Permanent, citable, technically rigorous publications documenting Synaptic Four's software, infrastructure, and reference implementations in bioinformatics, federated data systems, FAIR data, genomics, multi-omics, GA4GH standards, and privacy-preserving research platforms.
This repository is the canonical source for all Synaptic Four Technical Reports (SF-TR). It is designed for long-term maintenance, version control, automated rendering, DOI archival via Zenodo, and eventual adaptation to conference and journal formats.
Discovery: Published reports are listed at synapticfour.com/publications. This repository holds source, build tooling, and contributor documentation.
# Install Quarto: https://quarto.org/docs/get-started/
quarto --version
# Copy the template for a new report
cp -r templates/SF-TR-YYYY-NNN-template reports/SF-TR-2026-001
# Edit metadata and content in reports/SF-TR-2026-001/paper.qmd
quarto render reports/SF-TR-2026-001/paper.qmd
# Outputs appear in reports/SF-TR-2026-001/_output/technical-reports/
├── README.md # This file
├── CITATION.cff # Repository-level citation metadata
├── _quarto.yml # Quarto project configuration
├── .github/workflows/ # CI: render HTML and PDF
├── templates/
│ └── SF-TR-YYYY-NNN-template/ # Reusable report scaffold
├── reports/ # Published and in-progress reports
│ └── SF-TR-YYYY-NNN/ # One directory per report
├── figures/ # Shared figures (report-specific figures live in each report)
├── csl/ # Citation Style Language files
├── publications-index/ # Machine-readable catalogue of all reports
└── docs/ # Process, strategy, and contributor documentation
Every report receives a permanent identifier:
SF-TR-YYYY-NNN
| Component | Meaning |
|---|---|
SF-TR |
Synaptic Four Technical Report |
YYYY |
Year of initial publication |
NNN |
Three-digit sequence within that year (001–999) |
Examples: SF-TR-2026-001, SF-TR-2026-002, SF-TR-2027-001
See docs/numbering.md for allocation rules and versioning conventions.
| Document | Description |
|---|---|
| docs/workflow.md | End-to-end workflow: writing, releasing, DOI, website, versioning |
| docs/publication-strategy.md | Overall publication philosophy and goals |
| docs/website-publishing.md | Canonical workflow for synapticfour.com integration |
| docs/zenodo-integration.md | Zenodo DOI minting and GitHub integration |
| docs/citation-guide.md | How to cite reports; BibTeX examples |
| docs/publication-categories.md | Report type taxonomy and when to use each |
| docs/future-reports.md | Candidate topics (no fixed schedule) |
| docs/journal-conference-roadmap.md | How reports may evolve into formal publications |
| docs/contributing.md | Contributor guidelines |
| publications-index/README.md | Report catalogue and index format |
- Write — Author in Quarto/Markdown under
reports/SF-TR-YYYY-NNN/. - Review — Internal technical review; update
publications-index/. - Release — Create a GitHub Release tagged
SF-TR-YYYY-NNN-vX.Y.Z. - Archive — Zenodo mints a versioned DOI from the release (see docs/zenodo-integration.md).
- Publish — Add HTML/PDF and metadata to synapticfour.com publications hub.
- Maintain — Issue revised versions with new release tags; prior DOI versions remain archived.
| Tool | Role |
|---|---|
| Quarto | Authoring and rendering (HTML, PDF) |
| Markdown | Primary authoring format |
| BibTeX | Bibliography management |
| GitHub Actions | Automated rendering on push and release |
| GitHub Releases | Versioned distribution |
| Zenodo | Long-term DOI archival |
To cite this publication series repository:
@misc{synapticfour_technical_reports,
author = {{Synaptic Four}},
title = {Synaptic Four Technical Report Series},
year = {2026},
publisher = {GitHub},
howpublished = {\url{https://github.com/SynapticFour/technical-reports}},
note = {Technical report repository}
}See CITATION.cff and docs/citation-guide.md for per-report citation formats.
Report content is licensed individually; see each report's paper.qmd front matter. Repository infrastructure defaults to CC BY 4.0 unless otherwise stated.
Questions about the technical report series: contact@synapticfour.com