Skip to main content

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

This tutorial demonstrates the 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 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
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 covers an Introduction to neuron anatomy and signaling, and different types of models, including the Hodgkin-Huxley model.

Difficulty level: Beginner
Duration: 1:23:01
Speaker: : Gaute Einevoll

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

Difficulty level: Beginner
Duration: 1:01:36
Speaker: : Maryann Martone

Computational models provide a framework for integrating data across spatial scales and for exploring hypotheses about the biological mechanisms underlying neuronal and network dynamics. However, as models increase in complexity, additional barriers emerge to the creation, exchange, and re-use of models. Successful projects have created standards for describing complex models in neuroscience and provide open source tools to address these issues. This lecture provides an overview of these projects and make a case for expanded use of resources in support of reproducibility and validation of models against experimental data.

Difficulty level: Beginner
Duration: 1:00:39
Speaker: : Sharon Crook

Introduction to reproducible research. The lecture provides an overview of the core skills and practical solutions required to practice reproducible research. This lecture was part of the 2018 Neurohackademy, a 2-week hands-on summer institute in neuroimaging and data science held at the University of Washington eScience Institute.

Difficulty level: Beginner
Duration: 1:25:17
Speaker: : Fernando Perez

Since their introduction in 2016, the FAIR data principles have gained increasing recognition and adoption in global neuroscience.  FAIR defines a set of high-level principles and practices for making digital objects, including data, software, and workflows, Findable, Accessible,  Interoperable, and Reusable.  But FAIR is not a specification;  it leaves many of the specifics up to individual scientific disciplines to define.  INCF has been leading the way in promoting, defining, and implementing FAIR data practices for neuroscience.  We have been bringing together researchers, infrastructure providers, industry, and publishers through our programs and networks.  In this session, we will hear some perspectives on FAIR neuroscience from some of these stakeholders who have been working to develop and use FAIR tools for neuroscience.  We will engage in a discussion on questions such as:  how is neuroscience doing with respect to FAIR?  What have been the successes?  What is currently very difficult? Where does neuroscience need to go? This lecture covers the biomedical researcher's perspective on FAIR data sharing and the importance of finding better ways to manage large datasets.

Difficulty level: Beginner
Duration: 10:51
Speaker: : Adam Ferguson

Since their introduction in 2016, the FAIR data principles have gained increasing recognition and adoption in global neuroscience.  FAIR defines a set of high-level principles and practices for making digital objects, including data, software, and workflows, Findable, Accessible,  Interoperable, and Reusable.  But FAIR is not a specification;  it leaves many of the specifics up to individual scientific disciplines to define.  INCF has been leading the way in promoting, defining, and implementing FAIR data practices for neuroscience.  We have been bringing together researchers, infrastructure providers, industry, and publishers through our programs and networks.  In this session, we will hear some perspectives on FAIR neuroscience from some of these stakeholders who have been working to develop and use FAIR tools for neuroscience.  We will engage in a discussion on questions such as:  how is neuroscience doing with respect to FAIR?  What have been the successes?  What is currently very difficult? Where does neuroscience need to go? This lecture covers multiple aspects of FAIR neuroscience data: what makes it unique, the challenges to making it FAIR, the importance of overcoming these challenges, and how data governance comes into play.

Difficulty level: Beginner
Duration: 14:56
Speaker: : Damian Eke