Project Rephetio Manuscript Source
This repository contains the manuscript for Project Rephetio, an open project to repurpose drugs. The formal title of this study is Systematic integration of biomedical knowledge prioritizes drugs for repurposing. The manuscript is also available on Thinklab (as a project report), bioRxiv (as a preprint), and eLife (as a research article). The manuscript can be cited as:
Systematic integration of biomedical knowledge prioritizes drugs for repurposing
Daniel Scott Himmelstein, Antoine Lizee, Christine Hessler, Leo Brueggeman, Sabrina L Chen, Dexter Hadley, Ari Green, Pouya Khankhanian, Sergio E Baranzini
eLife (2017-09-22) https://doi.org/cdfk
DOI: 10.7554/elife.26726 · PMID: 28936969 · PMCID: PMC5640425
The fully-formatted author response to peer review from eLife is available in
Manubot is a system for writing scholarly manuscripts via GitHub. Manubot automates citations and references, versions manuscripts using git, and enables collaborative writing via GitHub.
Repository directories & files
The directories are as follows:
contentcontains the manuscript source, which includes markdown files as well as inputs for citations and references.
outputcontains the outputs (generated files) from the manubot including the resulting manuscripts. You should not edit these files manually, because they will get overwritten.
webpageis a directory meant to be rendered as a static webpage for viewing the HTML manuscript.
buildcontains commands and tools for building the manuscript.
cicontains files necessary for deployment via continuous integration. For the CI configuration, see
# Activate the manubot conda environment (assumes conda version >= 4.4) conda activate manubot # Build the manuscript, saving outputs to the output directory sh build/build.sh # At this point, the HTML & PDF outputs will have been created. The remaining # commands are for serving the webpage to view the HTML manuscript locally. # Configure the webpage directory python build/webpage.py # View the manuscript locally at http://localhost:8000/ cd webpage python -m http.server
Sometimes it's helpful to monitor the content directory and automatically rebuild the manuscript when a change is detected.
The following command, while running, will trigger both the
webpage.py scripts upon content changes:
Whenever a pull request is opened, Travis CI will test whether the changes break the build process to generate a formatted manuscript. The build process aims to detect common errors, such as invalid citations. If your pull request build fails, see the Travis CI logs for the cause of failure and revise your pull request accordingly.
When a commit to the
master branch occurs (for example, when a pull request is merged), Travis CI builds the manuscript and writes the results to the
gh-pages branch uses GitHub Pages to host the following URLs:
- HTML manuscript at https://dhimmel.github.io/rephetio-manuscript/
- PDF manuscript at https://dhimmel.github.io/rephetio-manuscript/manuscript.pdf
For continuous integration configuration details, see
Except when noted otherwise, the entirety of this repository is licensed under a CC BY 4.0 License (
LICENSE.md), which allows reuse with attribution.
Please attribute by linking to https://github.com/dhimmel/rephetio-manuscript.
Since CC BY is not ideal for code and data, certain repository components are also released under the CC0 1.0 public domain dedication (
All files matched by the following glob patterns are dual licensed under CC BY 4.0 and CC0 1.0:
All other files are only available under CC BY 4.0, including:
Please open an issue for any question related to licensing.