Open and Reproducible Neuroscience: Rough course outline

Schedule

Day 1	08:30	The layers of computing	Where, exactly, is my data? Where should it be? Where is the computer analyzing my data? Can I make it go faster? How do all of these places relate to each other? What is the shell and why do I care? What is python? What is IPython? What is Juypter? What are the tools we’ll be using in the course?
	09:00	Variables and Assignment	How can I store data in programs?
	09:20	Data Types and Type Conversion	What kinds of data do programs store? How can I convert one type to another?
	09:40	Built-in Functions and Help	How can I use built-in functions? How can I find out what they do? What kind of errors can occur in programs?
	10:05	Morning Coffee	Break
	10:20	Lists	How can I store multiple values?
	10:45	Iteration in Python	How can I make a program do many things?
	11:10	Introduction to the data	Where can I get neuroimaging data What is FAIR data
	11:35	Working with the command history and script-files	How can I save and edit my previous input commands conveniently?
	12:00	Open Science	Why the push for open science?
	12:30	Finish
Day 2	08:30	Libraries and pathlib	How can I use software that other people have written? How can I find out what that software does?
	09:00	Introduction to Version Control and Git	What is version control and why should I use it? How do I get set up to use Git? Where does Git store information?
	09:30	Versioning edits with Git	How do I record changes in Git? How do I record notes about what changes I made and why?
	10:00	Debugging	How can I debug my program?
	10:10	Conditionals	How can programs do different things for different data?
	10:30	Modular programming	How can I create my own functions?
	11:00	Keeping track of changes with Git	How can I identify old versions of files? How do I review my changes? How can I recover old versions of files?
	11:30	Pandas
	12:30	Finish
Day 3	08:30	Plotting with Seaborn
	09:00	Converting data to the BIDS directory structure
	09:30	Collaboration with Git and GitHub	How do I share my changes with others on the web? How can I use version control to collaborate with other people? What do I do when my changes conflict with someone else’s?
	10:30	Coffee	Break
	10:45	How to share neuroimaging data
	11:45	How to not fool yourself
	12:15	Finish
Day 4	08:30	Containers	What is a software container? What’s Docker? What’s Singularity? And what is each good for? How do I run software in a container? How do I build a container? What are some best practices to ensure reproducibility and ease of use? How do I use containers that are publicly available on Docker Hub and Singularity Hub? Where can I go to learn more?
	09:30	Standardization in Neuroimaging
	10:30	Coffee	Break
	10:45	Study pre-registration
	11:30	Pre-print servers
	11:45	Wrap-up
	12:30	Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.