Summer Report for the Vagelos Scholars Program in Molecular Life Science
Report detailing work done in the Greene Lab at the University of Pennsylvania for the Summer of 2017. Sparse matrix implementation of degree-weighted path count (DWPC) over a heterogeneous network of biomedical information. Summer research conducted as part of the Penn Vagelos Scholars Program in Molecular Life Science (MLS).
Continuous manuscripts written collaboratively on GitHub
Manubot Rootstock provides a system for collaboratively writing scholarly manuscripts via GitHub. This project aims to automate publishing. For example, citation and referencing are largely automated. This project originated with the Deep Review, but was moved here in hopes of making a general purpose template for the system.
A rootstock (or rhizome) is "a plant onto which another variety is grafted". This repository plays the role of a botanical trunk. Fork it and a manuscript will grow.
Instructions for using Manubot Rootstock for your own manuscript are still evolving. The recommended approach is to clone this repository, as detailed here.
Repository directories & files
USAGE.md for documentation on how to create or contribute to a manuscript.
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 source activate manubot # Build the manuscript sh build/build.sh # View the manuscript locally at http://localhost:8000/ cd webpage python -m http.server
When you make a pull request, Travis CI will test whether your changes break the build process to generate the formatted manuscript. The build process aims to detect common errors, such as invalid references. If your build fails, see the Travis CI logs for the cause of failure and revise your pull request accordingly.
- HTML manuscript at https://zietzm.github.io/Vagelos2017/
- PDF manuscript at https://zietzm.github.io/Vagelos2017/manuscript.pdf
For continuous integration configuration details, see
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.