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:

```yaml title: 'BioHackEU22 Report for Project 26: Shedding the light on unknown chemical substances' titleshort: '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 biohackathonname: "BioHackathon Europe 2022" biohackathonurl: "https://biohackathon-europe.org/" biohackathonlocation: "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.