Multiscale co-simulation design pattern for neuroscience applications

Authors: Lionel Kusch, Sandra Diaz-Pier, Wouter Klijn, Kim Sontheimer, Christophe Bernard, Abigail Morrison, Viktor Jirsa

Source: Frontiers in Neuroinformatics, Vol 18 (2024)

Subject Terms: co-simulation, multiscale, brain network model, spiking neural network, mouse brain, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fninf.2024.1156683/full; https://doaj.org/toc/1662-5196

Access URL: https://doaj.org/article/e90510803c42445ca83b752a4c6267b4

Brain simulation as a cloud service: The Virtual Brain on EBRAINS

Authors: Michael Schirner, Lia Domide, Dionysios Perdikis, Paul Triebkorn, Leon Stefanovski, Roopa Pai, Paula Prodan, Bogdan Valean, Jessica Palmer, Chloê Langford, André Blickensdörfer, Michiel van der Vlag, Sandra Diaz-Pier, Alexander Peyser, Wouter Klijn, Dirk Pleiter, Anne Nahm, Oliver Schmid, Marmaduke Woodman, Lyuba Zehl, Jan Fousek, Spase Petkoski, Lionel Kusch, Meysam Hashemi, Daniele Marinazzo, Jean-François Mangin, Agnes Flöel, Simisola Akintoye, Bernd Carsten Stahl, Michael Cepic, Emily Johnson, Gustavo Deco, Anthony R. McIntosh, Claus C. Hilgetag, Marc Morgan, Bernd Schuller, Alex Upton, Colin McMurtrie, Timo Dickscheid, Jan G. Bjaalie, Katrin Amunts, Jochen Mersmann, Viktor Jirsa, Petra Ritter

Source: NeuroImage, Vol 251, Iss , Pp 118973- (2022)

Subject Terms: Brain modelling, Cloud, Connectome, Neuroimaging, Network model, High performance computing, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S1053811922001021; https://doaj.org/toc/1095-9572

Access URL: https://doaj.org/article/0f18a5ffed99423bbcf750bc9eb638bf

Exploring Parameter and Hyper-Parameter Spaces of Neuroscience Models on High Performance Computers With Learning to Learn

Authors: Alper Yegenoglu, Anand Subramoney, Thorsten Hater, Cristian Jimenez-Romero, Wouter Klijn, Aarón Pérez Martín, Michiel van der Vlag, Michael Herty, Abigail Morrison, Sandra Diaz-Pier

Source: Frontiers in Computational Neuroscience, Vol 16 (2022)

Subject Terms: simulation, meta learning, hyper-parameter optimization, high performance computing, connectivity generation, parameter exploration, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fncom.2022.885207/full; https://doaj.org/toc/1662-5188

Access URL: https://doaj.org/article/48f75b596f42417a9a8e08f9f36d2677

Deploying and Optimizing Embodied Simulations of Large-Scale Spiking Neural Networks on HPC Infrastructure

Authors: Benedikt Feldotto, Jochen Martin Eppler, Cristian Jimenez-Romero, Christopher Bignamini, Carlos Enrique Gutierrez, Ugo Albanese, Eloy Retamino, Viktor Vorobev, Vahid Zolfaghari, Alex Upton, Zhe Sun, Hiroshi Yamaura, Morteza Heidarinejad, Wouter Klijn, Abigail Morrison, Felipe Cruz, Colin McMurtrie, Alois C. Knoll, Jun Igarashi, Tadashi Yamazaki, Kenji Doya, Fabrice O. Morin

Source: Frontiers in Neuroinformatics, Vol 16 (2022)

Subject Terms: spiking neural networks, embodiment, Neurorobotics Platform, high performance computing (HPC), NEST, musculoskeletal modeling, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fninf.2022.884180/full; https://doaj.org/toc/1662-5196

Access URL: https://doaj.org/article/27873b2367594477a8be12b4b7a80018

ConGen—A Simulator-Agnostic Visual Language for Definition and Generation of Connectivity in Large and Multiscale Neural Networks

Authors: Patrick Herbers, Iago Calvo, Sandra Diaz-Pier, Oscar D. Robles, Susana Mata, Pablo Toharia, Luis Pastor, Alexander Peyser, Abigail Morrison, Wouter Klijn

Source: Frontiers in Neuroinformatics, Vol 15 (2022)

Subject Terms: multiscale simulation, large scale simulation, visual language, neural networks, connectivity generation, connectome, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fninf.2021.766697/full; https://doaj.org/toc/1662-5196

Access URL: https://doaj.org/article/04eb2faa008747f785d189e9c44ae0fc

Editorial: Linking experimental and computational connectomics

Authors: Alexander Peyser, Sandra Diaz Pier, Wouter Klijn, Abigail Morrison, Jochen Triesch

Source: Harvard Data Science Review, Vol 3, Iss 4 (2021)

Subject Terms: Electronic computers. Computer science, QA75.5-76.95

File Description: electronic resource

Relation: https://doaj.org/toc/2644-2353

Access URL: https://doaj.org/article/173a0af3bc9640e2a5ba9cf4db8c6650

26th Annual Computational Neuroscience Meeting (CNS*2017): Part 2

Authors: Leonid L. Rubchinsky, Sungwoo Ahn, Wouter Klijn, Ben Cumming, Stuart Yates, Vasileios Karakasis, Alexander Peyser, Marmaduke Woodman, Sandra Diaz-Pier, James Deraeve, Eliana Vassena, William Alexander, David Beeman, Pawel Kudela, Dana Boatman-Reich, William S. Anderson, Niceto R. Luque, Francisco Naveros, Richard R. Carrillo, Eduardo Ros, Angelo Arleo, Jacob Huth, Koki Ichinose, Jihoon Park, Yuji Kawai, Junichi Suzuki, Hiroki Mori, Minoru Asada, Sorinel A. Oprisan, Austin I. Dave, Tahereh Babaie, Peter Robinson, Alejandro Tabas, Martin Andermann, André Rupp, Emili Balaguer-Ballester, Henrik Lindén, Rasmus K. Christensen, Mari Nakamura, Tania R. Barkat, Zach Tosi, John Beggs, Davide Lonardoni, Fabio Boi, Stefano Di Marco, Alessandro Maccione, Luca Berdondini, Joanna Jędrzejewska-Szmek, Daniel B. Dorman, Kim T. Blackwell, Christoph Bauermeister, Hanna Keren, Jochen Braun, João V. Dornas, Eirini Mavritsaki, Silvio Aldrovandi, Emma Bridger, Sukbin Lim, Nicolas Brunel, Anatoly Buchin, Clifford Charles Kerr, Anton Chizhov, Gilles Huberfeld, Richard Miles, Boris Gutkin, Martin J. Spencer, Hamish Meffin, David B. Grayden, Anthony N. Burkitt, Catherine E. Davey, Liangyu Tao, Vineet Tiruvadi, Rehman Ali, Helen Mayberg, Robert Butera, Cengiz Gunay, Damon Lamb, Ronald L. Calabrese, Anca Doloc-Mihu, Víctor J. López-Madrona, Fernanda S. Matias, Ernesto Pereda, Claudio R. Mirasso, Santiago Canals, Alice Geminiani, Alessandra Pedrocchi, Egidio D’Angelo, Claudia Casellato, Ankur Chauhan, Karthik Soman, V. Srinivasa Chakravarthy, Vignayanandam R. Muddapu, Chao-Chun Chuang, Nan-yow Chen, Mehdi Bayati, Jan Melchior, Laurenz Wiskott, Amir Hossein Azizi, Kamran Diba, Sen Cheng, Elena Y. Smirnova, Elena G. Yakimova, Anton V. Chizhov, Nan-Yow Chen, Chi-Tin Shih, Dorian Florescu, Daniel Coca, Julie Courtiol, Viktor K. Jirsa, Roberto J. M. Covolan, Bartosz Teleńczuk, Richard Kempter, Gabriel Curio, Alain Destexhe, Jessica Parker, Alexander N. Klishko, Boris I. Prilutsky, Gennady Cymbalyuk, Felix Franke, Andreas Hierlemann, Rava Azeredo da Silveira, Stefano Casali, Stefano Masoli, Martina Rizza, Martina Francesca Rizza, Yinming Sun, Willy Wong, Faranak Farzan, Daniel M. Blumberger, Zafiris J. Daskalakis, Svitlana Popovych, Shivakumar Viswanathan, Nils Rosjat, Christian Grefkes, Silvia Daun, Damiano Gentiletti, Piotr Suffczynski, Vadym Gnatkovski, Marco De Curtis, Hyeonsu Lee, Se-Bum Paik, Woochul Choi, Jaeson Jang, Youngjin Park, Jun Ho Song, Min Song, Vicente Pallarés, Matthieu Gilson, Simone Kühn, Andrea Insabato, Gustavo Deco, Katharina Glomb, Adrián Ponce-Alvarez, Petra Ritter, Adria Tauste Campo, Alexander Thiele, Farah Deeba, P. A. Robinson, Sacha J. van Albada, Andrew Rowley, Michael Hopkins, Maximilian Schmidt, Alan B. Stokes, David R. Lester, Steve Furber, Markus Diesmann, Alessandro Barri, Martin T. Wiechert, David A. DiGregorio, Alexander G. Dimitrov, Catalina Vich, Rune W. Berg, Antoni Guillamon, Susanne Ditlevsen, Romain D. Cazé, Benoît Girard, Stéphane Doncieux, Nicolas Doyon, Frank Boahen, Patrick Desrosiers, Edward Laurence, Louis J. Dubé, Russo Eleonora, Daniel Durstewitz, Dominik Schmidt, Tuomo Mäki-Marttunen, Florian Krull, Francesco Bettella, Christoph Metzner, Anna Devor, Srdjan Djurovic, Anders M. Dale, Ole A. Andreassen, Gaute T. Einevoll, Solveig Næss, Torbjørn V. Ness, Geir Halnes, Eric Halgren, Klas H. Pettersen, Marte J. Sætra, Espen Hagen, Alina Schiffer, Axel Grzymisch, Malte Persike, Udo Ernst, Daniel Harnack, Udo A. Ernst, Nergis Tomen, Stefano Zucca, Valentina Pasquale, Giuseppe Pica, Manuel Molano-Mazón, Michela Chiappalone, Stefano Panzeri, Tommaso Fellin, Kelvin S. Oie, David L. Boothe, Joshua C. Crone, Alfred B. Yu, Melvin A. Felton, Isma Zulfiqar, Michelle Moerel, Peter De Weerd, Elia Formisano, Kelvin Oie, Piotr Franaszczuk, Roland Diggelmann, Michele Fiscella, Domenico Guarino, Jan Antolík, Andrew P. Davison, Yves Frègnac, Benjamin Xavier Etienne, Flavio Frohlich, Jérémie Lefebvre, Encarni Marcos, Maurizio Mattia, Aldo Genovesio, Leonid A. Fedorov, Tjeerd M.H. Dijkstra, Louisa Sting, Howard Hock, Martin A. Giese, Laure Buhry, Clément Langlet, Francesco Giovannini, Christophe Verbist, Stefano Salvadé, Michele Giugliano, James A. Henderson, Hendrik Wernecke, Bulcsú Sándor, Claudius Gros, Nicole Voges, Paulina Dabrovska, Alexa Riehle, Thomas Brochier, Sonja Grün, Yifan Gu, Pulin Gong, Grégory Dumont, Nikita A. Novikov, Boris S. Gutkin, Parul Tewatia, Olivia Eriksson, Andrei Kramer, Joao Santos, Alexandra Jauhiainen, Jeanette H. Kotaleski, Jovana J. Belić, Arvind Kumar, Jeanette Hellgren Kotaleski, Masanori Shimono, Naomichi Hatano, Subutai Ahmad, Yuwei Cui, Jeff Hawkins, Johanna Senk, Karolína Korvasová, Tom Tetzlaff, Moritz Helias, Tobias Kühn, Michael Denker, PierGianLuca Mana, David Dahmen, Jannis Schuecker, Sven Goedeke, Christian Keup, Katja Heuer, Rembrandt Bakker, Paul Tiesinga, Roberto Toro, Wei Qin, Alex Hadjinicolaou, Michael R. Ibbotson, Tatiana Kameneva, William W. Lytton, Lealem Mulugeta, Andrew Drach, Jerry G. Myers, Marc Horner, Rajanikanth Vadigepalli, Tina Morrison, Marlei Walton, Martin Steele, C. Anthony Hunt, Nicoladie Tam, Rodrigo Amaducci, Carlos Muñiz, Manuel Reyes-Sánchez, Francisco B. Rodríguez, Pablo Varona, Joseph T. Cronin, Matthias H. Hennig, Elisabetta Iavarone, Jane Yi, Ying Shi, Bas-Jan Zandt, Werner Van Geit, Christian Rössert, Henry Markram, Sean Hill, Christian O’Reilly, Rodrigo Perin, Huanxiang Lu, Alexander Bryson, Michal Hadrava, Jaroslav Hlinka, Ryosuke Hosaka, Mark Olenik, Conor Houghton, Nicolangelo Iannella, Thomas Launey, Rebecca Kotsakidis, Jaymar Soriano, Takatomi Kubo, Takao Inoue, Hiroyuki Kida, Toshitaka Yamakawa, Michiyasu Suzuki, Kazushi Ikeda, Samira Abbasi, Amber E. Hudson, Detlef H. Heck, Dieter Jaeger, Joel Lee, Skirmantas Janušonis, Maria Luisa Saggio, Andreas Spiegler, William C. Stacey, Christophe Bernard, Davide Lillo, Spase Petkoski, Mark Drakesmith, Derek K. Jones, Ali Sadegh Zadeh, Chandra Kambhampati, Jan Karbowski, Zeynep Gokcen Kaya, Yair Lakretz, Alessandro Treves, Lily W. Li, Joseph Lizier, Cliff C. Kerr, Timothée Masquelier, Saeed Reza Kheradpisheh, Hojeong Kim, Chang Sub Kim, Julia A. Marakshina, Alexander V. Vartanov, Anastasia A. Neklyudova, Stanislav A. Kozlovskiy, Andrey A. Kiselnikov, Kanako Taniguchi, Katsunori Kitano, Oliver Schmitt, Felix Lessmann, Sebastian Schwanke, Peter Eipert, Jennifer Meinhardt, Julia Beier, Kanar Kadir, Adrian Karnitzki, Linda Sellner, Ann-Christin Klünker, Lena Kuch, Frauke Ruß, Jörg Jenssen, Andreas Wree, Paula Sanz-Leon, Stuart A. Knock, Shih-Cheng Chien, Burkhard Maess, Thomas R. Knösche, Charles C. Cohen, Marko A. Popovic, Jan Klooster, Maarten H.P. Kole, Erik A. Roberts, Nancy J. Kopell, Daniel Kepple, Hamza Giaffar, Dima Rinberg, Alex Koulakov, Caroline Garcia Forlim, Leonie Klock, Johanna Bächle, Laura Stoll, Patrick Giemsa, Marie Fuchs, Nikola Schoofs, Christiane Montag, Jürgen Gallinat, Ray X. Lee, Greg J. Stephens, Bernd Kuhn, Luiz Tauffer, Philippe Isope, Katsuma Inoue, Yoshiyuki Ohmura, Shogo Yonekura, Yasuo Kuniyoshi, Hyun Jae Jang, Jeehyun Kwag, Marc de Kamps, Yi Ming Lai, Filipa dos Santos, K. P. Lam, Peter Andras, Julia Imperatore, Jessica Helms, Tamas Tompa, Antonieta Lavin, Felicity H. Inkpen, Michael C. Ashby, Nathan F. Lepora, Aaron R. Shifman, John E. Lewis, Zhong Zhang, Yeqian Feng, Christian Tetzlaff, Tomas Kulvicius, Yinyun Li, Rodrigo F. O. Pena, Davide Bernardi, Antonio C. Roque, Benjamin Lindner, Sebastian Vellmer, Ausra Saudargiene, Tiina Maninen, Riikka Havela, Marja-Leena Linne, Arthur Powanwe, Andre Longtin, Jesús A. Garrido, Joe W. Graham, Salvador Dura-Bernal, Sergio L. Angulo, Samuel A. Neymotin, Srdjan D. Antic

Source: BMC Neuroscience, Vol 18, Iss S1, Pp 1-79 (2017)

Subject Terms: Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571, Neurophysiology and neuropsychology, QP351-495

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12868-017-0371-2; https://doaj.org/toc/1471-2202

Access URL: https://doaj.org/article/cb449872ac00401c841a6e1283c6594a

Brain simulation as a cloud service: The Virtual Brain on EBRAINS

Authors: Michael Schirner (Berlin Institute of Health at Charité, Universitätsmedizin Berlin), Lia Domide (Codemart), Dionysios Perdikis (Berlin Institute of Health at Charité, Universitätsmedizin Berlin), Paul Triebkorn (Berlin Institute of Health at Charité, Universitätsmedizin Berlin), Leon Stefanovski (Berlin Institute of Health at Charité, Universitätsmedizin Berlin), Roopa Pai (Berlin Institute of Health at Charité, Universitätsmedizin Berlin), Paula Prodan (Codemart), Bogdan Valean (Codemart), Jessica Palmer (Berlin Institute of Health at Charité, Universitätsmedizin Berlin), Chloê Langford (Berlin Institute of Health at Charité, Universitätsmedizin Berlin), André Blickensdörfer (Berlin Institute of Health at Charité, Universitätsmedizin Berlin), Michiel van der Vlag (SimLab Neuroscience, Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation, JARA, Forschungszentrum Jülich GmbH), Sandra Diaz-Pier (SimLab Neuroscience, Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation, JARA, Forschungszentrum Jülich GmbH), Alexander Peyser (SimLab Neuroscience, Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation, JARA, Forschungszentrum Jülich GmbH), Wouter Klijn (SimLab Neuroscience, Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation, JARA, Forschungszentrum Jülich GmbH), Dirk Pleiter (Jülich Supercomputer Centre, Forschungszentrum Jülich), Anne Nahm (Jülich Supercomputer Centre, Forschungszentrum Jülich), Oliver Schmid (Swiss Federal Institute of Technology Lausanne (EPFL)), Marmaduke Woodman (Institut de Neurosciences des Systèmes, Aix Marseille Université), Lyuba Zehl (Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich), Jan Fousek (Institut de Neurosciences des Systèmes, Aix Marseille Université), Spase Petkoski (Institut de Neurosciences des Systèmes, Aix Marseille Université), Lionel Kusch (Institut de Neurosciences des Systèmes, Aix Marseille Université), Meysam Hashemi (Institut de Neurosciences des Systèmes, Aix Marseille Université), Daniele Marinazzo (Department of Data-Analysis, Faculty of Psychology and Educational Sciences, Ghent University), Jean-François Mangin (Université Paris-Saclay, CEA, CNRS, Neurospin, Baobab), Agnes Flöel (Department of Neurology, University Medicine Greifswald), Simisola Akintoye (Leicester De Montfort Law School, De Montfort University), Bernd Carsten Stahl (Centre for Computing and Social Responsibility, De Montfort University), Michael Cepic (Department of Innovation and Digitalisation in Law, Faculty of Law, University of Vienna), Emily Johnson (Department of Innovation and Digitalisation in Law, Faculty of Law, University of Vienna), Gustavo Deco (Computational Neuroscience Group, Center for Brain and Cognition, Department of Information and Communication Technologies, Universitat Pompeu Fabra), Anthony R. McIntosh (Rotman Research Institute, Baycrest Health Sciences), Claus C. Hilgetag (Institute of Computational Neuroscience, University Medical Center Hamburg-Eppendorf), Marc Morgan (Swiss Federal Institute of Technology Lausanne (EPFL)), Bernd Schuller (Jülich Supercomputer Centre, Forschungszentrum Jülich), Alex Upton (CSCS Swiss National Supercomputing Centre), Colin McMurtrie (CSCS Swiss National Supercomputing Centre), Timo Dickscheid (Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich), Jan G. Bjaalie (Institute of Basic Medical Sciences, University of Oslo), Katrin Amunts (Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich), Jochen Mersmann (CodeBox GmbH), Viktor Jirsa (Institut de Neurosciences des Systèmes, Aix Marseille Université), Petra Ritter (Berlin Institute of Health at Charité, Universitätsmedizin Berlin)

Availability: http://data.europeana.eu/aggregation/europeana/1300/https___phaidra_univie_ac_at_o_1654579

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