PennLINC Project Setup Guide

Each project at PennLINC has several key elements to facilitate collaboration and ensure reproducbility. For clarity in naming, all elements should be named similarly– often Lastname_ProjectName with CamelCasing, where “Lastname” is the last name of the first author / trainee leading the project. Links to much of the relevant software can be found in the lab Software and Environments page.

GitHub repository

All code, from the beginning of the project, should be in a GitHub repository. This is a prerequisite for reproducible neuroscience – please start your project out on the right foot! These repos should reside in the PennLINC org, not your personal github.

Use the Template!

There is a GitHub repository template that you should use to create your project repository:

Project documentation on GitHub Pages

Careful tracking of your project is essential. While well-commented code, reproducible analytic notebooks, and an archived Slack channel are very helpful, an “overview” website also helps a lot to document how the different pieces of code fit together. This can be easily made using markdown and GitHub Pages (like this one). See the project docs page for how to do this with your project’s GitHub repository.


Your project website is very important! It is what your replication buddy will use at pre-defined checkpoints for replicating your code; see the project reproducibility guide for more info.

Slack channel

All projects in the lab are collaborative, and furthermore form a knowledge and code base for other subsequent projects. A lot of valuable knowledge (esp re: troubleshooting) tends to be captured in correspondence. As such, it is critical for the lab that this knowledge is not “locked away” in inaccessible repositories like private email inboxes or direct message channels on slack. As such nearly all project discussion should occur in a project specific slack channel; this will be created (by Ted) when the project is initiated. Please try to avoid using direct message channels on slack for project communication.

Ted is a slack admin and can add you to the “BBL” slack, which encompasses all the labs in LiBI and the Psychosis and Development Section; PennLINC is a member.

The main execption to this are documents (e.g., manuscripts) that need review; please send these directly to Ted via email. See also the note on Communication and Collaboration.

Zotero library

While some projects can be done locally on your laptop, many require more computing resources. In general, we now reccomend projects use the PMACS LPC; see the PMACS pages for details. However, some projects may be best served by using the computational resources of CUBIC; see the CUBIC pages for more details. Regardless, each project should use a common directory structure to ensure reproducibility.