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Kusch L, Diaz-Pier S, Klijn W, Sontheimer K, Bernard C, Morrison A, Jirsa V. Multiscale co-simulation design pattern for neuroscience applications. Front Neuroinform 2024; 18:1156683. [PMID: 38410682 PMCID: PMC10895016 DOI: 10.3389/fninf.2024.1156683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 01/19/2024] [Indexed: 02/28/2024] Open
Abstract
Integration of information across heterogeneous sources creates added scientific value. Interoperability of data, tools and models is, however, difficult to accomplish across spatial and temporal scales. Here we introduce the toolbox Parallel Co-Simulation, which enables the interoperation of simulators operating at different scales. We provide a software science co-design pattern and illustrate its functioning along a neuroscience example, in which individual regions of interest are simulated on the cellular level allowing us to study detailed mechanisms, while the remaining network is efficiently simulated on the population level. A workflow is illustrated for the use case of The Virtual Brain and NEST, in which the CA1 region of the cellular-level hippocampus of the mouse is embedded into a full brain network involving micro and macro electrode recordings. This new tool allows integrating knowledge across scales in the same simulation framework and validating them against multiscale experiments, thereby largely widening the explanatory power of computational models.
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Affiliation(s)
- Lionel Kusch
- Institut de Neurosciences des Systèmes (INS), UMR1106, Aix-Marseille Université, Marseilles, France
| | - Sandra Diaz-Pier
- Simulation and Data Lab Neuroscience, Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation, JARA, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Wouter Klijn
- Simulation and Data Lab Neuroscience, Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation, JARA, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Kim Sontheimer
- Simulation and Data Lab Neuroscience, Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation, JARA, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Christophe Bernard
- Institut de Neurosciences des Systèmes (INS), UMR1106, Aix-Marseille Université, Marseilles, France
| | - Abigail Morrison
- Simulation and Data Lab Neuroscience, Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation, JARA, Forschungszentrum Jülich GmbH, Jülich, Germany
- Forschungszentrum Jülich GmbH, IAS-6/INM-6, JARA, Jülich, Germany
- Computer Science 3 - Software Engineering, RWTH Aachen University, Aachen, Germany
| | - Viktor Jirsa
- Institut de Neurosciences des Systèmes (INS), UMR1106, Aix-Marseille Université, Marseilles, France
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Schlick T, Portillo-Ledesma S, Blaszczyk M, Dalessandro L, Ghosh S, Hackl K, Harnish C, Kotha S, Livescu D, Masud A, Matouš K, Moyeda A, Oskay C, Fish J. A MULTISCALE VISION-ILLUSTRATIVE APPLICATIONS FROM BIOLOGY TO ENGINEERING. INTERNATIONAL JOURNAL FOR MULTISCALE COMPUTATIONAL ENGINEERING 2021; 19:39-73. [PMID: 35330633 PMCID: PMC8942125 DOI: 10.1615/intjmultcompeng.2021039845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Modeling and simulation have quickly become equivalent pillars of research along with traditional theory and experimentation. The growing realization that most complex phenomena of interest span many orders of spatial and temporal scales has led to an exponential rise in the development and application of multiscale modeling and simulation over the past two decades. In this perspective, the associate editors of the International Journal for Multiscale Computational Engineering and their co-workers illustrate current applications in their respective fields spanning biomolecular structure and dynamics, civil engineering and materials science, computational mechanics, aerospace and mechanical engineering, and more. Such applications are highly tailored, exploit the latest and ever-evolving advances in both computer hardware and software, and contribute significantly to science, technology, and medical challenges in the 21st century.
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Affiliation(s)
- Tamar Schlick
- Department of Chemistry, New York University, New York, New York 10003, USA
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA
- NYU-ECNU Center for Computational Chemistry, NYU Shanghai, China
| | | | - Mischa Blaszczyk
- Institute of Mechanics of Materials, Ruhr-University Bochum, Bochum 44721, Germany
| | - Luke Dalessandro
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana 47405, USA
| | - Somnath Ghosh
- Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Klaus Hackl
- Institute of Mechanics of Materials, Ruhr-University Bochum, Bochum, 44721, Germany
| | - Cale Harnish
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Shravan Kotha
- Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Daniel Livescu
- Computer and Computational Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Arif Masud
- Department of Civil and Environmental Engineering, University of Illinois, Urbana, Illinois 61801, USA
| | - Karel Matouš
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | | | - Caglar Oskay
- Department of Civil and Environmental Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Jacob Fish
- Department of Civil Engineering and Engineering Mechanics, Columbia University, New York, New York 10027, USA
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