Skip to content

elixir-europe/intoxicom-workshop-report-template

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

4 Commits
 
 
 
 
 
 

Repository files navigation

BioHackrXiv Template for INTOXICOM Workshop Reports

Minimal example of a BioHackrXiv publication that can be generated with the Preview Service for an INTOXICOM Workshop Report. Each of the workshops will write one report.

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:

Screenshot of the green "Use this template" button.

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: 'INTOXICOM Workshop Report: Shedding the light on unknown chemical substances'
title_short: 'INTOXIOM #1: unknown chemical substances'
tags:
  - toxicology
  - PubChem
  - unknown chemical substances
authors:
  - name: Marvin Martens
    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: INTOXICOM
biohackathon_name: "INTOXICOM Workshops"
biohackathon_url:   "https://elixir-europe.org/internal-projects/commissioned-services/integrating-toxicology-community"
biohackathon_location: "Basel, Switserland, 2024"
group: Workshop 1
# 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: Martens \emph{et al.}

Which metadata to update?

To change

The following fields should be changed:

  • title
  • title_short
  • tags
  • authors
  • 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:

Only update for other BioHackathons

The following fields should only be changed if you are not writing for the INTOXICOM Workshops:

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.

About

INTOXICOM Workshop Report Template

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages