Free Online Course on Simulation Neuroscience

Free Online Course on Simulation Neuroscience
Certificate fee scholarship is available for this course.

Institution: Ecole Polytechnique Federale de Lausanne
Start Date: November 2, 2017  

Ecole Polytechnique Federale de Lausanne is proud to announce you a free online course named as “Simulation Neuroscience”. 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.  You will learn how to digitally reconstruct a single neuron to better study the biological mechanisms of brain function, behavior, and disease. This course will start on November 2, 2017.

Course Summary

  • Duration: 6 weeks
  • Commitment: 5-8 hours per week
  • Subject: Biology & Life Sciences
  • Institution: Ecole Polytechnique Federale de Lausanne
  • Languages: English
  • Price: Free
  • Session: Starts on November 2, 2017
  • Requirement: Anyone
  • Certificate Available: Yes

Who Developed the Course

  • About University: EPFL is the Swiss Federal Institute of Technology in Lausanne. The past decade has seen EPFL ascend to the very top of European institutions of science and technology: it is ranked #1 in Europe in the field of Engineering by the Times Higher Education (based on publications and citations), Leiden Rankings, and the Academic Ranking of World Universities.
  • Mission of University: The university complex has three main world-rank missions: education, research, and technology transfer at the highest international level.

Target Audience

No prior programming experience is needed.

Where Could This Lead You

  • Importance of the Subject in Today’s Scenario: Simulation Neuroscience is an emerging approach to integrate the knowledge dispersed throughout the field of neuroscience. This is achieved by integrating diverse data sources across the various scales of experimental neuroscience, from molecular to clinical, into computer simulations.
  • Your Career Option: After successfully completing the course you can build your career in the following:
  1. Virtual Program Design Consultant
  2. Research Scientist I, Drug Product Development
  3. Molecular Discovery

 Get Extra Benefits

Pursue a Verified Certificate to highlight the knowledge and skills you gain ($49)

  • Official and Verified: Receive an instructor-signed certificate with the institution’s logo to verify your achievement and increase your job prospects
  • Easily Shareable: Add the certificate to your CV or resume, or post it directly on LinkedIn
  • Proven Motivator: Give yourself an additional incentive to complete the course

 How to Join This Course

You should register yourself through the given link of join this free online course:

Course Format

Week 1: Simulation neuroscience: An introduction,
Understanding the brain
Approaches and Rationale of Simulation Neuroscience
The principles of simulation neuroscience
Data strategies
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
Synaptic dynamics

Week 2: Neuroinformatics
Introduction to neuroinformatics
Text mining
Data integration and knowledge graphs
Knowledge graphs
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
Creating your own domain
Acquisition of neuron electrophysiology and morphology data
Generating data
Using data
Design an entity
An entity design and the provenance model
Morphological feature extraction
Morphological structures,
Understanding neuronal morphologies using NeuroM
Statistics and visualization of morphometric data

Week 3: Modeling neurons
Introduction to the single neuron
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 synapse
Compiling your modifies
Hosting & testing your synapse model
Reconfigure your synapse to biological ranges
Defining a mod file for a dynamic TM synapse
Compiling and testing the modified

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          

 Learning Outcomes

Students will gain skills:

  • 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 behavioral aspects
  • Model a neuron with all its parts (soma, dendrites, axon, synapse) and its behavior
  • Use experimental data on neuronal activity to constrain a model

 Who Will You Learn With

  • Henry Markram: Henry Markram is a professor of neuroscience at the Swiss Federal Institute of Technology (EPFL), director of the Laboratory of Neural Microcircuitry (LNMC) and the founder and Director of the Blue Brain Project.
  • Idan Segev: Prof. Idan Segev is the David & Inez Myers Professor in Computational Neuroscience and former director of the Interdisciplinary Center for Neural Computation (ICNC) at the Hebrew University of Jerusalem, where he received B.Sc. in Math, and Ph.D. in experimental and theoretical neurobiology.
  • Sean Hill: Sean Hill is co-Director of Blue Brain, a Swiss national brain initiative, where he leads the Neuroinformatics division, based at the Campus Biotech in Geneva, Switzerland. He also directs the Laboratory for the Neural Basis of Brain States at the École Polytechnique Fédérale de Lausanne (EPFL).
  • Felix Schürmann: Felix Schürmann is an adjunct professor at the Ecole Polytechnique Fédérale de Lausanne, co-director of the Blue Brain Project and involved in several research challenges of the European Human Brain Project. He studied physics at the University of Heidelberg, Germany, supported by the German National Academic Foundation.
  • Eilif Muller: Dr. Eilif Benjamin Muller is the Section Manager of Cells & Circuits in the Simulation Neuroscience Division. Dr. Muller leads the team of researchers at Blue Brain who develop, refine and study our flagship simulations of neocortical tissue, under the direction of Prof. Henry Markram, and in close collaboration with Prof.
  • Srikanth Ramaswamy: Dr. Srikanth Ramaswamy is a Senior Scientist in the Cells & Circuits Section of the Simulation Neuroscience Division. Dr. Ramaswamy leads the effort in modeling synaptic transmission and neuromodulation in the Blue Brain Project’s flagship simulations of neocortical tissue, under the direction of Prof.
  • Werner Van Geit: Werner is a systems specialist in Blue Brain, where he is responsible for the software used in Blue Brain’s single cell modeling He mainly focuses on automated parameter optimisation for Blue Brain’s open source BluePyOpt tool, but he is also active in maintaining and extending other Blue Brain software packages.
  • Samuel Kerrien: Samuel Kerrien is the section manager of the Neuroinformatics Software Engineering section in the Neuroinformatics Division headed by Professor Sean Hill. He has extensive experience with the Java and big data ecosystems, data integration in life science as well as making software development teams more effective using agile processes.
  • Lida Kanari: Lida Kanari is a D. student in the Molecular Systems Section in the Simulation Neuroscience Division. Lida’s main focus is to understand the fundamental principles of neuronal morphologies in order to artificially reproduce them so that they are statistically indistinguishable from the biological ones.

Suggested Reading

You can cite these books:

  • The Future of the Brain – Essays by the World`s Leading Neuroscientists by Gary Marcus, Jeremy Freeman, May-britt Moser, Edvard I. Moser
  • Mechanisms of Morphogenesis by Jamie A. Davies
  • Organic Mechanisms: Reactions, Methodology, and Biological Applications by Xiaoping Sun
  • Biological mechanisms of attachment by Werner Nachtigall


  • Importance of Course: At the end of this course you will gain the knowledge and skills needed to create simulations of biological neurons and synapses.   Model a neuron with all its parts (soma, dendrites, axon, synaps) and its behavior.
  • Importance of Certificate: You can get a verified certificate to highlight the knowledge and skills you gain. You can prove your success when applying for jobs or courses and display on your LinkedIn or CV.

Detailed Information

  •  For more information about the course, you may visit the given link:!

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