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The International Brain Initiative (IBI)

INCF

The International Brain Initiative (IBI) is a consortium of the world’s major large-scale brain initiatives and other organizations with a vested interest in catalyzing and advancing neuroscience research through international collaboration and knowledge sharing. This session will introduce the IBI and the current efforts of the Data Standards and Sharing Working Group with a view to gain input from a wider neuroscience and neuroinformatics community. 

 

Module 3: Computational Models

Mike X. Cohen

This module introduces computational neuroscience by simulating neurons according to the AdEx model. You will learn about generative modeling, dynamical systems, and F-I curves. The MATLAB code introduces live scripts and functions.

 

Introductory Concepts

Krembil Centre for Neuroinformatics

This couse is the opening module for the University of Toronto's Krembil Centre for Neuroinformatics' virtual learning series Solving Problems in Mental Health Using Multi-Scale Computational Neuroscience. Lessons in this course introduce participants to the study of brain disorders, starting from elemental units like genes and neurons, eventually building up to whole-brain modelling and global activity patterns.

 

Fundamental Methods for Genomic Analysis

Krembil Centre for Neuroinformatics

This course includes both lectures and tutorials around the management and analysis of genomic data in clinical research and care. Participants are led through the basics of genome-wide association studies (GWAS), genotypes, and polygenic risk scores, as well as novel concepts and tools for more sophisticated consideration of population stratification in GWAS.

 

Module 5: Calcium Imaging

Mike X. Cohen

In this course, you will learn about working with calcium-imaging data, including image processing to remove background "blur", identifying cells based on threshold spatial contiguity, time-series filtering, and principal component analysis (PCA). The MATLAB code shows data animations, capabilities of the image processing toolbox, and PCA.

 

Module 4: fMRI

Mike X. Cohen

This module covers fMRI data, including creating and interpreting flatmaps, exploring variability and average responses, and visual eccenticity. You will learn about processing BOLD signals, trial-averaging, and t-tests. The MATLAB code introduces data animations, multicolor visualizations, and linear indexing.

 

Open Data in Neuroscience: Data Sharing in EBRAINS

Maaike van Swieten, Ida Aasebø, the EBRAINS curation services and HBP-EBRAINS

There is a broad consensus among researchers, publishers, and funding bodies that open sharing of data is needed to address major reproducibility and transparency challenges that currently exist in all scientific disciplines. In addition to potentially increasing the utilization of shared data through re-analysis and integration with other data, data sharing is beneficial for individual researchers through data citation and increased exposure of research.

 
INCF TrainingSpace

Preprocessing Data in EEGLAB

Swartz Center for Computational Neuroscience

EEGLAB is an interactive MATLAB toolbox for processing continuous and event-related EEG, MEG, and other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics, and several useful modes of visualization of the averaged and single-trial data.

 
INCF TrainingSpace

Deep Learning: Advanced Energy-Based Models

NYU Center for Data Science

This module is intended to provide a foundation in energy-based models. It is a part of the Deep Learning Course at NYU's Center for Data Science. Prerequisites for this module include: Introduction to Deep Learning (module 1 of the course), Parameter Sharing (module 2 of the course),

 

Statistical Software

These courses give introductions and overviews of some of the major statistics software packages currently used in neuroscience research.

 

Bayesian Models of Learning and Integration of Neuroimaging Data

Krembil Centre for Neuroinformatics

Bayesian inference (using prior knowledge to generate more accurate predictions about future events or outcomes) has become increasingly applied to the fields of neuroscience and neuroinformatics. In this course, participants are taught how Bayesian statistics may be used to build cognitive models of processes like learning or perception. This course also offers theoretical and practical instruction on dynamic causal modeling as applied to fMRI and EEG data.

 

Applied Ethics in Machine Learning and Mental Health

Krembil Centre for Neuroinformatics

This course tackles the issue of maintaining ethical research and healthcare practices in the age of increasingly powerful technological tools like machine learning and artificial intelligence. While there is great potential for innovation and improvement in the clinical space thanks to AI development, lecturers in this course advocate for a greater emphasis on human-centric care, calling for algorithm design which takes the full intersectionality of individuals into account.

 

Module 3: Computational Models

Mike X. Cohen

This module introduces computational neuroscience by simulating neurons according to the AdEx model. You will learn about generative modeling, dynamical systems, and F-I curves. The MATLAB code introduces live scripts and functions.

 

Module 3: Computational Models

Mike X. Cohen

This module introduces computational neuroscience by simulating neurons according to the AdEx model. You will learn about generative modeling, dynamical systems, and F-I curves. The MATLAB code introduces live scripts and functions.

 

Module 5: Calcium Imaging

Mike X. Cohen

In this course, you will learn about working with calcium-imaging data, including image processing to remove background "blur", identifying cells based on threshold spatial contiguity, time-series filtering, and principal component analysis (PCA). The MATLAB code shows data animations, capabilities of the image processing toolbox, and PCA.

 

Model Types

Neuromatch Academy

Neuromatch Academy aims to introduce traditional and emerging tools of computational neuroscience to trainees.

 
INCF TrainingSpace

Deep Learning: Foundations of Energy-Based Models

NYU Center for Data Science

This module is intended to provide a foundation in energy-based models, and is a part of the Deep Learning Course at NYU's Center for Data Science, a course that covered the latest techniques in deep learning and representation learning, focusing on supervised and unsupervised deep learning, embedding methods, metric learning, convolutional and recurrent nets, with applications to computer vision, natural language understanding, and speech recognition. Prerequisites for this mo

 

Machine Learning

Neuromatch Academy

Neuromatch Academy aims to introduce traditional and emerging tools of computational neuroscience to trainees.

 

INCF Short Course: Introduction to Neuroinformatics

INCF

The emergence of data-intensive science creates a demand for neuroscience educators worldwide to deliver better neuroinformatics education and training in order to raise a generation of modern neuroscientists with FAIR capabilities, awareness of the value of standards and best practices, knowledge in dealing with big datasets, and the ability to integrate knowledge over multiple scales and methods.

 

Data Management, Repositories, & Search Engines

The importance of Research Data Management in the conduct of open and reproducible science is better understood and technically supported than ever, and many of the underlying principles apply as much to everyday activities of a single researcher as to large-scale, multi-center open data sharing.