We share all code and additional data for all publications from the lab. To make this a bit easier, we have a template repository to get you started. The template contains:

• pre-filled README with general instructions and explanations
• the open source license from the lab policies
• a code of conduct
• customized templates for bug reports and feature requests
• automated documentation builder using Material for Mkdocs through Github Actions

The general steps for any data-based research project are the following:

Login to Github and go to our Lab Organization. Click on the green New Button to create a new repository.

Choose the template dienerlab/template and fill out all other parts. For a repository name we recommend something in the form of YEAR-my-project (for instance 2025-fancy-probiotic) because that makes it easier to screen how old a repository is.

Make sure it is private at this stage. After this create the repository. You can now clone it locally and add files etc. Some tools that can help with that (any one will do the job):

• Github Desktop
• Github CLI
• VS Code
• barebone git

Make sure to replace all instances of template with your project name with a global search and replace.

As soon as the preprint has been deposited you can make the repository public. For this go to your project page like https://github.com/dienerlab/2025-fancy-probiotic and make it public by:

1. Clicking on Settings
2. Scrolling down to the red area called Danger Zone
3. Click on Change visibility > Change to public and follow the prompts

Add the link to the Data and Code Availability of the paper and, if it exists, the author checklist provided by the journal.

All scripts, notebooks, and additional metadata required to reproduce the analyses and figures in this manuscript can be found at https://github.com/dienerlab/2025-fancy-probiotics.

If at all possible check the repository in regular intervals for reported issues or discussion topics and engage with the community. Keeping the repository functional will increase the usability for the community and probably also the number of citations.