Learn how to simulate a Hippocampus Microcircuit – new MOOC

© 2021 EPFL

© 2021 EPFL

The hippocampus is a major component of the mammalian brain, which contributes to important cognitive functions such as memory consolidation and recall, and spatial navigation. The EPFL Blue Brain Project has launched a brand new Massive Open Online Course (MOOC) to enable students to learn how to simulate a Hippocampus Microcircuit and learn more about this fascinating brain region.

This course is part of a series of courses, where you will learn to use state-of-the-art modeling tools to simulate neurons, build neural networks, and perform your own simulation experiments. We start with an introduction into the role of the hippocampus in fundamental cognitive functions such as learning, memory, and spatial navigation. Then we focus on identifying typical electrophysiological behaviours of neuronal circuits in the hippocampus and understand their functional role. Next, we will continue with how modeling and simulation can enhance our understanding of the brain, and how we can analyze and simulate microcircuit models of the rodent hippocampus. You will conduct actual simulations of a microcircuit model and also analyze a simulation of a microcircuit and validate its behavior against empirical data.

In addition, the course has a theory component, where experts introduce the subject, explain the ideas and present the approach. While, in the practical part of the course, you will actually get your hands on the tools, workflows and model. This is done in a pre-installed e-environment accessible through the web browser and not requiring any other resources from you. If you want to continue to use the approaches of the MOOC for your own research, you can use the open source software on your own or use it via the EBRAINS platform (https://ebrains.eu), which offers access to the same pre-installed modeling and simulation tools freely via the web. If you are interested in further research around the hippocampus, you may also want to check out the Hippocampus Hub (https://www.hippocampushub.eu).

Meet the MOOC organizer - Dr. Annechien Helsdingen and instructor and Hippocampus expert, Dr. Armando Romani.

Why are you excited about launching this MOOC?

Armando - In this MOOC, we move from single cell to network modeling. With thousands of cells and millions of synapses, the students will start to appreciate the complexity and beauty of the brain. Despite this complexity, we can now create computer representation of neuronal tissue and we are developing technologies to make this accessible to everyone.

The brain has hundreds of regions so why the Hippocampus?

Armando - The hippocampus has fascinated researchers for more than 100 years with its well-organized anatomical structure and for its fundamental role in cognitive function such as memory and spatial navigation. The Hippocampus also receives attention because it is particularly compromised in pathologies such as Alzheimer’s disease, epilepsy or strokes.

Who is teaching this MOOC?

Annechien - We have a very diverse group of researchers and scientists from in and outside the Blue Brain Project, each teaching their own individual specialism. Externally, we invited established scientists like Dr. Michele Migliore (National Research Council Italy), Prof. Audrey Mercer (UCL School of Pharmacy) and Dr. Szalbocs Kàli (Hungarian Academy of Sciences) to lecture on their specific area of expertise. And, from inside the Blue Brain, we have both upcoming and established scientists: Prof. Felix Schürmann, Dr. Judit Planas, Dr. Michael Reimann, András Ecker, Dr. Srikanth Ramaswamy - who is now at Newcastle University - and Dr. Armando Romani. At the same time, we also have technical specialists like Werner van Geit, Fabien Petitjean and Jean-Denis Courcol to teach us how to use the different tools. I think this diversity in teachers really reflects the diversity that is needed in Neuroscience as a whole.

Who is this MOOC for?

Annechien - This MOOC is for people with an interest in modeling biological or neurological systems and phenomena. They need to have a solid background in cell biology, and know Python programming.

That being said, our learners are very diverse. They can be practitioners in the medical field who want to know more about how modeling and simulation can help increase our understanding of the structures, processes and functions of the brain. Or, they can be students or researchers who are preparing for a project or study and want to know more about which databases, atlases or simulation tools are available and how to utilize them. Alternatively, they could be other life-science teachers that want to include part of our course materials in their own teaching. For example, our wonderful brain visualization tool - the Blue Brain Cell Atlas is a great resource for teaching.

The course is open to everyone and we invite them to come and have a look!

Tell us more about the background to the series of MOOCs on offer

Annechien - We believe that MOOCs offer a powerful and flexible channel to disseminate the new findings of the Blue Brain Project to a wider public, and they allow us to train other researchers in how to use our datasets and tools. Thus, we can help other brain initiatives and the wider scientific community to achieve their goals.

Finally, what’s next?

Annechien - This is the third MOOC on Simulation Neuroscience. The first is on simulation of a single neuron, the second is on the multi-scale brain and this new one is on simulating a microcircuit. These MOOCs are for advanced audiences that have a specific interest in modeling and simulation.

We are now working on a series of MOOCs on the principles of neuroscience. The first of these will be a more generic MOOC on Neuroscience aimed at a broader audience. This MOOC will also address the specifics of modeling and simulation, as we think that this has become a central approach in life sciences. However, the focus will be on the what and why of modeling and simulation in neuroscience, not so much on how to do it yourself. Find out more here - portal.bluebrain.epfl.ch/resources/online-learning/neuroscience-reconstructed-towards-an-integrative-approach.

For more information on the MOOCs, please contact Anne Helsdingen


This MOOC was created with funding from the Patrick and Lina Drahi Foundation and funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne, from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.

During the development of the MOOC, compute services of EBRAINS were used, supported by the EBRAINS research infrastructure, funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3).

The software tools and model used in the MOOC in part have received funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 785907 (Human Brain Project SGA2).


About the EPFL Blue Brain Project

The aim of the EPFL Blue Brain Project, a Swiss brain research initiative founded and directed by Professor Henry Markram, is to establish simulation neuroscience as a complementary approach alongside experimental, theoretical and clinical neuroscience to understanding the brain, by building the world’s first biologically detailed digital reconstructions and simulations of the mouse brain. https://www.epfl.ch/research/domains/bluebrain/


EBRAINS is a new digital research infrastructure, created by the EU-funded Human Brain Project, to foster brain-related research and to help translate the latest scientific discoveries into innovation in medicine and industry, for the benefit of patients and society.

It draws on cutting-edge neuroscience and offers an extensive range of brain data sets, a multilevel brain atlas, modelling and simulation tools, easy access to high-performance computing resources and to robotics and neuromorphic platforms.

All academic researchers have open access to EBRAINS’ state-of-the art services. Industry researchers are also very welcome to use the platform under specific agreements. For more information about EBRAINS, please contact us at [email protected] or visit www.ebrains.eu.