Submit a software paper to JOSS (Journal of Open Source Software)

[AlexisJanin]

Why

JOSS is the standard peer-reviewed venue for research software. A JOSS paper gives ClinicalScope a proper academic citation (DOI, indexed by Google Scholar / Crossref) that clinical and ML researchers can reference — distinct from the software deposit on Zenodo (#46).

The review process is light: it checks software quality (docs, tests, license), not scientific novelty. Typical turnaround is 4–8 weeks.

Blocked by

• Choose and add a LICENSE file #38 — an OSI-approved LICENSE file is required by JOSS
• Deposit on Zenodo to obtain a citable DOI #46 — Zenodo DOI should exist before submission (JOSS references it)

What JOSS requires

Artifact	Description
paper.md	~1 000-word Markdown paper at repo root
paper.bib	BibTeX references for the paper
LICENSE	OSI-approved (MIT / Apache 2.0 / CeCILL-B)
Tests	Automated test suite — already present ✓
Documentation	User-facing docs — already present ✓

paper.md outline

# Summary
One paragraph: what ClinicalScope does and why it matters.

# Statement of Need
What gap does it fill? Who is the target user?
Distinguish from existing tools (e.g. wfdb, MNE, LabChart).

# Functionality
Key features: multi-source loading, annotation, Python API, inspection view.

# Acknowledgements
Institution, funding sources if any.

# References

Steps

1. Write paper.md + paper.bib (see outline above)
2. Preview locally: docker run --rm -it -v "$PWD":/data openjournals/joss-publishing-tools
3. Submit at https://joss.theoj.org/papers/new
4. Once accepted: add preferred-citation block to CITATION.cff

Acceptance Criteria

• paper.md and paper.bib committed at repo root
• Paper renders without errors with the JOSS Docker tool
• Submission opened at joss.theoj.org
• After acceptance: preferred-citation block added to CITATION.cff

[AlexisJanin]

The repo needs to be public for at least 6 months, have research paper associated, more tests,... this is not ready at this day

19/05/2026

[kernelpanic888]

Hi,

I found this issue and I think I can help with a small, bounded cleanup.

My fit is research package review, documentation, README/CITATION/release
readiness, LaTeX/Markdown/PDF cleanup, and reproducible build notes.

I can start with a concise public review note or a small PR so maintainers can
judge the value before anything larger.

If useful, I can prepare a short Research Package Passport: structure, claim
boundary, sources, risks, readiness, and next steps.

Best,
Aleksey

[AlexisJanin]

Hi Aleksey, thanks for the offer and for taking the time to look at the project.

As noted above, a JOSS submission is on hold until ClinicalScope meets the prerequisites (public for 6+ months, an associated research paper, and broader test coverage), so there's nothing actionable on this front right now. We're keeping contributions in-house for the moment, but I appreciate you reaching out.

Best,
Alexis