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This tutorial demonstrates the UCSC Genome Browser Data Integrator, a tool that allows combination and intersection of data from up to five primary tables. In the example, data are extracted showing SNPs, genes, and phenotypes from a genomic region.

Difficulty level: Beginner
Duration: 6:24

This tutorial shows how to obtain coordinates of genes, then input those coordinates into the UCSC Genome Browser for display. The regions do not have to be continuous in the genome.

Difficulty level: Beginner
Duration: 9:04

This tutorial demonstrates the Multi-Region Exon-Only Display mode of the UCSC Genome Browser.

Difficulty level: Beginner
Duration: 5:15

This tutorial demonstrates viewing alternate haplotypes with the UCSC Genome Browser.

Difficulty level: Beginner
Duration: 7:04

The Genome Browser in the Cloud (GBiC) program is a convenient tool that automates the setup of a UCSC Genome Browser mirror​ on a cloud instance or a dedicated physical server.

Difficulty level: Beginner
Duration: 4:16

This tutorial gives a demonstration of species/genome assembly selection page (Gateway) on the UCSC Genome Browser.

Difficulty level: Beginner
Duration: 3:18

This tutorial demonstrates how to get the coordinates and sequences of exons using the UCSC Genome Browser.

Difficulty level: Beginner
Duration: 8:11

This tutorial will demonstrate how to locate amino acid numbers for coding genes using the UCSC Genome Browser.

Difficulty level: Beginner
Duration: 8:01

This tutorial will demonstrate how to find the tables in the UCSC database that are associated with the data tracks in the Genome Browser graphical viewer.

Difficulty level: Beginner
Duration: 8:39

This tutorial shows how to navigate between exons of a gene using the UCSC Genome Browser.

Difficulty level: Beginner
Duration: 4:24

This lecture explains the concept of federated analysis in the context of medical data, associated challenges. The lecture also presents an example of hospital federations via the Medical Informatics Platform.

Difficulty level: Intermediate
Duration: 19:15
Speaker: : Yannis Ioannidis

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.

Difficulty level: Beginner
Duration: 1:16:04

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. 

Difficulty level: Beginner
Duration: 52:26

This is a tutorial on how to simulate neuronal spiking in brain microcircuit models, as well as how to analyze, plot, and visualize the corresponding data. 

Difficulty level: Intermediate
Duration: 1:39:50
Speaker: : Frank Mazza

In this third and final hands-on tutorial from the Research Workflows for Collaborative Neuroscience workshop, you will learn about workflow orchestration using open source tools like DataJoint and Flyte. 

Difficulty level: Intermediate
Duration: 22:36
Speaker: : Daniel Xenes

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

Difficulty level: Beginner
Duration: 58:05

In this lecture, you will learn about current methods, approaches, and challenges to studying human neuroanatomy, particularly through the lense of neuroimaging data such as fMRI and diffusion tensor imaging (DTI). 

Difficulty level: Intermediate
Duration: 1:35:14
Speaker: : Matt Glasser

This lesson provides a thorough description of neuroimaging development over time, both conceptually and technologically. You will learn about the fundamentals of imaging techniques such as MRI and PET, as well as how the resultant data may be used to generate novel data visualization schemas. 

Difficulty level: Beginner
Duration: 1:43:57
Speaker: : Jack Van Horn

This video will document the process of creating a pipeline rule for batch processing on brainlife.

Difficulty level: Intermediate
Duration: 0:57
Speaker: :

This video will document the process of launching a Jupyter Notebook for group-level analyses directly from brainlife.

Difficulty level: Intermediate
Duration: 0:53
Speaker: :