Manipulate the default connectome provided with TVB to see how structural lesions effect brain dynamics. In this hands-on session you will insert lesions into the connectome within the TVB graphical user interface (GUI). Afterwards, the modified connectome will be used for simulations and the resulting activity will be analysed using functional connectivity.
This lecture covers a wide range of aspects regarding neuroinformatics and data governance, describing both their historical developments and current trajectories. Particular tools, platforms, and standards to make your research more FAIR are also discussed.
EyeWire is a game to map the brain. Players are challenged to map branches of a neuron from one side of a cube to the other in a 3D puzzle. Players scroll through the cube and reconstruct neurons with the help of an artificial intelligence algorithm developed at Seung Lab in Princeton University. EyeWire gameplay advances neuroscience by helping researchers discover how neurons connect to process visual information.
This is a hands-on tutorial on PLINK, the open source whole genome association analysis toolset. The aims of this tutorial are to teach users how to perform basic quality control on genetic datasets, as well as to identify and understand GWAS summary statistics.
This is a tutorial on using the open-source software PRSice to calculate a set of polygenic risk scores (PRS) for a study sample. Users will also learn how to read PRS into R, visualize distributions, and perform basic association analyses.
This lesson contains the slides (pptx) of a lecture discussing the necessary concepts and tools for taking into account population stratification and admixture in the context of genome-wide association studies (GWAS). The free-access software Tractor and its advantages in GWAS are also discussed.
This is a tutorial introducing participants to the basics of RNA-sequencing data and how to analyze its features using Seurat.
This tutorial demonstrates how to perform cell-type deconvolution in order to estimate how proportions of cell-types in the brain change in response to various conditions. While these techniques may be useful in addressing a wide range of scientific questions, this tutorial will focus on the cellular changes associated with major depression (MDD).
This lesson provides an overview of GeneWeaver, a web application for the integrated cross-species analysis of functional genomics data to find convergent evidence from heterogeneous sources.
This lesson provides a demonstration of GeneWeaver, a system for the integration and analysis of heterogeneous functional genomics data.
This lecture outlines GeneNetwork.org, a group of linked data sets and tools used to study complex networks of genes, molecules, and higher order gene function and phenotypes.
This tutorial shows how to use the UCSC genome browser to find a list of genes in a given genomic region.
This tutorial shows how to find all the single nucleotide polymorphisms (SNPs) upstream from genes using the UCSC Genome Browser.
This tutorial demonstrates how to find all the single nucleotide polymorphisms (SNPs) in a gene using the UCSC Genome Browser.
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. This feature offers a great way to keep track of your thinking on a particular topic.
The Track Collection Builder is a new tool in the UCSC Genome Browser that provides a way to create grouped collections of sub-tracks with native tracks, custom tracks, or hub tracks of continuous value graphing data types.
This tutorial demonstrates the visibility controls on the Genome Browser, showing the effect on BED tracks, wiggle tracks, and Conservation tracks. It also discusses supertracks and composite tracks.
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 on human and mouse DNA/RNA. It also demonstrates how to use the Browser to obtain DNA sequences from the genome.
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.