Community-based reconstruction and simulation of a full-scale model of the rat hippocampus CA1 region
The CA1 region of the hippocampus is one of the most studied regions of the rodent brain, thought to play an important role in cognitive functions such as memory and spatial navigation. Despite a wealth of experimental data on its structure and function, it has been challenging to integrate information obtained from diverse experimental approaches. To address this challenge, we present a community-based, full-scale in silico model of the rat CA1 that integrates a broad range of experimental data, from synapse to network, including the reconstruction of its principal afferents, the Schaffer collaterals, and a model of the effects that acetylcholine has on the system. We tested and validated each model component and the final network model, and made input data, assumptions, and strategies explicit and transparent. The unique flexibility of the model allows scientists to potentially address a range of scientific questions. In this article, we describe the methods used to set up simulations to reproduce in vitro and in vivo experiments. Among several applications in the article, we focus on theta rhythm, a prominent hippocampal oscillation associated with various behavioral correlates and use our computer model to reproduce experimental findings. Finally, we make data, code, and model available through the hippocampushub.eu portal, which also provides an extensive set of analyses of the model and a user-friendly interface to facilitate adoption and usage. This community-based model represents a valuable tool for integrating diverse experimental data and provides a foundation for further research into the complex workings of the hippocampal CA1 region.
Authors
- Mohameth François Sy (ORCID: https://orcid.org/0000-0002-4603-9838)
- Carmen Alina Lupaşcu (ORCID: https://orcid.org/0000-0002-7870-5620)
- Juan Luis Riquelme (ORCID: https://orcid.org/0000-0003-4604-7405)
- Joanne Falck (ORCID: https://orcid.org/0000-0003-2185-3750)
- Marwan Abdellah (ORCID: https://orcid.org/0000-0003-0751-2300)
- Alberto Antonietti (ORCID: https://orcid.org/0000-0003-0388-6321)
- Huanxiang Lu (ORCID: https://orcid.org/0000-0003-3377-9359)
- Alexis Arnaudon (ORCID: https://orcid.org/0000-0001-9486-1458)
- Werner Van Geit (ORCID: https://orcid.org/0000-0002-2915-720X)
- Lida Kanari (ORCID: https://orcid.org/0000-0002-9539-5070)
- Michael Gevaert (ORCID: https://orcid.org/0000-0002-7547-3297)
- András Ecker
- Ying Shi (ORCID: https://orcid.org/0000-0002-6442-9880)
- Srikanth Ramaswamy (ORCID: https://orcid.org/0000-0001-6642-7136)
- Nadir Román Guerrero (ORCID: https://orcid.org/0000-0001-7528-2549)
- Szabolcs Káli (ORCID: https://orcid.org/0000-0002-2740-6057)
- Genrich Ivaska
- Sára Sáray (ORCID: https://orcid.org/0000-0002-4341-177X)
- Rosanna Migliore (ORCID: https://orcid.org/0000-0001-9034-7849)
- Armando Romani (ORCID: https://orcid.org/0000-0001-6388-4286)
- Anna-Kristin Kaufmann (ORCID: https://orcid.org/0000-0002-6084-418X)
- Vishal Sood (ORCID: https://orcid.org/0000-0002-2167-7710)
- Jean-Denis Courcol (ORCID: https://orcid.org/0000-0002-9351-1461)
- Liesbeth Vanherpe (ORCID: https://orcid.org/0000-0002-1226-0526)
- Julian M. L. Budd (ORCID: https://orcid.org/0000-0001-8614-9989)
- Juan Hernando (ORCID: https://orcid.org/0000-0002-8562-8213)
- Judit Planas (ORCID: https://orcid.org/0000-0002-8221-7988)
- Tamás F. Freund (ORCID: https://orcid.org/0000-0002-9139-8370)
- Joni Herttuainen (ORCID: https://orcid.org/0000-0001-7301-2350)
- Henry Markram (ORCID: https://orcid.org/0000-0001-6164-2590)
- E. Giacalone (ORCID: https://orcid.org/0009-0006-1072-299X)
- Sigrun Lange (ORCID: https://orcid.org/0000-0002-7193-3102)
- Kerem Kurban (ORCID: https://orcid.org/0000-0003-4990-9541)
- Fabien Petitjean (ORCID: https://orcid.org/0000-0002-1321-4433)
- Pramod Kumbhar (ORCID: https://orcid.org/0000-0002-1756-801X)
- Michele Migliore
- Thomas Delemontex (ORCID: https://orcid.org/0000-0003-3218-5137)
- Felix Schürmann
- Michael Reimann (ORCID: https://orcid.org/0000-0003-3455-2367)
- Cristina Colangelo (ORCID: https://orcid.org/0009-0004-7974-5124)
- Cyrille Favreau (ORCID: https://orcid.org/0000-0003-1381-1585)
- James King (ORCID: https://orcid.org/0000-0003-0906-8389)
- Eilif Müller (ORCID: https://orcid.org/0000-0003-4309-8266)
- Elvis Boci (ORCID: https://orcid.org/0009-0002-5871-4164)
- Pranav Rai (ORCID: https://orcid.org/0009-0007-3639-4530)
- Davide Bella (ORCID: https://orcid.org/0000-0002-7389-0337)
- Audrey Mercer (ORCID: https://orcid.org/0000-0002-5086-2560)
- Alex M. Thomson
Institutions
- Centre Hospitalier Universitaire Sainte-Justine (CA)
- Pázmány Péter Catholic University (HU)
- HUN-REN Institute of Experimental Medicine (HU)
- National Research Council (IT)
- Mila - Quebec Artificial Intelligence Institute (CA)
- University College London (GB)
- École Polytechnique Fédérale de Lausanne (CH)
- Université de Montréal (CA)
- Newcastle University (GB)
- University of Westminster (GB)
Publication Details
- Journal
- PLoS Biology
- Published
- 2024-11-05
- DOI
- https://doi.org/10.1371/journal.pbio.3002861
- Citations
- 25
- Primary Topic
- Neuroscience and Neuropharmacology Research
- Type
- article
- Field-Weighted Citation Impact
- 6.71
Funders
- Wellcome Trust
- Board of the Swiss Federal Institutes of Technology
- Centro Svizzero di Calcolo Scientifico
- Novartis Pharma
- Horizon 2020 Framework Programme
- Medical Research Council