How to contribute to Human GEM

Contributions to Human-GEM are very welcome and greatly appreciated! Credit is given to everyone who contributes.

You can contribute in 2 major ways: by creating issues, and by sending pull requests (PRs) with additions, deletions, corrections, etc. to the yml model and/or tsv annotation files. Please follow the following guidelines:

Reporting issues

Report an issue at here, if you notice any of the following:

• Incorrect annotation for any model components.
• Missing feature or field you would like the model to have.
• Bug/weird simulation results.
• Lacking documentation.
• Any type of feedback.

If you are unsure about the issue, consider asking first in our Gitter chat room.

When creating issue or discussion, please make sure:

• You checked that a similar issue does not exist already
• You tested your code (if any) with all requirements for running the model.
• You did your analysis in the main branch of the repository.
• You provide any necessary files/links needed for understanding the issue.
• To reserve enough time for communication and debate, issues and discussions should be kept open for at least one week before closing.
• "We should forget about small efficiencies, say about 97% of the time: premature optimization is the root of all evil."

Feel free to also comment on any of the open issues.

Contributing to the model/annotation

If you want to contribute to the model with some additions or improvements, please always start by raising an issue for asking/describing what you want to achieve. This way, we reduce the risk of duplicated efforts and you may also get suggestions on how to best proceed, e.g. there may be half-finished work in some branch that you could work with. Also, feel free to browse our open issues and our ongoing projects: Anything tagged with "help wanted" is open to whoever wants to implement it.

Here's how to set up Human-GEM to contribute small features or changes. This should work for most curation work.

1. Fork the Human-GEM repository to your local, by clicking on the upper right corner. Then, switch to the develop branch before starting to work in the forked repository.

2. Modify model file Human-GEM.yml and/or annotation files reactions.tsv, metabolites.tsv, and genes.tsv, and commit changes as suggested below in "Semantic commits".

3. Submit a pull request from the develop branch of the forked repository to the develop branch of the original SysBioChalmers/Human-GEM repository. We recommend ticking the box "Allow edits from maintainers" if you wish for us to be able to contribute directly to your branch (speeding-up the reviewing process).

Finally, and for larger features that you want to work on collaboratively, you may consider to first request to join our development team to get write access to the repository so that you can create a branch directly in the main repository (or simply ask the administrator to create a branch for you). Once you have a new branch, you can push your changes directly to the main repository and when finished, submit a pull request from that branch to develop.

Thank you very much for contributing to Human-GEM!