BioHackrXiv Publication Template

Minimal example of a BioHackrXiv publication that can be generated with the Preview Service.

Step 1: Clone this Template Repository

This repository is a template repository. This means that you can hit the green "Use this template" button (after logging in) to use it as a template to start a new BioHackrXiv Publication:

Step 2: Configuring the Markdown

The publication Markdown is found in the paper/paper.md file. At the top you can edit the YAML code with metadata. It is important to get this part correct, because otherwise the PDF generation will fail. The metadata looks like this:

title: 'BioHackEU22 Report for Project 26: Shedding the light on unknown chemical substances'
title_short: 'BioHackEU22 #26: unknown chemical substances'
tags:
  - cheminformatics
  - PubChem
  - unknown chemical substances
authors:
  - name: Egon Willighagen
    orcid: 0000-0001-7542-0286
    affiliation: 1
affiliations:
  - name: Dept of Bioinformatics - BiGCaT, NUTRIM, FHML, Maastricht University, Maastricht, NL
    index: 1
date: 7 November 2022
cito-bibliography: paper.bib
event: BH22EU
biohackathon_name: "BioHackathon Europe 2022"
biohackathon_url:   "https://biohackathon-europe.org/"
biohackathon_location: "Paris, France, 2022"
group: Unknown chemical substances group
# URL to project git repo --- should contain the actual paper.md:
git_url: https://github.com/biohackrxiv/publication-template
# This is the short authors description that is used at the
# bottom of the generated paper (typically the first two authors):
authors_short: Egon Willighagen \emph{et al.}

Which metadata to update?

To change

The following fields should be changed:

• title
• title_short
• tags
• authors (name and optionally their ORCID identifier)
• affiliations
• date
• group
• authors_short

Particularly important to update is the following field, which should point to your clone of the template, instead of the template itself:

• git_url: https://github.com/biohackrxiv/publication-template

Only update for other BioHackathons

The following fields should only be changed if you are not writing for the BioHackathon Europe 2022:

• event: BH22EU
• biohackathon_name: "BioHackathon Europe 2022"
• biohackathon_url: "https://biohackathon-europe.org/"
• biohackathon_location: "Paris, France, 2022"

Step 3: Writing the article

A full Markdown example is given in paper/paper.md. This includes instructions how to include figures, tables, and annotate citations with the Citation Typing Ontology.

Step 4: Previewing the paper as PDF

This repository can be converted into a preview PDF with BioHackrXiv Preview Server. The preview website asks for the link to your repository and will automatically find the paper.md and create an PDF.