{"id":27332450,"url":"https://github.com/beaherrera/2-compartments_l5-pc_model","last_synced_at":"2025-04-12T13:54:16.053Z","repository":{"id":195871370,"uuid":"229796891","full_name":"beaherrera/2-compartments_L5-PC_model","owner":"beaherrera","description":"A Minimal Biophysical Model of Neocortical Pyramidal Cells: Implications for Frontal Cortex Microcircuitry and Field Potential Generation","archived":false,"fork":false,"pushed_at":"2022-07-26T15:18:59.000Z","size":8005,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2023-09-19T23:55:49.235Z","etag":null,"topics":["ca-spikes","cognitive-control","eeg","lfp-sources","pyramidal-cells"],"latest_commit_sha":null,"homepage":"https://doi.org/10.1523/JNEUROSCI.0221-20.2020","language":"MATLAB","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/beaherrera.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2019-12-23T17:35:15.000Z","updated_at":"2023-09-19T23:55:50.690Z","dependencies_parsed_at":"2023-09-20T00:11:19.134Z","dependency_job_id":null,"html_url":"https://github.com/beaherrera/2-compartments_L5-PC_model","commit_stats":null,"previous_names":["beaherrera/2-compartments_l5-pc_model"],"tags_count":null,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/beaherrera%2F2-compartments_L5-PC_model","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/beaherrera%2F2-compartments_L5-PC_model/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/beaherrera%2F2-compartments_L5-PC_model/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/beaherrera%2F2-compartments_L5-PC_model/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/beaherrera","download_url":"https://codeload.github.com/beaherrera/2-compartments_L5-PC_model/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248576706,"owners_count":21127459,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["ca-spikes","cognitive-control","eeg","lfp-sources","pyramidal-cells"],"created_at":"2025-04-12T13:54:15.469Z","updated_at":"2025-04-12T13:54:16.039Z","avatar_url":"https://github.com/beaherrera.png","language":"MATLAB","funding_links":[],"categories":[],"sub_categories":[],"readme":"# 2-compartments_L5-PC_model\nTwo-compartments Layer 5 Pyramidal Cell Model\n\nThe basal-dendritic/somatic compartment includes the classic Hodgkin-Huxley sodium (I_Na) and potassium delayed rectifier (I_Kdr) currents (Hodgkin and Huxley, 1952). The apical-dendrite/trunk compartment includes persistent Na^+ current (I_Nap) (Magistretti and Alonso, 1999), Ca^(2+) L-type current (I_CaL) (Lytton and Sejnowski, 1991), hyperpolarization-activated non-specific cation current (I_h) (Kole et al., 2006), muscarinic K+ current (I_M) (Adams et al., 1982), and the slow-inactivating potassium current (I_Ks) (Korngreen and Sakmann, 2000).\n\n## Plataform\nMatLab (release 2018b)\n\nA memory of at least 16 GB is needed to run the trials to create the f-I curves. \n\n## Dependencies\nFor the numerical simulations and data processing the following MatLab toolboxes were used:\n- [CSDplotter-master](https://github.com/espenhgn/CSDplotter)\n- [RasterPlot](https://www.mathworks.com/matlabcentral/fileexchange/45671-flexible-and-fast-spike-raster-plotting)\n- [SDETools-master](https://github.com/horchler/SDETools)\n- [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php), specifically the function [eegfilt.m](https://sccn.ucsd.edu/~arno/eeglab/auto/eegfilt.html).\nYou can download them from the links or find them in the folder [Toolbox](Toolbox).\n\n## Description\n- [InputCurrents](InputCurrents): contains the functions used to generate the input currents.\n- [IonicCurrents](IonicCurrents): contains the channels kinetics and a test function to visualize the channel kinetics curves: activation/inactivation and time constants.\n- [SingleNeuron](SingleNeuron): contains the model codes with Ih blocked and without blocking Ih for a single neuron. **Add [InputCurrents](InputCurrents) and [IonicCurrents](IonicCurrents) to the MATLAB path before running scripts.**\n- [L5PCs](L5PCs): contains the model codes with Ih blocked and without blocking Ih for a collaction of L5-PCs located randomly in a cortical column. It also contains the codes for the local field potentials (LFPs) and current source density (CSD) estimations. **Add [InputCurrents](InputCurrents) and [IonicCurrents](IonicCurrents) to the MATLAB path before running scripts.**\n- [GenerateFigures](GenerateFigures): contains the programs used to create the figures.\n\n## License\nCopyright (C) 2020 Beatriz Herrera, Amirsaman Sajad, Geoffrey F. Woodman, Jeffrey D. Schall, Jorge J. Riera.\n\nThis program is free software: you can redistribute it and/or modify\nit under the terms of the GNU General Public License as published by\nthe Free Software Foundation, either version 3 of the License, or\n(at your option) any later version.\n\nThis program is distributed in the hope that it will be useful,\nbut WITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\nGNU General Public License for more details.\n\n[GNU GPLv3](https://choosealicense.com/licenses/gpl-3.0/)\n\n## Citation\nHerrera B, Sajad A, Woodman GF, Schall JD, Riera JJ. A minimal biophysical model of neocortical pyramidal cells: implications for frontal cortex microcircuitry and field potential generation. J Neurosci **40**, 8513-8529 (2020); DOI: https://doi.org/10.1523/JNEUROSCI.0221-20.2020.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbeaherrera%2F2-compartments_l5-pc_model","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbeaherrera%2F2-compartments_l5-pc_model","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbeaherrera%2F2-compartments_l5-pc_model/lists"}