Please see USAGE.md for information on how to use the Manubot for writing the manuscript.
Below you'll find information on the contribution workflow for the OpenPBTA manuscript.
We use issues for discussion of papers, section outlines, and other structural components of the paper.
Contributions to the analysis repository operate on a pull request model. We expect participants to actively review pull requests, with a particular focus on pull requests that include analyses within their areas of expertise.
The ultimate goal of this is effort is to describe the results from OpenPBTA-analysis in this manuscript. We will use the ICMJE Guidelines. We expect authors to contribute to the overall design of the project by participating in issues and to contribute to the text by contributing sections and/or revisions to sections through pull requests in this repository. It is important to note that, for authorship, these should be substantial intellectual contributions.
All pull requests will undergo peer review. Participants in this project should review pull requests, which can be done using GitHub's review interface. They should suggest modifications or, potentially, directly edit the pull request to make suggested changes. As a reviewer, it's helpful to note the type of review you performed: did you look over the source code, did you run the source code, did you look at and interpret the results or a combination of these?
Before a repository maintainer merges a pull request, there must be at least one affirmative review. If there is any unaddressed criticism or disapproval, a repository maintainer will determine how to proceed and may wait for additional feedback.