This repo hosts a work-in-progress list of drug candidates for SARS-CoV-2 (COVID-19). Most information comes from literature reviews and preprints.

Drug candidates are not clinically validated. Do not attempt to self-medicate based on this information.

There are two steps that can be done locally: updating the data, and building the website. These are independent, so you can skip one or the other depending on your needs. For instance, building the website can be skipped by pushing the data to github.

The first step is to check out the repository from git:

git clone [email protected]:paulscherrerinstitute/covid-drugs.git

Updating the data uses bash and python scripts. Easiest is to use conda to set up the python environment:

conda env create -f environment.yml

Then activate:

conda activate covid-drugs

Currently data is drawn from a google sheet. To update the website to match the spreadsheet:

1. Activate your environment: conda activate covid-drugs
2. Run scripts/update_data.sh
3. (Optional) If major changes such as renaming columns occurred, run jekyll locally (see below) to ensure there are no errors

The update script is written as a jupyter notebook using the py:percent syntax. The jupytext extension will be installed by conda in order to properly edit and execute this format. If you use jupyter elsewhere, you may have to specify your kernel to the script:

$ jupyter kernelspec list
Available kernels:
  python3    /usr/local/miniconda3/envs/covid-drugs/share/jupyter/kernels/python3
$ scripts/update_data.sh python3

If no major changes are expected and you don't feel the need to rebuild the website, just commit the updated data to github.

git add _data
git commit -m "Update data"
git push

Pushing changes to github automatically triggers the site to build. Building locally requires ruby 2.5 and bundler. To install:

gem install bundler jekyll
bundle

To run a local webserver:

bundle exec jekyll serve

Site is licensed CC-0.

If you use the data, please cite the original references.