This repository contains and data and scripts for reproducing the results accompanying the manuscript
Author One1, Author Two2, and John P. Barton1,2,#
1 Department of Physics and Astronomy, University of California, Riverside
2 Department of Computational and Systems Biology, University of Pittsburgh School of Medicine
# correspondence to jpbarton@pitt.edu
The preprint is available at INSERT LINK HERE.
Describe the contents of the repository, and which pieces do what. You can use code text to refer to specific files or directories, like this: a_file.ipynb, a_folder/. In this template, the figures.ipynb contains a template Jupyter notebook for reproducing the figures accompanying the paper. Generally, the generated figures should be placed in the figures/ directory.
If the analysis uses data that is maintained by a third party or stored separately (e.g., on Zenodo), then it can be linked to here. If the paper develops a method, then a test script should be included that implements the method, allowing users to verify the results before applying the method to their own data.
In general, local data should be organized in the data/ directory and appropriate sub-folders. This should include raw data that we use (including from simulations) and processed data, which is saved separately.
Significant code should be in the src/ directory. Code that is just used for making figures or minor data processing could be included here in the top-level directory.
Paper drafts, including cover letters, etc., can be placed in the drafts/ directory. This directory also contains a .gitignore file that will make it such that the contents of this directory are not synced with GitHub.
To sync the above folders on GitHub, placeholder files have been placed in the data/, figures/, and src/ directories. These files should be deleted when the template is copied for a project and files appear in each folder.
Here's an example statement about the need for external software to execute any part of the code: Parts of the analysis are implemented in C++11 and the GNU Scientific Library.
This repository is dual licensed as GPL-3.0 (source code) and CC0 1.0 (figures, documentation, and our presentation of the data).