{"id":20956570,"url":"https://github.com/bluebrain/emodel-generalisation","last_synced_at":"2025-05-14T05:32:10.579Z","repository":{"id":178875446,"uuid":"662445885","full_name":"BlueBrain/emodel-generalisation","owner":"BlueBrain","description":"Generalisation of electrical models of neurons with MCMC","archived":true,"fork":false,"pushed_at":"2025-02-26T13:06:30.000Z","size":18053,"stargazers_count":4,"open_issues_count":4,"forks_count":5,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-05-11T15:03:18.110Z","etag":null,"topics":["electrophysiology","generalisation","mcmc","neuron"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BlueBrain.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS.md","dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2023-07-05T06:48:24.000Z","updated_at":"2025-02-26T13:06:34.000Z","dependencies_parsed_at":null,"dependency_job_id":"dd511a47-8827-4c66-a9ef-ba3731851489","html_url":"https://github.com/BlueBrain/emodel-generalisation","commit_stats":null,"previous_names":["bluebrain/emodel-generalisation"],"tags_count":16,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2Femodel-generalisation","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2Femodel-generalisation/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2Femodel-generalisation/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2Femodel-generalisation/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BlueBrain","download_url":"https://codeload.github.com/BlueBrain/emodel-generalisation/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253584492,"owners_count":21931547,"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":["electrophysiology","generalisation","mcmc","neuron"],"created_at":"2024-11-19T01:26:57.757Z","updated_at":"2025-05-14T05:32:05.549Z","avatar_url":"https://github.com/BlueBrain.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![DOI](https://zenodo.org/badge/662445885.svg)](https://zenodo.org/badge/latestdoi/662445885)\n\n# emodel-generalisation\n\nGeneralisation of neuronal electrical models on a morphological population with Markov Chain Monte-Carlo.\n\nThis code accompanies the paper:\n\n[Arnaudon, A., Reva, M., Zbili, M., Markram, H., Van Geit, W., \u0026 Kanari, L. (2023). Controlling morpho-electrophysiological variability of neurons with detailed biophysical models. iScience, 2023.](https://www.cell.com/iscience/fulltext/S2589-0042%2823%2902299-X)\n\n## Installation\n\nThis code can be installed via [pip](https://pip.pypa.io/en/stable/) from pypi with\n\n```\npip install emodel-generalisation\n```\n\nor from github with\n\n```\ngit clone git@github.com:BlueBrain/emodel-generalisation.git\npip install .\n```\n\n## Documentation\n\nThe documentation can be found here: https://emodel-generalisation.readthedocs.io/en/latest/\n\n## Code structure\n\nThis code contains several modules, the most important are:\n* [model](emodel_generalisation/model) contains an adapted version of BlueBrain/BluePyEmodel core functionalities for evaluating electrical models, built on top of BlueBrain/BluePyOpt\n* [tasks](emodel_generalisation/tasks) contains the luigi workflows to run MCMC, adapt and generalise electrical model\n* [bluecellulab_evaluator](emodel_generalisation/bluecellulab_evaluator.py) contains functions to compute currents with BlueBrain/BlueCelluLab and hoc files of models\n* [mcmc](emodel_generalisation/mcmc.py) contains the code to run MCMC sampling of electrical models\n* [information](emodel_generalisation/information.py) contains some WIP code to compute information theory measures on sampled electrical models\n\n\n## Examples\n\nWe provide several examples of the main functionalities of the ```emodel-generalisation``` code:\n* run MCMC on a simple single compartment model in [examples/mcmc/mcmc_singlecomp](examples/mcmc/mcmc_singlecomp)\n* run MCMC on a simple multi-compartment model in [examples/mcmc/mcmc_simple_multicomp](examples/mcmc/mcmc_simple_multicomp)\n* run the entire generalisation worklow on a simplified version of the L5PC model of the paper in [examples/workflow](examples/workflow)\n* provide all the scripts necessary to reproduce the figures of the paper. For the scripts to run, one has to download the associated dataset on dataverse  with the script ```get_data.sh``` in [examples/paper_figures](examples/paper_figures)\n\n\n## Citation\n\nWhen you use the ``emodel-generalisation`` code or method for your research, we ask you to [cite](https://www.cell.com/iscience/fulltext/S2589-0042%2823%2902299-X):\n\n\u003e Arnaudon, A., Reva, M., Zbili, M., Markram, H., Van Geit, W., \u0026 Kanari, L. (2023). Controlling morpho-electrophysiological variability of neurons with detailed biophysical models. iScience, 2023.\n\nTo get this citation in another format, please use the `Cite this repository` button in the sidebar of the [code's github page](https://github.com/BlueBrain/emodel-generalisation).\n\n## Funding \u0026 Acknowledgment\n\nThe development of this code was supported by funding to the Blue Brain Project, a research\ncenter of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH\nBoard of the Swiss Federal Institutes of Technology.\n\nFor license and authors, see `LICENSE.txt` and `AUTHORS.md` respectively.\n\nCopyright 2022-2023 Blue Brain Project/EPFL\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Femodel-generalisation","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbluebrain%2Femodel-generalisation","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Femodel-generalisation/lists"}