- From www.edx.org
Simulation Neuroscience
- Self-paced
- Free Access
- Fee-based Certificate
- 6 Sequences
- Advanced Level
Course details
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
Prerequisite
Knowledge of ordinary differential equations, and their numerical solution
Knowledge of programming in one of Python (preferred), C/C++, Java, MATLAB, R.
Instructors
Henry Markram
Professor
École polytechnique fédérale de Lausanne
Idan Segev
Professor
École polytechnique fédérale de Lausanne
Sean Hill
Professor
École polytechnique fédérale de Lausanne
Felix Schürmann
Adjunct Professor
EPFL
Eilif Muller
Section Manager of Cells & Circuits in the Simulation Neuroscience Division
École polytechnique fédérale de Lausanne
Srikanth Ramaswamy
Senior Scientist in the Cells & Circuits Section of the Simulation Neuroscience Division
École polytechnique fédérale de Lausanne
Werner Van Geit
Systems Specialist
EPFL
Samuel Kerrien
Section Manager, Neuroinformatics Software Engineering
École polytechnique fédérale de Lausanne
Lida Kanari
PhD student, Molecular Systems, Simulation Neuroscience Division
École polytechnique fédérale de Lausanne
Anne-Kristin Kaufmann
Dr
EPFL
Editor
The École polytechnique fédérale de Lausanne (EPFL, English: Swiss Federal Institute of Technology in Lausanne) is a research university in Lausanne, Switzerland, that specialises in physical sciences and engineering.
One of the two Swiss Federal Institutes of Technology, the school was founded by the Swiss Federal Government with the stated mission to:
Educate engineers and scientists to the highest international standing
Be a national center of excellence in science and technology
Provide a hub for interaction between the scientific community and the industry
EPFL is considered one of the most prestigious universities in the world for engineering and sciences, ranking 17th overall and 10th in engineering in the 2015 QS World University Rankings; 34th overall and 12th in engineering in the 2015 Times Higher Education World University Rankings.
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