Simulation Neuroscience

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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!

What you will learn

• Discuss the different types of data for simulation neuroscience
• How to collect, annotate and register different types of neuroscience data
• Describe the simulation neuroscience strategies
• Categorize different classification features of neurons
• List different characteristics of synapses and behavioural aspects
• Model a neuron with all its parts (soma, dendrites, axon, synaps) and its behaviour
• Use experimental data on neuronal activity to constrain a model

Skills you learn

• Artificial Neural Networks
• Biology
• Simulations
• Computer Simulation

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

Auto Summary

"Simulation Neuroscience" is an expert-level course designed for learners passionate about integrating neuroscience knowledge through computer simulations. Offered by edX and taught by a team of world-renowned scientists, this 6-week course focuses on creating simulations of biological neurons and synapses, using state-of-the-art modeling tools. Ideal for those in Science & Engineering, it forms part of a series aimed at understanding brain functions, behavior, and diseases. Available with a Starter subscription, it’s perfect for those eager to delve into cutting-edge neuroscience research.