Course:

This lesson provides an introduction to biologically detailed computational modelling of neural dynamics, including neuron membrane potential simulation and F-I curves.

Difficulty level: Intermediate

Duration: 8:21

Speaker: : Mike X. Cohen

Course:

In this lesson, users learn how to use MATLAB to build an adaptive exponential integrate and fire (AdEx) neuron model.

Difficulty level: Intermediate

Duration: 22:01

Speaker: : Mike X. Cohen

Course:

In this lesson, users learn about the practical differences between MATLAB scripts and functions, as well as how to embed their neuronal simulation into a callable function.

Difficulty level: Intermediate

Duration: 11:20

Speaker: : Mike X. Cohen

Course:

This lesson teaches users how to generate a frequency-current (F-I) curve, which describes the function that relates the net synaptic current (I) flowing into a neuron to its firing rate (F).

Difficulty level: Intermediate

Duration: 20:39

Speaker: : Mike X. Cohen

This is the first of two workshops on reproducibility in science, during which participants are introduced to concepts of FAIR and open science. After discussing the definition of and need for FAIR science, participants are walked through tutorials on installing and using Github and Docker, the powerful, open-source tools for versioning and publishing code and software, respectively.

Difficulty level: Intermediate

Duration: 1:20:58

Speaker: : Erin Dickie and Sejal Patel

This lesson continues with the second workshop on reproducible science, focusing on additional open source tools for researchers and data scientists, such as the R programming language for data science, as well as associated tools like RStudio and R Markdown. Additionally, users are introduced to Python and iPython notebooks, Google Colab, and are given hands-on tutorials on how to create a Binder environment, as well as various containers in Docker and Singularity.

Difficulty level: Beginner

Duration: 1:16:04

Speaker: : Erin Dickie and Sejal Patel

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.

Difficulty level: Beginner

Duration: 52:26

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.

Difficulty level: Intermediate

Duration: 1:27:18

Speaker: : Dan Felsky

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.

Difficulty level: Intermediate

Duration: 1:53:34

Speaker: : Dan Felsky

This is a tutorial introducing participants to the basics of RNA-sequencing data and how to analyze its features using Seurat.

Difficulty level: Intermediate

Duration: 1:19:17

Speaker: : Sonny Chen

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).

Difficulty level: Intermediate

Duration: 1:15:14

Speaker: : Keon Arbabi

This is a tutorial on how to simulate neuronal spiking in brain microcircuit models, as well as how to analyze, plot, and visualize the corresponding data.

Difficulty level: Intermediate

Duration: 1:39:50

Speaker: : Frank Mazza

Course:

This tutorial introduces pipelines and methods to compute brain connectomes from fMRI data. With corresponding code and repositories, participants can follow along and learn how to programmatically preprocess, curate, and analyze functional and structural brain data to produce connectivity matrices.

Difficulty level: Intermediate

Duration: 1:39:04

Speaker: : Erin Dickie and John Griffiths

Course:

In this tutorial on simulating whole-brain activity using Python, participants can follow along using corresponding code and repositories, learning the basics of neural oscillatory dynamics, evoked responses and EEG signals, ultimately leading to the design of a network model of whole-brain anatomical connectivity.

Difficulty level: Intermediate

Duration: 1:16:10

Speaker: : John Griffiths

This is a tutorial on designing a Bayesian inference model to map belief trajectories, with emphasis on gaining familiarity with Hierarchical Gaussian Filters (HGFs).

This lesson corresponds to slides 65-90 of the PDF below.

Difficulty level: Intermediate

Duration: 1:15:04

Speaker: : Daniel Hauke

Tutorial on how to simulate brain tumor brains with TVB (reproducing publication: Marinazzo et al. 2020 Neuroimage). This tutorial comprises a didactic video, jupyter notebooks, and full data set for the construction of virtual brains from patients and health controls. Authors: Hannelore Aerts, Michael Schirner, Ben Jeurissen, DIrk Van Roost, Eric Achten, Petra Ritter, Daniele Marinazzo

Difficulty level: Intermediate

Duration: 10:01

Speaker: :

This lecture 1/15 is part of the Computational Modeling of Neuronal Plasticity Course that aims to teach users how to build a mathematical model of a neuron, its inputs, and its neuronal plasticity mechanisms, by writing your own Python program. This lecture provides users with a brief video introduction to the concepts that serves as a companion to the lecture notes and solution figures.

Authors: Florence I. Kleberg and Prof. Jochen Triesch.

Difficulty level: Intermediate

Duration: 0:40

Speaker: : Florence I. Kleberg

This lecture (2/15) is part of the Computational Modeling of Neuronal Plasticity Course that aims to teach users how to build a mathematical model of a neuron, its inputs, and its neuronal plasticity mechanisms, by writing your own Python program. This lecture provides users with a brief video introduction to the concepts that serves as a companion to the lecture notes and solution figures.

Authors: Florence I. Kleberg and Prof. Jochen Triesch.

Difficulty level: Intermediate

Duration: 1:23

Speaker: : Florence I. Kleberg

This lecture (3/15) is part of the Computational Modeling of Neuronal Plasticity Course that aims to teach users how to build a mathematical model of a neuron, its inputs, and its neuronal plasticity mechanisms, by writing your own Python program. This lecture provides users with a brief video introduction to the concepts that serves as a companion to the lecture notes and solution figures.

Authors: Florence I. Kleberg and Prof. Jochen Triesch.

Difficulty level: Intermediate

Duration: 1:20

Speaker: : Florence I. Kleberg

This lecture (4/15) is part of the Computational Modeling of Neuronal Plasticity Course that aims to teach users how to build a mathematical model of a neuron, its inputs, and its neuronal plasticity mechanisms, by writing your own Python program. This lecture provides users with a brief video introduction to the concepts that serves as a companion to the lecture notes and solution figures.

Authors: Florence I. Kleberg and Prof. Jochen Triesch.

Difficulty level: Intermediate

Duration: 1:08

Speaker: : Florence I. Kleberg

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