Module for Molecular & Cell Biology
Instructor: Robin Ball
The goal of this module is to provide two 30-minute data science explorations using data from the Allen Brain Atlas API to supplement the 3 hour Lab on Mouse Brain Connectivity. Students will first be introduced to the world of Jupyter Notebooks, Python and statistical analysis (bootstrapping & hypothesis testing). In the first 30 minute exploration, we quantify projection densities between the Subiculum and other brain structures to conduct a hypothesis test on whether a given projection belongs to those of the Primary Visual Area. In the latter exploration, we learn how to calculate and graph gene expression densities across various regions of the brain; students will explore and analyze a gene and brain region of their choosing using skills acquired in this module.
Developers: Daniel Lopez, Elias Saravia, Kayli Jiang, Keiko Kamei
Introduction Notebook adapted from Intro-to-Python-and-Jupyter.ipynb by Keeley Takimoto.
| Notebook | Data File | Data Source | Reason for use |
|---|---|---|---|
| Intro-to-Python-and-Jupyter | primary_auditory_area.csv; math_110_grade_distribution.csv | Allen Brain Atlas API; UC Berkeley Math Department | Introducing Table Manipulation |
| Lab1: Mouse Brain Connectivity | n/a | Allen Brain Atlas API | Explore Structural Mouse Brain Connectivity & Projection |
| Lab2: Gene Expression | convertcsv.csv | Mouse Brain Atlas | Explore Gene Expression Density across Various Structures |