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. 

In this hands-on session, you will learn how to explore and work with DataLad datasets, containers, and structures using Jupyter notebooks. 

This video demonstrates each required step for preprocessing T1w anatomical data in brainlife.io.

In this tutorial, you will learn the basic features of uploading and versioning your data within OpenNeuro.org.

This tutorial shows how to share your data in OpenNeuro.org.

Following the previous two tutorials on uploading and sharing data with OpenNeuro.org, this tutorial briefly covers how to run various analyses on your datasets.

This tutorial is part 1 of 2. It aims to provide viewers with an understanding of the fundamentals of R tool. Note: parts 1 and 2 of this tutorial are part of the same YouTube video; part 1 ends at 17:42. 

The Allen Mouse Brain Atlas is a genome-wide, high-resolution atlas of gene expression throughout the adult mouse brain. This tutorial describes the basic search and navigation features of the Allen Mouse Brain Atlas.

The Allen Developing Mouse Brain Atlas is a detailed atlas of gene expression across mouse brain development. This tutorial describes the basic search and navigation features of the Allen Developing Mouse Brain Atlas.

This tutorial demonstrates how to use the differential search feature of the Allen Mouse Brain Atlas to find gene markers for different regions of the brain, as well as to visualize this gene expression in three-dimensional space. Differential search is also available for the Allen Developing Mouse Brain Atlas and the Allen Human Brain Atlas.

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. 

Research Resource Identifiers (RRIDs) are ID numbers assigned to help researchers cite key resources (e.g., antibodies, model organisms, and software projects) in biomedical literature to improve the transparency of research methods.

This lesson introduces the EEGLAB toolbox, as well as motivations for its use.

In this lesson, you will learn about the biological activity which generates and is measured by the EEG signal.

This lesson goes over the characteristics of EEG signals when analyzed in source space (as opposed to sensor space). 

This lesson describes the development of EEGLAB as well as to what extent it is used by the research community.

This lesson provides instruction as to how to build a processing pipeline in EEGLAB for a single participant. 

Whereas the previous lesson of this course outlined how to build a processing pipeline for a single participant, this lesson discusses analysis pipelines for multiple participants simultaneously. 

In addition to outlining the motivations behind preprocessing EEG data in general, this lesson covers the first step in preprocessing data with EEGLAB, importing raw data.