Simulating a hippocampus microcircuit

EPFL

About This Course

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. In this course, you will gain the knowledge and skills needed to analyze and simulate microcircuit models of the rodent hippocampus. This course is part of a series of three courses, where you will learn to use state-of-the-art modeling tools of the Human Brain Project 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!

Requirements

Python programming, basic neuroscience knowldge, cell biology.

Course Staff

Armando Romani

Armando Romani is a Postdoctoral Fellow and Cortex Junior Group Leader within the Simulation Neuroscience Division. Armando joined Blue Brain to work on a biophysically detailed model of the hippocampus. The hippocampus plays a key role in memory formation, spatial navigation, and other fundamental cognitive functions. Before moving to Blue Brain, Armando spent two years as a collaborator at the Laboratory of Computational Embodied Neuroscience, group leader Dr. Gianluca Baldassarre, Institute of Cognitive Sciences and Technologies, National Research Council (Rome, Italy). Prior to that, he was a PhD student at the ‘Molecular Mechanisms of Synaptic Plasticity’ laboratory, group leader Dr. Hélène Marie, European Brain Research Institute, Rita Levi-Montalcini Foundation (Rome, Italy). Armando has a degree in Biology from the University ‘Roma Tre’, Italy and a PhD in Neuroscience from the University ‘Tor Vergata’, Rome, Italy.

Course Staff

Srikanth Ramaswamy

Dr. Srikanth Ramaswamy is a tenure-track Principal Investigator and Group Leader in Computational Neuroscience at Newcastle University. He directs the Neural Circuits Laboratory at Newcastle University. At his lab they employ multidisciplinary approaches at the interface of theory and experiments to understand how neuromodulators shape learning and cognition in neocortical circuits.

In 2017, he was one of the winners of the FENS – Australasian Neuroscience Society exchange award for young researchers and he won the 2017 Japan Neuroscience Society young investigator award.

Course Staff

Felix Schürmann

Felix Schürmann is 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. Later, as a Fulbright Scholar, he obtained his Master’s degree (M.S.) in Physics from the State University of New York, Buffalo, USA, under the supervision of Richard Gonsalves. During these studies, he became curious about the role of different computing substrates and dedicated his master thesis to the simulation of quantum computing. He studied for his Ph.D. at the University of Heidelberg, Germany, under the supervision of Karlheinz Meier. For his thesis he co-designed an efficient implementation of a neural network in hardware.

Course Staff

Judit Planas

Judit Planas is the Section Manager of Scientific Visualization in the Computing Division. Judit manages the research and development of tools that scientific users need to support their science. These tools enable scientists to visualize and analyze the different aspects of neural circuit reconstructions and simulations at large scale. Judit joined Blue Brain in 2015 as Post-doctoral Researcher in large-scale data analysis and I/O-intensive applications in supercomputing. In 2019, she became the Scientific Coordinator of the Computing Division, which gave her the opportunity to tackle a broader range of topics and in 2020, she was appointed the Section Manager of the Scientific Visualization team. Judit received her Bachelors, Masters and PhD in Computer Science at the Polytechnic University of Catalonia (UPC), Spain. She developed her Masters and PhD at the Barcelona Supercomputing Center, focused on programming models for heterogeneous and high-performance computing systems.

Course Staff

Werner van Geit

Werner is the Group Leader of the Cells team within the Simulation Neuroscience Division in Blue Brain. Werner obtained his Masters degree in Informatics from the University of Ghent in 2003, after which he worked as a researcher in the Computational Neuroscience at the University of Antwerp under the supervision of Prof. Erik De Schutter. He then relocated to the Okinawa Institute of Science and Technology in Japan for three and a half years. After joining Blue Brain in 2011 he has been involved both as researcher and system engineer in the single cell building pipeline.

Michael Reimann

Michael Reimann is the Group Leader for Connectomics within the Simulation Neuroscience Division. Michael develops methods to derive/predict the local synaptic connectivity in a neocortical microcircuit. Additionally, he analyzes the trends found in connectivity and how it relates to the electrical activity (structural to functional relation). Before joining Blue Brain, he worked with Prof. Christoph von Lassberg, on the analysis of data streams from simultaneous recordings of eye movement, EMG and full body tracking in collaboration. His research also included integration of vestibular information in humans. Michael studied Bioinformatics at the University of Tuebingen, Germany, specializing in neuroinformatics and coding theory before joining Blue Brain as a PhD student.

Course Staff

Audrey Mercer

Following a DEA (french predoctoral qualification) at the University of Montpellier, Dr Mercer moved to the department of Physiology, Royal Free Hospital Medical School, where she started a PhD under the supervision of Professor Alex Thomson. In 2003, she moved to the School of Pharmacy and was awarded her PhD in 2005. Dr Mercer became a RCUK Academic Fellow at the School in 2007, was appointed as a lecturer in 2012 and as Associate Professor in 2019.

Course Staff

Michele Migliori

Senior scientist at the Institute of Biophysics, National Research Council, Italy

Course Staff

Szalbocs Kàli

Senior scientist at Institute of Experimental Medicine, Hungarian Academy of Sciences, Hungary

Course Staff

Jean-Denis Courcol

Jean-Denis Courcol is the Section Manager of the Neuroscientific Software Engineering team and Deputy Head of the Computing Division. He leads the development of Blue Brain’s Neuroscientific Software team, who engineer tools for single cell model building, detailed model circuit building and, circuit and simulation analysis. The team aims to implement facilities for scientific workflows and for user interaction with scientific applications. An engineer graduate from the ‘Grande Ecole’ ENSIMAG (the National Superior School of Computer Science and Applied Mathematics of Grenoble), Jean-Denis spent 10 years at Dassault Systèmes developing CATIA, the industrial renowned computer-aided design software before joining Blue Brain.

Course Staff

Fabien Petitjean

Fabien is a Software Engineer born in Berlin of an Italian mother and a French father. When he is not running day and night in the mountain among ibexes, you can find him in front of a black board fighting with mathematical puzzles, or behind his computer screen writing thousands of lines of mysterious code, or drinking an old Rum while debating philosophical questions with his friends. To reconcile his passion for hiking and algorithms, he created the website “http://trail-passion.net“.

Course Staff

Andras Ecker

András Ecker is a PhD student, supervised by Henry Markram and co-supervised by Srikanth Ramaswamy, in the Circuits team in the Simulation Neuroscience Division. His focus is on a biophysically detailed synaptic plasticity in the somatosensory cortex, with implications on learning and memory storage. András has a Master’s degree from EPFL in Life Science Engineering where he was a research scholar and awarded best master’s thesis in the section. He has Bachelors in the same subject from Pazmany Peter Catholic University, Hungary and was granted an Excellence Fellowship by the Hungarian Republic.

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