https://github.com/jervenbolleman/swat4hcls-2024-beyond-the-void

SWAT4HCLS beyond the VoID hackathon project report
https://github.com/jervenbolleman/swat4hcls-2024-beyond-the-void

Last synced: 19 days ago
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SWAT4HCLS beyond the VoID hackathon project report

• Host: GitHub
• URL: https://github.com/jervenbolleman/swat4hcls-2024-beyond-the-void
• Owner: JervenBolleman
• License: cc0-1.0
• Created: 2024-02-29T08:50:43.000Z (10 months ago)
• Default Branch: main
• Last Pushed: 2024-02-29T08:50:45.000Z (10 months ago)
• Last Synced: 2024-05-18T07:42:17.174Z (8 months ago)
• Language: TeX
• Size: 28.3 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# BioHackrXiv Publication Template

Minimal example of a [BioHackrXiv](https://biohackrxiv.org/) publication that can be generated with the

[Preview Service](http://preview.biohackrxiv.org/).

## 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.](paper/use-this-template.png)

## 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'

title_short: 'BioHackEU22 #26: unknown chemical substances'

tags:

  - cheminformatics

  - PubChem

  - unknown chemical substances

authors:

  - name: Egon Willighagen

    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

* 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](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](http://preview.biohackrxiv.org/).

The preview website asks for the link to your repository and will automatically find the `paper.md` and create an PDF.