Course Description: Project-based course in which students will use computational notebooks to perform exploratory data analyses and to test hypotheses in large neuroscience datasets, including the differences between unique neuron types, leveraging text mining of the neuroscience literature, and human neuroimaging analyses.
- Write and edit Python code, particularly in Jupyter Notebooks
- Develop hypotheses specific to big data environments in neuroscience
- Design a big data experiment and excavate data from open sources
- Integrate data from multiple datasets to answer a biological question
- In-class work & participation: This is a small seminar, and we will be actively working through materials during lecture. You will need to make up in-class work that you miss.
- Assignments: Weekly take-home coding assignments will support your progression through the course topics and will directly relate to the larger class projects.
- Projects: Includes the project proposal, code, and deliverables.
- The first project will ask you to investigate a specific cell type in the brain, combining information across electrophysiology, gene expression, visual responses, and activity.
- In the second project you’ll choose one brain region in humans and integrate three different datasets of your choosing to address the function of that brain region and identify possible links between genes, circuits, and behavior.
- Final Exam
There is no official textbook for this course. Instead, we’ll be relying on several online resources:
- VanderPlas, Whirlwind Tour of Python
- VanderPlas, Python Data Science Handbook -- this book is available free online or in print.
- Wallisch, Neural Data Science
- Adhikari & DeNero, The Foundations of Data Science
- Software Carpentry, Plotting and Programming in Python
We’ll be working together to create an equitable and inclusive environment of mutual respect, in which we all feel comfortable to share our moments of confusion, ask questions, and challenge our understanding. Everyone should be able to succeed in this course. If you do not feel that is the case please let me know.
If you need accommodations for this course due to a disability, please contact the Office for Students with Disabilities (osd@ucsd.edu) for an Authorization for Accommodation letter. Please speak with me in the first week of class if you intend to apply for accommodations. For more information, visit http://disabilities.ucsd.edu.
So, you won’t benefit if others do your work. Cases of academic dishonesty or cheating will be first handled by me, and then by the Academic Integrity Office. If you become aware of cheating in this class, you can anonymously report it: https://academicintegrity.ucsd.edu/
Request a schedule for a specific quarter by emailing ajuavine@ucsd.edu.
Weeks 1-3: Intro to Data Science, Programming fundamentals, object-oriented programming, and scientific computing packages
Weeks 4-7: Introduction to various data sets, including multiple Allen Institute for Brain Science datasets, Neurosynth, and Human Brain Project data
Weeks 8-9: Additional uses of coding in neuroscience, including dimensionality reduction & signal processing.
Week 10: The future of neural data science & final projects.