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Simulation Neuroscience

École Polytechnique Fédérale de Lausanne via edX

students interested
  • Provider edX
  • Subject Biology
  • $ Cost Free Online Course
  • Session Self Paced
  • Language English
  • Certificate $49 Certificate Available
  • Effort 5-8 hours a week
  • Start Date
  • Duration 6 weeks long

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Overview

Simulation Neuroscience is an emerging approach to integrate the knowledge dispersed throughout the field of neuroscience.

The aim is to build a unified empirical picture of the brain, to study the biological mechanisms of brain function, behaviour and disease. This is achieved by integrating diverse data sources across the various scales of experimental neuroscience, from molecular to clinical, into computer simulations.

This is a unique, massive open online course taught by a multi-disciplinary team of world-renowned scientists. In this first course, you will gain the knowledge and skills needed to create simulations of biological neurons and synapses.

This course is part of a series of three courses, where you will learn to use state-of-the-art modeling tools of the HBP Brain Simulation Platform to simulate neurons, build neural networks, and perform your own simulation experiments. We invite you to join us and share in our passion to reconstruct, simulate and understand the brain!

Syllabus

Week 1: Simulation neuroscience: An introduction,
Understanding the brain
Approaches and Rationale of Simulation Neuroscience
The principles of simulation neuroscience
Data strategies
Neuroinformatics
Reconstruction and simulation strategies
Summary and Caveats Experimental data
Single neuron data collection techniques 
Morphological profiles
Electrophysiological profiles
Caveats and summary of experimental data techniques Single neuron data
Ion channels
Combining profiles
Cell densities
Summary and Caveats
Synapses
Synapses
Synaptic dynamics Week 2: Neuroinformatics
Introduction to neuroinformatics
Text mining
Data integration and knowledge graphs
Knowledge graphs 
Ontologies 
Neuroinformatics
Brain atlases and knowledge space
Motivation of data-integration
Fixed data approach to data integration
Blue Brain Nexus
Architecture of Blue Brain Nexus
Design a provenance entity
Ontologies
Creating your own domain
MINDS
Conclusion
Acquisition of neuron electrophysiology and morphology data
Generating data
Using data
Design an entity
An entity design and the provenance model
Conclusion
Morphological feature extraction
Morphological structures,
Understanding neuronal morphologies using NeuroM
Statistics and visualisation of morphometric data Week 3: Modeling neurons
Introduction to the single neuron
Introduction 
Motivation for studying the electrical brain  
The neuron
A structural introduction 
An electrical device 
Electrical neuron model
Modeling the electrical activity  
Hodgkin & Huxley
Tutorial creating single cell electrical models
Single cell electrical model: passive
Making it active
Adding a dendrite
Connecting cells Week 4: Modeling synapses
Modeling synaptic potential
Modeling the potential
Rall’s cable model
Modeling synaptic transmission between neurons
Synaptic transmission
Modeling synaptic transmission
Modeling dynamic synapses tutorial
Defining your synaps
Compiling your modifies
Hosting & testing your synaps model
Reconfigure your synaps to biological ranges
Defining a modfile for a dynamic TM synapse
Compiling and testing the modfile Week 5: Constraining neurons models with experimental data
Constraining neuron models with experimental data
Constraining neuron model with experimental data.
Computational aspects of optimization
Tools for constraining neuron models
Tutorials for optimization
Setting up the components Week 6: Exam week
NMC portal
Accessing the NMC portal
Running models on your local computer
Downloading and interacting with the single cell models 
Injecting a current

Taught by

Henry Markram , Idan Segev , Sean Hill , Dr. Felix Schürmann , Dr. Eilif Muller , Dr. Srikanth Ramaswamy , Werner Van Geit , Samuel Kerrien and Lida Kanari

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Reviews for edX's Simulation Neuroscience
5.0 Based on 3 reviews

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  • 1
Pablo O
5.0 9 months ago
by Pablo is taking this course right now.
Magnificent course where you will learn to use the Human Brain Project tools to simulate neurons. It is recommended that you know how to program in python before you take this course.
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Michal K
5.0 4 months ago
Michal audited this course, spending 10 hours a week on it and found the course difficulty to be medium.
This is a very specialized course. But if you want an introduction to the NEURON simulator in Python or you are interested how folks at the Blue Brain Project approach their cortical tissue reconstruction effort this information source is invaluable.
Was this review helpful to you? Yes
Kevin D
5.0 7 months ago
Kevin completed this course, spending 7 hours a week on it and found the course difficulty to be medium.
Very good introductory course to the basics of Neuroscience. It was very interesting to use the resources from the Human Brain Project!
Was this review helpful to you? Yes
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