Workshop

09:00 – 09:30 Welcome and Introduction to the Workshop (Local Organizer & M. Migliore)

09:30 – 10:30 First steps into the ECEMP (L. L. Bologna)

10:30 – 10:45 Coffee / Tea break

10:45 – 11:30 Electrophysiological features extraction (R. Migliore)

11:30 – 12:30 Scientific drive: Single cell modeling – how it is done (M. Migliore)

12:30 – 14:30 Lunch break

14:30 – 17:30 Hands-on session I: (includes a coffee / Tea break in the middle)

                Dealing with 3D cell morphologies (C.A. Lupascu)

Electrophysiological features extraction: practice; speakers: L.L. Bologna, R. Migliore

              Build your own single-cell model; speakers: R. Migliore, P. Vitale, E. Giacalone

09:00 – 10:30 The NEURON-python simulation environment (C.A. Lupascu)

10:30 – 10:45 Coffee / Tea break

10:45 – 11:30 Scientific drive: ion channels (M. Migliore)

11:30 – 12:00 Introduction to visualization tools (O.D.R. Sánchez)

12:00 – 12:30 Single Cell Model optimization (P. Vitale)

12:30 – 14:30 Lunch break

14:30 – 17:30 Hands-on session II: (includes a coffee / Tea break in the middle)

                  The Virtual Brain environment for whole brain models; speakers: E. Baspinar and D. Depannemaecker

09:00 – 10:30 Student Presentations

10:30 – 10:45 Coffee / Tea break

10:45 – 11:30 Scientific drive: Full-scale models of brain area, olfactory bulb & hippocampus (M. Migliore)

11:30 – 12:30 Implementing simplified models (A. Marasco, C.. Tribuzi)

12:30 – 14:30 Lunch break

14:30 – 17:30 Hands-on session III: (includes a coffee / Tea break in the middle)

Visualization tools (O.D.R. Sánchez, S.M. Fernández)                 

The NEST simulator; speaker: S. Solinas
 

Social Dinner (Time TBD)

09:00 – 10:00 Network of spiking neurons and their response to perturbations (M. Mattia, M. Giugliano)

10:00 – 10:30 The NEST simulation II (S. Solinas)

10:30 – 10:45 Coffee / Tea break

10:45 – 11:30 Scientific drive: Modeling Pathological conditions (M. Migliore)

11:30 – 12:30 In silico experiments using circuits (L.L. Bologna)

12:30 – 14:30 Lunch break

14:30 – 17:30 Hands-on session IV: (includes a coffee / Tea break in the middle)

                  Run your network of spiking neurons; speakers: A. Galluzzi, G.V. Vinci, C. Capone

09:00 – 09:45 Getting supercomputing resources (C. Padrin)

09:45 – 10:45 Netpyne for large network simulations using NEURON (W. Lytton)

10:45 – 11:00 Coffee / Tea break

11:00 – 12:30 Using CoreNEURON (M. Hines)

12:30 – 14:30 Lunch break

14:30 – 17:00 Hands-on session V: (includes a coffee / Tea break in the middle)

                  Implementing and running efficient simulations on parallel supercomputer systems; speakers: M. Hines, W. Lytton

17:00 – 18:00 Q&A, discussion, conclusions

He received his master degree in Biomedical Engineering from Eindhoven University of Technology (Netherlands) in 2013, on curve reconstruction via sub-Riemannian geometry and its application to retinal vessel tracking, aiming early detection of diabetes. He did his PhD in Mathematics at University of Bologna (Italy), working on minimal surfaces in sub-Riemannian structures and functional geometry of the visual cortex. Then he did a one year in the Department of Mathematics of University of Bologna, then two and a half years at Inria (Sophia Antipolis, France) where he focused on multiple-timescale dynamical systems applied to neuronal population models, finally two and a half years in Paris-Saclay Institute of Neuroscience (NeuroPSI) where he worked on biophysically realistic modeling of decision-making neuronal populations. He has been a permanent researcher (CRCN) at Inria since October 2023. He works in mathematical neuroscience, and his research is based on modeling neuronal populations via dynamical systems and sub-Riemannian geometries.

Research Scientist, Institute of Biophysics of the Italian National Research Council (Palermo). PhD in Neuro-engineering at the Italian Institute of Technology (IIT, Genoa), investigating in-vitro cortical cultures behaviour through both an experimental and modelling approach. During a post-doctoral period at the Université Pierre et Marie Curie (UPMC, Paris), he studied information neurotransmission in the somatosensory system via a neuromimetic software architecture. He is currently involved in the design and implementation of web applications and software tools for data analysis and computational modelling for the EBRAINS Reaserch Infrastructure, in the framework of the EBRAINS-Italy project.

He is a theoretical physicist, and a researcher in theoretical and computational neuroscience, devoted to understanding biological and artificial intelligence. He got his PhD at La Sapienza University, and have held postdoctoral positions at the European Institute of Theoretical Neuroscience in Paris and the APE Lab (High-Performance and Parallel Computing Lab) at the Istituto Nazionale di Fisica Nucleare in Rome. Currently, I am a researcher at the Istituto Superiore di Sanità (Italian Institute of Health) in Rome, Italy.

He earned a Bachelor's degree in Physics at the University of Aix-Marseille (France), followed by a Master degree in Life Sciences at the École Pratique des Hautes Études (EPHE) in Paris. Wanting to contribute to scientific research, he embarked on a PhD at the Federal University of São Paulo (UNIFESP) and at the Federal University of Sao Joao (UFSJ) in Brazil. His research activities continued in theoretical and computational neuroscience at the Institute of Neuroscience of Paris-Saclay in France (NeuroPSI), and currently at the Institute of Systems Neuroscience (INS) at Timone in Marseille. He is interested in theoretical neuroscience and potential clinical applications, as well as the integration of scales, and, in the construction process of models and their domains of application.

Researcher at the National Center for Radiation Protection and Computational Physics, part of the Istituto Superiore di Sanità (Italian Institute of Health) in Rome, Italy. Theoretical Physics with a PhD in Applied Mathematics, my research initially focused on statistical mechanics models for neural networks and modeling biological systems is now centered on cortical network dynamics and artificial intelligence within the fields of theoretical physics and computational neuroscience.

PhD Student, Institute of Biophysics of the Italian National Research Council (Palermo). Master’s degree in applied physics at the University of Bologna, Alma Mater Studiorum, in 2017, with a thesis focusing on a graph-based analysis of the brain structural connectivity using Diffusion-Weighted magnetic resonance Imaging (DWI). She is now involved in developing biophysically and morphologically accurate computational models of neurons using the NEURON-Python environment on parallel supercomputers, and in the analysis of the information processing in the hippocampus using the EBRAINS cellular level model circuits.

He is Principal Investigator and Associate Professor of Bioengineering at the Univ. of Modena and Reggio Emilia (Italy). He retains a small and temporary appointment as a Professor of Physiology at SISSA. He obtained his PhD in Biomedical Engineering from the Univ. of Genova (Italy) in 2001, then held a “long-term fellowship” by Human Frontiers Science Program Organization at the University of Bern (Switzerland). In 2005, he joined the experimental lab of Prof. Dr. H. Markram as a junior group leader at the Brain Mind Institute of the Swiss Federal Institute of Technology of Lausanne (EPFL). In 2008, he joined as a “tenure-track” Assistant Professor of Neuroscience the the Dept. of Biomedical Sciences of the Univ. of Antwerp (Belgium). In 2019, he left Belgium to join as a Professor of Physiology the International School of Advanced Studies (SISSA) of Trieste, Italy, moving my team at SISSA’s Neuroscience Area, and starting the Neuronal Dynamics Laboratory. In 2024, he was appointed Professor of Bioengineering by the Univ. of Modena and Reggio Emilia, joining its Dept. of Biomedical, Metabolic and Neural Sciences, and the newly launched Master in Biomedical Engineering, contributing with his vision on Neural Engineering.

Neuroscience Department, Yale University, USA. He is a developer and beginning author of the NEURON Simulation Environment. He has been associated with the Blue Brain and European Human Brain Projects from their beginning.

Biography

Department of Mathematics, University of Naples “Federico II”, Naples, Italy. Mathematical engineer, co-founder of Nova Analysis, where she has worked on innovation and product development through multiphysics simulations and data science. In 2022 she joined University of Naples Federico II in the frame of HBP project, where she works on computational neuroscience, implementing mathematical modeling and supporting data exploration and model analysis.

Dr. Lytton is a practicing neurologist who sees patients with brain disease. His research focus is to bring the tools of computational neuroscience into clinical practice. Computational neuroscience can provide mechanistic causality to explain clinical correlations, linking scales ranging from the molecular scale of drugs up to the behavioral scale of disordered cognition and movement. He has worked in epilepsy, stroke, schizophrenia, Parkinsons, Alzheimers, pain and other brain and spinal cord disorders.

Associate Professor of Mathematical Physics, University of Naples Federico II, Naples, Italy. Ph.D. in Applied Mathematics and Informatics (2003). My research interests have been focused on continuum mechanics, dynamical systems, mathematical models, analytic and computational methods for nonlinear problems in applied sciences, mathematical models, and computational Neuroscience. Coordinator and Principal Investigator (PI) of several scientific projects with national and international funding. Member of the editorial boards and guest editor for scientific journals, author of over 50 scientific publications, and three volumes for Springer.

Susana Mata works as an associate professor at Universidad Rey Juan Carlos in Madrid. She is part of the VG-Lab research group and has been involved in the Human Brain Project. She is currently involved in the EBRAINS 2.0 and in the Virtual Brain Twin Project. She has taken part in the development of SimVisSuite, the Simulation Data Visualization Suite, that provides tools for interactive visual exploration of neuroscience data for the analysis of complex scenarios, based on an approach that structures and depicts the information at different levels of abstraction, combining schematic and realistic representations.

Senior Researcher at the Natl. Center for Radiation Protection and Computational Physics of the Istituto Superiore di Sanità (Italian Institute of Health) in Rome, Italy. Physicist by training with a PhD in Neurophysiology, my research activity aims at bridging the gap between theory and experimental evidence on cortical network dynamics within the framework of theoretical physics and computational/systems neuroscience. I published over 60 journal papers and participated in several EU funded projects. I am currently adjunct professor of Neural Networks at the Physics Dept. of “Sapienza” University of Rome, Italy.

Research Scientist, Institute of Biophysics of the Italian National Research Council (Palermo). PhD in Theoretical Physics at the University of Palermo in 2004. Until 2010, her research interests were focused on superconducting mesoscopic devices interacting with quantized electromagnetic fields. The currently main field of interest is computational neuroscience, with focus on detailed modeling of neurons and small networks (mainly from hippocampus), effects of dendritic ionic channels on firing properties and synaptic integration, kinetic models of synaptic transmission and plasticity.

Senior Associate, Institute of Biophysics of the Italian National. Research Council (Palermo). D.Phil. in Physics (1980, University of Palermo, Italy). He has been Research Director of the Italian National Research Council (1983-2024), Director of the Palermo section of the Institute of Biophysics (2015-2017), Visiting Professor of Computational Neuroscience at the University of Rome La Sapienza (Italy, 2018-2023), Visiting Professor of Cybernetics at the Department of Mathematics and Informatics of the University of Palermo (Italy, 2000-2018), and Visiting Scientist at the Department of Neuroscience of the Yale University School of Medicine (New Haven, USA, 2000-2020). His lab is involved in modelling realistic neurons and networks, synaptic integration processes, and plasticity mechanisms. The main long-term goal is to understand the emergence of higher brain functions and dysfunctions from cellular processes, implementing new tools and using state of the art simulation environments on different supercomputer systems.

Dr. Cristiano Padrin is a HPC Scientific Application Engineer senior at CINECA with roles of Project Manager and Project Coordinator in Italian and EU projects. Main institutional roles covered are CINECA representative in EBRAINS Italian Community, EBRAINS Italian National Node and in EBRAINS AISBL. Main duties covered at CINECA are the supervision of support activities for developing RIs. He takes care of coordination activities for research in-house in EBRAINS Italy. 

Óscar David Robles Sánchez works as associate professor at Universidad Rey Juan Carlos in Madrid. He is part of the VG-Lab research group and was involved in the HBP since its very beginning. He is currently involved in the Virtual Brain Twin project, and is also part of EBRAINS 2.0. His group has developed  SimVisSuite, the Simulation Data Visualization Suite, that provides tools for interactive visual exploration of neuroscience data for the analysis of complex scenarios.

He is a Physicist, Master at University of Bologna (Italy), with a PhD in Biomedical Sciences at the University of Antwerp (Belgium) specialized in the simulation of biologically realistic and artificial Neural Networks of the Hippocampus and Cerebellum on HPC systems. He is currently a Researcher in Tenure Track at the University of Sassari teaching Artificial intelligence and Automatic Controls and developing Mixed Reality tools for the visualization of neural network activity within the EBRAINs-Italy Research Infrastructure.

He is a theoretical physicist, who got his PhD in Physics from the University of Rome Tor Vergata. He is currently a postdoc at the Istituto Superiore di Sanità (Italian Institute of Health) in Rome, Italy. He is fascinated by the behavior of complex dynamical systems. His main focus is in computational and theoretical neuroscience. In particular he is interested in deriving from first principles, a general theory of neuronal dynamics and in understanding how neural computation emerges from interacting neurons.

Research Scientist, Institute of Biophysics of the Italian National Research Council (Palermo). PhD in Chemistry from University of Palermo in 2014. Since graduation, her research interest was focused on supramolecular chemistry. In particular, she studied self-assemby processes in organic salts leading to gel phase formation, molecular recognition processes and ionic liquids organization. Her currently research field is computational neuroscience, implementing data-driven subcellular models of the biochemical pathways involved in synaptic plasticity and single neuron, mainly from the hippocampus region, under both physiological and pathological conditions.