eprintid: 10199884 rev_number: 6 eprint_status: archive userid: 699 dir: disk0/10/19/98/84 datestamp: 2024-11-11 11:48:23 lastmod: 2024-11-11 11:48:23 status_changed: 2024-11-11 11:48:23 type: article metadata_visibility: show sword_depositor: 699 creators_name: Romani, Armando creators_name: Antonietti, Alberto creators_name: Bella, Davide creators_name: Budd, Julian creators_name: Giacalone, Elisabetta creators_name: Kurban, Kerem creators_name: Sáray, Sára creators_name: Abdellah, Marwan creators_name: Arnaudon, Alexis creators_name: Boci, Elvis creators_name: Colangelo, Cristina creators_name: Courcol, Jean-Denis creators_name: Delemontex, Thomas creators_name: Ecker, András creators_name: Falck, Joanne creators_name: Favreau, Cyrille creators_name: Gevaert, Michael creators_name: Hernando, Juan B creators_name: Herttuainen, Joni creators_name: Ivaska, Genrich creators_name: Kanari, Lida creators_name: Kaufmann, Anna-Kristin creators_name: King, James Gonzalo creators_name: Kumbhar, Pramod creators_name: Lange, Sigrun creators_name: Lu, Huanxiang creators_name: Lupascu, Carmen Alina creators_name: Migliore, Rosanna creators_name: Petitjean, Fabien creators_name: Planas, Judit creators_name: Rai, Pranav creators_name: Ramaswamy, Srikanth creators_name: Reimann, Michael W creators_name: Riquelme, Juan Luis creators_name: Román Guerrero, Nadir creators_name: Shi, Ying creators_name: Sood, Vishal creators_name: Sy, Mohameth François creators_name: Van Geit, Werner creators_name: Vanherpe, Liesbeth creators_name: Freund, Tamás F creators_name: Mercer, Audrey creators_name: Muller, Eilif creators_name: Schürmann, Felix creators_name: Thomson, Alex M creators_name: Migliore, Michele creators_name: Káli, Szabolcs creators_name: Markram, Henry title: Community-based reconstruction and simulation of a full-scale model of the rat hippocampus CA1 region ispublished: pub divisions: UCL divisions: B02 divisions: C08 divisions: D10 divisions: D11 divisions: G10 divisions: G12 note: This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third-party material in this article are included in the Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ abstract: 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. date: 2024-11-05 date_type: published publisher: Public Library of Science (PLoS) official_url: http://dx.doi.org/10.1371/journal.pbio.3002861 oa_status: green full_text_type: pub language: eng primo: open primo_central: open_green verified: verified_manual elements_id: 2334350 doi: 10.1371/journal.pbio.3002861 lyricists_name: Mercer, Audrey lyricists_name: Lange, Sigrun lyricists_id: AMERC74 lyricists_id: SLANG65 actors_name: Harris, Jean actors_id: JAHAR68 actors_role: owner full_text_status: public publication: PLOS Biology volume: 22 number: 11 article_number: e3002861 editors_name: Csicsvari, Jozsef citation: Romani, Armando; Antonietti, Alberto; Bella, Davide; Budd, Julian; Giacalone, Elisabetta; Kurban, Kerem; Sáray, Sára; ... Markram, Henry; + view all <#> Romani, Armando; Antonietti, Alberto; Bella, Davide; Budd, Julian; Giacalone, Elisabetta; Kurban, Kerem; Sáray, Sára; Abdellah, Marwan; Arnaudon, Alexis; Boci, Elvis; Colangelo, Cristina; Courcol, Jean-Denis; Delemontex, Thomas; Ecker, András; Falck, Joanne; Favreau, Cyrille; Gevaert, Michael; Hernando, Juan B; Herttuainen, Joni; Ivaska, Genrich; Kanari, Lida; Kaufmann, Anna-Kristin; King, James Gonzalo; Kumbhar, Pramod; Lange, Sigrun; Lu, Huanxiang; Lupascu, Carmen Alina; Migliore, Rosanna; Petitjean, Fabien; Planas, Judit; Rai, Pranav; Ramaswamy, Srikanth; Reimann, Michael W; Riquelme, Juan Luis; Román Guerrero, Nadir; Shi, Ying; Sood, Vishal; Sy, Mohameth François; Van Geit, Werner; Vanherpe, Liesbeth; Freund, Tamás F; Mercer, Audrey; Muller, Eilif; Schürmann, Felix; Thomson, Alex M; Migliore, Michele; Káli, Szabolcs; Markram, Henry; - view fewer <#> (2024) Community-based reconstruction and simulation of a full-scale model of the rat hippocampus CA1 region. PLOS Biology , 22 (11) , Article e3002861. 10.1371/journal.pbio.3002861 <https://doi.org/10.1371/journal.pbio.3002861>. Green open access document_url: https://discovery.ucl.ac.uk/id/eprint/10199884/1/journal.pbio.3002861.pdf