Write and Submit a BioHackrXiv Preprint

BioHackrXiv preprints are written in Markdown and converted to PDF. Follow the steps below to write, preview, and submit your paper.

Prerequisites

  • Your event must be registered with BioHackrXiv. Check the Meetings page to see if your event is listed. If not, ask your event organizer to register it.

Step 1: Create your paper repository

  1. Go to the publication-template on GitHub
  2. Click “Use this template” → “Create a new repository”
  3. Name your repository (e.g., biohackeu25-paper-projectname)

Step 2: Write your paper

Edit paper/paper.md in your repository. The template includes detailed comments explaining each section.

Required YAML metadata

Your paper must include the following fields in the YAML front matter:

---
title: "Your Paper Title"
title_short: "Short Title \\emph{et al.}"
tags:
  - tag1
  - tag2
authors:
  - name: First Author
    affiliation: 1
    orcid: 0000-0000-0000-0000
  - name: Second Author
    affiliation: 2
affiliations:
  - name: First Affiliation
    index: 1
  - name: Second Affiliation
    index: 2
date: 1 January 2026
cito-bibliography: paper.bib
event: BH25EU
biohackathon_name: "BioHackathon Europe 2025"
biohackathon_url: "https://biohackathon-europe.org/"
biohackathon_location: "Berlin, Germany, 2025"
group: "Project 1"
git_url: https://github.com/yourusername/your-paper-repo
authors_short: "First Author \\emph{et al.}"
---

Tip: Find the correct values for event, biohackathon_name, biohackathon_url, and biohackathon_location on your event’s page at the Meetings page. Each event page shows the exact YAML snippet to use.

References

Add your references to paper/paper.bib in BibTeX format. Cite them in your text using [@citationkey].

BioHackrXiv supports CiTO (Citation Typing Ontology) annotations. You can specify the type of citation:

[@usesMethodIn:citationkey]
[@extends:citationkey]
[@citesAsAuthority:citationkey]

Optional metadata

  • ORCID: Add orcid field for each author
  • ROR: Add ror field for each affiliation
  • CRediT roles: Add role field for each author (e.g., “Conceptualization, Writing – original draft”)

Step 3: Preview your PDF

You have two options:

Push your changes to the main branch of your repository. GitHub Actions will automatically build the PDF.

  1. Go to the Actions tab of your repository
  2. Click the latest workflow run
  3. Download the PDF from the Artifacts section

Option B: Preview server

Visit preview.biohackrxiv.org and either:

  • Paste your repository URL, or
  • Upload a ZIP file containing your paper.md and paper.bib

Step 4: Submit to BioHackrXiv

Once your PDF is ready, submit it through the BioHackrXiv submission portal on OSF.

Questions?