments to the updated metadata and reference before publication. This curation process ensures the article and its supplements have high-quality metadata, properly integrated into the publication. After publication, the reference/citation data is also part of the published metadata of the scholarly article. The metadata will be used in the scholarly article. If it hasn’t been published elsewhere, it will also be published on the DROPS publication server. This published metadata will also be transferred to Software Heritage for long-term availability.

How does it work: a step-by-step guide

Once invited, authors can upload their research software as supplementary material linked to their scholarly article. The updated workflow is available for most series and journals of Dagstuhl Publishing including:

• LIPIcs: Leibniz International Proceedings in Informatics,
• OASIcs: Open Access Series in Informatics,
• TGDK: Transactions on Graph Data and Knowledge, and
• LITES: Leibniz Transactions on Embedded Systems

After registering on DSUB, authors gain access to the submission workflow. Dagstuhl Publishing collects all relevant information via a form. The relevant steps are:

1. Providing Metadata: Authors can now submit basic metadata, including a URL, and classify their materials using the DataCite vocabulary (e.g., software, dataset) in the DSUB service. If the materials are hosted in Git or SVN repositories, authors can request long-term preservation in Software Heritage (SWH) through Dagstuhl Publishing.
2. Adding Extended Metadata: Authors can enrich their metadata at any stage of the submission process, such as author names, software descriptions, titles, programming language, and other relevant details. If a GitHub link is provided, the submission form can fetch metadata from the repository automatically. If the author is the same as for the research software, this information can be copied from the main article with a single click.
3. Internal Processing: The Publishing team standardizes and reviews the metadata to ensure all required fields are complete and accurate. For scholarly articles, this includes author affiliations with city and country details. For supplementary materials, at least a URL and proper classification are required.
4. Publication: The supplementary material is published in the Artifacts collection on DROPS, where it receives a DOI for citation purposes. While the metadata is curated the source code itself is not reviewed — only the associated article undergoes a formal peer review.
5. Long-term archiving in Software Heritage: If an author requests preservation during submission, Dagstuhl Publishing archives the software source code in Software Heritage (SWH). This archived version is linked to the DROPS publication, ensuring that the software remains accessible and verifiable over time.

For a detailed overview of the process, refer to Zenodo.

Disclaimer

This contribution has previously been published in two separate articles that appeared on softwarehertitage.org[1] and dagstuhl.de[2].

About Dagstuhl

Dagstuhl has been the publishing arm of the Leibniz Center for Informatics since 1990 and ventured into open-access publishing in 2008. They’re best known for their LIPIcs series, which has proceedings from top computer science conferences. But they also publish reports, manifestos, the LITES journal (embedded systems), TGDK (graphs for data management), and DARTS (evaluated artifacts).

[1] Bozaci, S. (2025): Citable, Discoverable, Preserved: Connecting Software with Publications. https://www.dagstuhl.de/en/institute/news/2025/citable-discoverable-preserved-connecting-software-with-publications

[2] Software Heritage, ed. (2025): Inside Dagstuhl Publishing’s drive to preserve code. https://www.softwareheritage.org/2025/04/16/dagstuhl_softwareheritage_collaboration/