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Enabling neuroscience research using high performance computing

Difficulty level: Beginner
Duration: 39:27
Speaker: : Subha Sivagnanam

Lecture on functional brain parcellations and a set of tutorials on bootstrap agregation of stable clusters (BASC) for fMRI brain parcellation which were part of the 2019 Neurohackademy, a 2-week hands-on summer institute in neuroimaging and data science held at the University of Washington eScience Institute.

Difficulty level: Advanced
Duration: 50:28
Speaker: : Pierre Bellec

This lecture provides an overview of depression (epidemiology and course of the disorder), clinical presentation, somatic co-morbidity, and treatment options.

Difficulty level: Beginner
Duration: 37:51

Overview of the Braintorm package for analyzing extracellular electrophysiology, including preprocessing, spike sorting, trial alignment, and spectrotemporal decomposition

Difficulty level: Intermediate
Duration: 47:47

Overview of the CaImAn package, and demonstration of usage with NWB

Difficulty level: Intermediate
Duration: 44:37

Overview of the SpikeInterface package, including demonstration of data loading, preprocessing, spike sorting, and comparison of spike sorters

Difficulty level: Intermediate
Duration: 1:10:28
Speaker: : Alessio Buccino

Overview of the NWBWidgets package, including coverage of different data types, and information for building custom widgets within this framework

Difficulty level: Intermediate
Duration: 47:15
Speaker: : Ben Dichter

An overview of some of the essential concepts in neuropharmacology (e.g. receptor binding, agonism, antagonism), an introduction to pharmacodynamics and pharmacokinetics, and an overview of the drug discovery process relative to diseases of the Central Nervous System.

Difficulty level: Beginner
Duration: 45:47

How genetics can contribute to our understanding of psychiatric phenotypes.

Difficulty level: Beginner
Duration: 55:15
Speaker: : Sven Cichon

GeneWeaver is a web application for the integrated cross-species analysis of functional genomics data to find convergent evidence from heterogeneous sources. The application consists of a large database of gene sets curated from multiple public data resources and curated submissions, along with a suite of analysis tools designed to allow flexible, customized workflows through web-based interactive analysis or scripted API driven analysis. Gene sets come from multiple widely studied species and include ontology annotations, brain gene expression atlases, systems genetic study results, gene regulatory information, pathway databases, drug interaction databases and many other sources. Users can retrieve, store, analyze and share gene sets through a graded access system. Analysis tools are based on combinatorics and statistical methods for comparing, contrasting, and classifying gene sets based on their members.

Difficulty level: Beginner
Duration: 1:03:26
Speaker: : Erich J. Baker

GeneWeaver is a web application for the integrated cross-species analysis of functional genomics data to find convergent evidence from heterogeneous sources. The application consists of a large database of gene sets curated from multiple public data resources and curated submissions, along with a suite of analysis tools designed to allow flexible, customized workflows through web-based interactive analysis or scripted API driven analysis. Gene sets come from multiple widely studied species and include ontology annotations, brain gene expression atlases, systems genetic study results, gene regulatory information, pathway databases, drug interaction databases and many other sources. Users can retrieve, store, analyze and share gene sets through a graded access system. Analysis tools are based on combinatorics and statistical methods for comparing, contrasting and classifying gene sets based on their members.

Difficulty level: Beginner
Duration: 25:53
Speaker: :

This tutorial shows how to use the UCSC genome browser to find a list of genes in a given genomic region.

Difficulty level: Beginner
Duration: 4:32

This tutorial shows how to find all the single nucleotide polymorphisms upstream from genes using the UCSC Genome Browser.

Difficulty level: Beginner
Duration: 8:13

This tutorial demonstrates how to find all the single nucleotide polymorphisms in a gene using the UCSC Genome Browser.

Difficulty level: Beginner
Duration: 6:12

The Saved Sessions feature of the Browser has been around for quite some time, but many of our users have not made full use of it. It offers a great way to keep track of your thinking on a particular topic.

Difficulty level: Beginner
Duration: 7:16

This tutorial demonstrates the visibility controls on the Genome Browser, showing the affect on BED tracks, wiggle tracks and Conservation tracks. It also discusses supertracks and composite tracks.

Difficulty level: Beginner
Duration: 14:30

This tutorial describes the isPCR tool and demonstrates how to use it for predicting the size and location of PCR products and visualizing the genomic location on the genome. The tool operates on DNA templates for all organisms and DNA or RNA on human and mouse. It also demonstrates how to use the Browser to obtain DNA sequences from the genome.

Difficulty level: Beginner
Duration: 8:01

This tutorial describes the dbSNP resources in the UCSC Genome Browser, including display conventions and the subdivision of the data into several useful subset tracks, especially the Common SNPs. There is also a discussion about changes to the genome assemblies from one version to another, and of two ways to navigate between different assemblies of the human genome in the Browser.

Difficulty level: Beginner
Duration: 17:41