{"id":45924660,"url":"https://github.com/dbbs-lab/cerebellar-models","last_synced_at":"2026-02-28T09:01:32.625Z","repository":{"id":298787712,"uuid":"337954925","full_name":"dbbs-lab/cerebellar-models","owner":"dbbs-lab","description":"Models of the cerebellum","archived":false,"fork":false,"pushed_at":"2026-02-25T14:07:42.000Z","size":87336,"stargazers_count":4,"open_issues_count":10,"forks_count":1,"subscribers_count":6,"default_branch":"master","last_synced_at":"2026-02-25T15:07:12.453Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"agpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dbbs-lab.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":"codemeta.json","zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2021-02-11T07:10:01.000Z","updated_at":"2025-12-16T11:35:13.000Z","dependencies_parsed_at":null,"dependency_job_id":"3a90cbd2-7b71-439d-9b4c-ff8a59e3d596","html_url":"https://github.com/dbbs-lab/cerebellar-models","commit_stats":null,"previous_names":["dbbs-lab/cerebellar-models"],"tags_count":10,"template":false,"template_full_name":null,"purl":"pkg:github/dbbs-lab/cerebellar-models","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dbbs-lab%2Fcerebellar-models","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dbbs-lab%2Fcerebellar-models/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dbbs-lab%2Fcerebellar-models/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dbbs-lab%2Fcerebellar-models/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dbbs-lab","download_url":"https://codeload.github.com/dbbs-lab/cerebellar-models/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dbbs-lab%2Fcerebellar-models/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29929115,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-27T19:37:42.220Z","status":"online","status_checked_at":"2026-02-28T02:00:07.010Z","response_time":90,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":[],"created_at":"2026-02-28T09:01:32.149Z","updated_at":"2026-02-28T09:01:32.609Z","avatar_url":"https://github.com/dbbs-lab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Build and Test](https://github.com/dbbs-lab/cerebellar-models/actions/workflows/integration.yml/badge.svg)](https://github.com/dbbs-lab/cerebellar-models/actions/workflows/integration.yml)\n[![Documentation Status](https://readthedocs.org/projects/cerebellar-models/badge/?version=latest)](https://cerebellar-models.readthedocs.io/en/latest/?badge=latest)\n[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)\n[![codecov](https://codecov.io/gh/dbbs-lab/cerebellar-models/graph/badge.svg?token=KBEE3D83YQ)](https://codecov.io/gh/dbbs-lab/cerebellar-models)\n\n# DBBS Cerebellar models: Models of the cerebellum, using the BSB.\nThis repository provides the code, configuration and morphology data to reconstruct and simulate \ncerebellar cortex circuits using the [Brain Scaffold Builder](https://github.com/dbbs-lab/bsb) \nframework. These models are based on the iterative work of the [Department of Brain and Behavioral \nSciences](https://dbbs.dip.unipv.it/en) (DBBS) of the university of Pavia. \n\n\u003ch3\u003e:closed_book: Read the documentation on  https://cerebellar-models.readthedocs.io/en/latest\n\n## Installation\n`cerebellar-models` is a package that contains implementation of connectivity or placement rules for BSB.\nThe `cerebellar-models` package requires Python 3.10+.\n\n### Pre-requirements\n\nBSB parallelizes the network reconstruction using MPI, and translates simulator instructions to \nthe simulator backends with it as well, for effortless parallel simulation. \nTo use MPI from Python the mpi4py package is required, which in turn needs a working MPI \nimplementation installed in your environment.\n\nOn your local machine you can install OpenMPI:\n```bash\nsudo apt-get update \u0026\u0026 sudo apt-get install -y libopenmpi-dev openmpi-bin\n```\n\nThen, depending on the types of simulations, you want to perform you will need to install the \nsimulator(s) of your interest. Please follow the instructions:\n- For the [NEST](https://nest-simulator.readthedocs.io/en/stable/installation/index.html) simulator\n- For the [NEURON](https://nrn.readthedocs.io/en/8.2.4/install/install.html) simulator\n\n### Cerebellar-models installation\n\n#### pip\nCerebellar-models can be installed from PyPI through `pip`:\n```bash\npip install cerebellar-models\n```\n\n#### Developers\nDevelopers best use pip's *editable* install. This creates a live link between the\ninstalled package and the local git repository:\n\n```bash\n git clone git@github.com:dbbs-lab/cerebellar-models\n cd cerebellar_models\n pip install -e .\n```\n\n## Contents\n\n### Morphologies\nCerebellar cortex neuron morphology reconstructions used in our microcircuits are stored in the \n[morphologies](https://github.com/dbbs-lab/cerebellar-models/tree/master/configurations) folder. \nThe folder contains also more information about each file.\n\n### BSB configuration files for cerebellar cortex circuits\nIn this repository, the BSB configurations are stored in the \n[configurations](https://github.com/dbbs-lab/cerebellar-models/tree/master/configurations) folder. \nSub-folders within `configurations` corresponds to different species reconstructions. Each specie \nhave its default configuration to reconstruct the models as well as `extensions` that can be added \nto override or extend the default one. This includes the different simulation' paradigms.\n\n## Building a circuit\n\nDepending on the circuit you wish to obtain and/or simulate, the process will vary.\nThis package provides a command-line interface to generate the BSB configuration \nof the canonical circuits developed by the DBBS based on a few choices.\n\nAssuming you are in the `cerebellar-models` folder, run the following command in your terminal:\n```bash\ncerebellar-models configure\n```\nOnce you filled the forms provided by the command within your terminal, your BSB configuration\nshould be ready to be compiled:\n\n```bash\nbsb compile circuit.yaml -v4 --clear\n```\nThis command will produce the desired circuit of the cerebellar cortex and store it in\nan `.hdf5` file. This process might take a while depending on your machine.\n\n## Running a simulation\nAs for the previous paragraph the following command might vary depending on your reconstruction and \nsimulation. \n\nAssuming you are in the `cerebellar-models` folder, and you want to run the simulation `simulation_name`, \nrun the following command in your terminal:\n```bash\nbsb simulate cerebellum.hdf5 simulation_name -o output_file_name -v4\n```\n\n## Acknowledgements\nThis research has received funding from the European Union’s Horizon 2020 Framework\nProgram for Research and Innovation under the Specific Grant Agreement No. 945539\n(Human Brain Project SGA3) and Specific Grant Agreement No. 785907 (Human Brain\nProject SGA2) and from Centro Fermi project “Local Neuronal Microcircuits” to ED.\nThe project is also receiving funding from the Virtual Brain Twin Project under the \nEuropean Union's Research and Innovation Program Horizon Europe under grant agreement\nNo 101137289.\n\nWe acknowledge the use of EBRAINS platform and Fenix Infrastructure resources, which are\npartially funded from the European Union’s Horizon 2020 research and innovation\nprogramme under the Specific Grant Agreement No. 101147319 (EBRAINS 2.0 Project) and \nthrough the ICEI project under the grant agreement No. 800858 respectively.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdbbs-lab%2Fcerebellar-models","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdbbs-lab%2Fcerebellar-models","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdbbs-lab%2Fcerebellar-models/lists"}