This lecture covers visualizing extracellular neurotransmitter dynamics
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.
This lesson provides an overview of how to construct computational pipelines for neurophysiological data using DataJoint.
This lesson introduces several open science tools like Docker and Apptainer which can be used to develop portable and reproducible software environments.
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.
This video demonstrates each required step for preprocessing T1w anatomical data in brainlife.io.
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.
In this lesson you will learn how to simulate seizure events and epilepsy in The Virtual Brain. We will look at the paper On the Nature of Seizure Dynamics, which describes a new local model called the Epileptor, and apply this same model in The Virtual Brain. This is part 1 of 2 in a series explaining how to use the Epileptor. In this part, we focus on setting up the parameters.
Brief introduction to Research Resource Identifiers (RRIDs), persistent and unique identifiers for referencing a research resource.
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.
The Mouse Phenome Database (MPD) provides access to primary experimental trait data, genotypic variation, protocols and analysis tools for mouse genetic studies. Data are contributed by investigators worldwide and represent a broad scope of phenotyping endpoints and disease-related traits in naïve mice and those exposed to drugs, environmental agents or other treatments. MPD ensures rigorous curation of phenotype data and supporting documentation using relevant ontologies and controlled vocabularies. As a repository of curated and integrated data, MPD provides a means to access/re-use baseline data, as well as allows users to identify sensitized backgrounds for making new mouse models with genome editing technologies, analyze trait co-inheritance, benchmark assays in their own laboratories, and many other research applications. MPD’s primary source of funding is NIDA. For this reason, a majority of MPD data is neuro- and behavior-related.
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.
KnowledgeSpace is a community-based encyclopedia that links brain research concepts to data, models, and literature. It provides users with access to anatomy, gene expression, models, morphology, and physiology data from over 15 different neuroscience data/model repositories, such as Allen Institute for Brain Science and the Human Brain Project.
Longitudinal Online Research and Imaging System (LORIS) is a web-based data and project management software for neuroimaging research studies. It is an open source framework for storing and processing behavioural, clinical, neuroimaging and genetic data. LORIS also makes it easy to manage large datasets acquired over time in a longitudinal study, or at different locations in a large multi-site study.
This talk highlights a set of platform technologies, software, and data collections that close and shorten the feedback cycle in research.
This talk covers the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC), a free one-stop-shop collaboratory for science researchers that need resources such as neuroimaging analysis software, publicly available data sets, or computing power.
This lesson outlines NeuroMorpho.org, a centrally curated inventory of digitally reconstructed neurons, which contrains contributions from dozens of laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared.