Open Science in Undergraduate Education Workshop (2025)

Tutorial notebooks and slides for the Allen Institute Open Science in Undergraduate Education Workshop workshop "Integrating programming into biology and neuroscience courses."

There are three different ways you can interact with these materials from your browser:

1. We will predominantly be working on Google Colab:

2. But Binder is another option: Binder

3. And a third option (necessary for working with NWB datasets) is cloning this repo in the Dandihub.

There are several ways to implement these notebooks in your class:

• Run notebooks via Binder or Colab, as demonstrated above
• Set up a JupyterHub for your course or university (e.g., the UCSD DataHub)
• Ask students to download the VS Code or the Anaconda Distribution of Python, which includes Jupyter Notebook, many useful packages and more, to run these notebooks locally

Teaching resources related to this workshop:

• Various Lesson Plans with the Allen Institute for Brain Science resources
• Webinar on Allen Cell Types Data
• Neurobiology Lab JupyterBook
• Introduction to Python for Biologists Course Materials

More advanced materials for teaching neural data science

• Neural Data Science Course Materials
• Neurodata Without Borders for Education
• OpenScope Databook
• Sample Dandi Notebooks

Questions? Get in touch.

Email ajuavine[at]ucsd.edu