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.

This lesson contains both a lecture and a tutorial component. The lecture (0:00-20:03 of YouTube video) discusses both the need for intersectional approaches in healthcare as well as the impact of neglecting intersectionality in patient populations. The lecture is followed by a practical tutorial in both Python and R on how to assess intersectional bias in datasets. Links to relevant code and data are found below. 

This lesson is an overview of transcriptomics, from fundamental concepts of the central dogma and RNA sequencing at the single-cell level, to how genetic expression underlies diversity in cell phenotypes. 

This lesson describes the principles underlying functional magnetic resonance imaging (fMRI), diffusion-weighted imaging (DWI), tractography, and parcellation. These tools and concepts are explained in a broader context of neural connectivity and mental health. 

This lesson delves into the the structure of one of the brain's most elemental computational units, the neuron, and how said structure influences computational neural network models. 

This lesson goes over the basic mechanisms of neural synapses, the space between neurons where signals may be transmitted. 

While the previous lesson in the Neuro4ML course dealt with the mechanisms involved in individual synapses, this lesson discusses how synapses and their neurons' firing patterns may change over time. 

Whereas the previous two lessons described the biophysical and signalling properties of individual neurons, this lesson describes properties of those units when part of larger networks. 

This lesson explores how researchers try to understand neural networks, particularly in the case of observing neural activity. 

As the previous lesson of this course described how researchers acquire neural data, this lesson will discuss how to go about interpreting and analysing the data. 

This lecture focuses on how the immune system can target and attack the nervous system to produce autoimmune responses that may result in diseases such as multiple sclerosis, neuromyelitis, and lupus cerebritis manifested by motor, sensory, and cognitive impairments. Despite the fact that the brain is an immune-privileged site, autoreactive lymphocytes producing proinflammatory cytokines can cause active brain inflammation, leading to myelin and axonal loss.

This lecture will provide an overview of neuroimaging techniques and their clinical applications.

This lecture gives an introduction to the types of glial cells, homeostasis (influence of cerebral blood flow and influence on neurons), insulation and protection of axons (myelin sheath; nodes of Ranvier), microglia and reactions of the CNS to injury.

This lesson gives an introductory presentation on how data science can help with scientific reproducibility.

This lesson discusses FAIR principles and methods currently in development for assessing FAIRness.

This lecture provides an introduction to the Brain Imaging Data Structure (BIDS), a standard for organizing human neuroimaging datasets.

This lecture presents an overview of functional brain parcellations, as well as a set of tutorials on bootstrap agregation of stable clusters (BASC) for fMRI brain parcellation.

This lecture covers FAIR atlases, including their background and construction, as well as how they can be created in line with the FAIR principles.

This lecture covers the needs and challenges involved in creating a FAIR ecosystem for neuroimaging research.

This lecture covers how to make modeling workflows FAIR by working through a practical example, dissecting the steps within the workflow, and detailing the tools and resources used at each step.