This lecture focuses on where and how Jupyter notebooks can be used most effectively for education.

JupyterHub is a simple, highly extensible, multi-user system for managing per-user Jupyter Notebook servers, designed for research groups or classes. This lecture covers deploying JupyterHub on a single server, as well as deploying with Docker using GitHub for authentication.

This lesson introduces the practical usage of The Virtual Brain (TVB) in its graphical user interface and via python scripts. In the graphical user interface, you are guided through its data repository, simulator, phase plane exploration tool, connectivity editor, stimulus generator, and the provided analyses. The implemented iPython notebooks of TVB are presented, and since they are public, can be used for further exploration of TVB. 

This lesson provides a brief overview of the Python programming language, with an emphasis on tools relevant to data scientists.

This tutorial covers the fundamentals of collaborating with Git and GitHub.

This book was written with the goal of introducing researchers and students in a variety of research fields to the intersection of data science and neuroimaging. This book reflects our own experience of doing research at the intersection of data science and neuroimaging and it is based on our experience working with students and collaborators who come from a variety of backgrounds and have a variety of reasons for wanting to use data science approaches in their work. The tools and ideas that we chose to write about are all tools and ideas that we have used in some way in our own research. Many of them are tools that we use on a daily basis in our work. This was important to us for a few reasons: the first is that we want to teach people things that we ourselves find useful. Second, it allowed us to write the book with a focus on solving specific analysis tasks. For example, in many of the chapters you will see that we walk you through ideas while implementing them in code, and with data. We believe that this is a good way to learn about data analysis, because it provides a connecting thread from scientific questions through the data and its representation to implementing specific answers to these questions. Finally, we find these ideas compelling and fruitful. That’s why we were drawn to them in the first place. We hope that our enthusiasm about the ideas and tools described in this book will be infectious enough to convince the readers of their value.

Following the previous lesson on neuronal structure, this lesson discusses neuronal function, particularly focusing on spike triggering and propogation. 

This lesson introduces the practical exercises which accompany the previous lessons on animal and human connectomes in the brain and nervous system. 

In this lecture, attendees will learn how Mutant Mouse Resource and Research Center (MMRRC) archives, cryopreserves, and distributes scientifically valuable genetically engineered mouse strains and mouse ES cell lines for the genetics and biomedical research community.

Learn how to create a standard extracellular electrophysiology dataset in NWB using Python.

Learn how to create a standard calcium imaging dataset in NWB using Python.

In this tutorial, you will learn how to create a standard intracellular electrophysiology dataset in NWB using Python.

Learn how to create a standard intracellular electrophysiology dataset in NWB.

This lesson gives an overview of the Brainstorm package for analyzing extracellular electrophysiology, including preprocessing, spike sorting, trial alignment, and spectrotemporal decomposition.

This lesson provides an overview of the CaImAn package, as well as a demonstration of usage with NWB.

This lesson gives an overview of the SpikeInterface package, including demonstration of data loading, preprocessing, spike sorting, and comparison of spike sorters.

In this lesson, users will learn about the NWBWidgets package, including coverage of different data types, and information for building custom widgets within this framework.

This lecture will provide an overview of the INCF Training Suite, a collection of tools that embraces the FAIR principles developed by members of the INCF Community. This will include an overview of TrainingSpace, Neurostars, and KnowledgeSpace.

This lesson provides an overview of how to construct computational pipelines for neurophysiological data using DataJoint.

This lesson continues with the second workshop on reproducible science, focusing on additional open source tools for researchers and data scientists, such as the R programming language for data science, as well as associated tools like RStudio and R Markdown. Additionally, users are introduced to Python and iPython notebooks, Google Colab, and are given hands-on tutorials on how to create a Binder environment, as well as various containers in Docker and Singularity.