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 (antibodies, model organisms and software projects) in the biomedical literature to improve transparency of research methods.

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.

Introduction to the Brain Imaging Data Structure (BIDS): a standard for organizing human neuroimaging datasets. 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.

NWB: An ecosystem for neurophysiology data standardization

NWB: An ecosystem for neurophysiology data standardization

Enabling neuroscience research using high performance computing

This lecture and tutorial focuses on measuring human functional brain networks. The lecture and tutorial 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.

Neuronify is an educational tool meant to create intuition for how neurons and neural networks behave. You can use it to combine neurons with different connections, just like the ones we have in our brain, and explore how changes on single cells lead to behavioral changes in important networks. Neuronify is based on an integrate-and-fire model of neurons. This is one of the simplest models of neurons that exist. It focuses on the spike timing of a neuron and ignores the details of the action potential dynamics. These neurons are modeled as simple RC circuits. When the membrane potential is above a certain threshold, a spike is generated and the voltage is reset to its resting potential. This spike then signals other neurons through its synapses.

Neuronify aims to provide a low entry point to simulation-based neuroscience.

Tutorial describing the basic search and navigation features of the Allen Mouse Brain Atlas

Tutorial describing the basic search and navigation features of the Allen Developing Mouse Brain Atlas

Tutorial describing the basic features of the Brain Explorer® 3-D viewer for the mouse brain

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 and 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.

Learn how to create a standard extracellular electrophysiology dataset in NWB using Python

Learn how to create a standard calcium imaging dataset in NWB using Python

Learn how to create a standard intracellular electrophysiology dataset in NWB

Learn how to use the icephys-metadata extension to enter meta-data detailing your experimental paradigm

Learn how to create a standard extracellular electrophysiology dataset in NWB using MATLAB

Learn how to create a standard calcium imaging dataset in NWB using MATLAB

Learn how to create a standard intracellular electrophysiology dataset in NWB