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
    ror: 02jz4aj89
    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.

Troubleshooting

The first page is badly formatted

Sometimes the list of authors plus affiliations runs over the page. We are working on a fix, but in the mean time you can try to shorten the affiliations. If that does not work move the affiliations into a repo and put the affiliations on a web page and use something like

affiliations:
  - name: For remaining affiliations see \url{https://github.com/project/etc} \vspace{0.2in}
    index: \*