{"id":20956443,"url":"https://github.com/bluebrain/me-features-to-mo-id-mapping","last_synced_at":"2025-05-14T05:31:45.578Z","repository":{"id":40511320,"uuid":"444848610","full_name":"BlueBrain/me-features-to-mo-ID-mapping","owner":"BlueBrain","description":null,"archived":false,"fork":false,"pushed_at":"2022-05-04T07:21:28.000Z","size":1807,"stargazers_count":4,"open_issues_count":0,"forks_count":1,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-04-02T13:22:31.813Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BlueBrain.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2022-01-05T15:11:42.000Z","updated_at":"2024-04-04T07:39:24.000Z","dependencies_parsed_at":"2022-08-09T22:30:40.724Z","dependency_job_id":null,"html_url":"https://github.com/BlueBrain/me-features-to-mo-ID-mapping","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2Fme-features-to-mo-ID-mapping","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2Fme-features-to-mo-ID-mapping/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2Fme-features-to-mo-ID-mapping/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2Fme-features-to-mo-ID-mapping/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BlueBrain","download_url":"https://codeload.github.com/BlueBrain/me-features-to-mo-ID-mapping/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254076977,"owners_count":22010630,"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":[],"created_at":"2024-11-19T01:26:01.580Z","updated_at":"2025-05-14T05:31:41.012Z","avatar_url":"https://github.com/BlueBrain.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# BBP-me-type-to-mol-ID\n\n## Description:\nThis is a repository containing configuration code that use me-types-mapper to reproduce results from *Roussel et al., \n2021* (https://www.biorxiv.org/content/10.1101/2021.11.24.469815v1)\n\n## Installation:\n\nTo install this tool, run the following steps in your shell:\n\n```\ngit clone https://bbpgitlab.epfl.ch/molsys/bbp_me_type_to_mol_id.git\npip install -r bbp_me_type_to_mol_id/requirements.txt\npip install git+https://bbpgitlab.epfl.ch/molsys/me_types_mapper.git\npip install git+https://github.com/BlueBrain/BluePyEfe@da783256a4212b14d4f152687238754a99d1a78b\n```\n\n## How to use:\nStep 1 and 2 are optional as we made the extracted features available in the `feature_extraction folder`.\n\n### Step 1: Download the data (optional)\nGo into `downloader` directory\n####  Morphologies and electrophysiological recording from Gouwens et al., 2019:\nDue to open source license issues, the python script for downloading AIBS data from Gouwens et al. (2019) could not be \nincluded.\nPlease refer to `allensdk` from Allen Institute for Brain Science to download data from the Gouwens et al paper. \nClear instructions on how to download morphological and electrophysiological data are provided in the `allensdk`\ndocumentation:\nElectrophysiology: https://allensdk.readthedocs.io/en/latest/_static/examples/nb/cell_types.html#Cell-Types-Database\nMorphologies: https://allensdk.readthedocs.io/en/latest/_static/examples/nb/cell_types.html#Cell-Morphology-Reconstructions\nThe cell ids used in the manuscript are provided in the `downloader/41593_2019_417_MOESM5_ESM.xlsx` file.\nData should be stored in the `downloader` directory in a new folder named after the dataset name (i.e. `Gouwens_2019`)\nand organized  into two sub-directories: one named as `ephys_traces` containing the raw traces in nwb format and another\nnamed `morphologies` containing the morphology reconstruction in swc format.\nDownloading of AIBS data should be done in a dedicated virtual environment.\n####  Morphologies and electrophysiological recording from Blue Brain Project:\nCreate a dedicated virtual environment for downloading BBP data. Install dependencies using\n`pip install -r requirements_BBP_dl.txt`. Finally, run `python BBP_downloader.py`.\n\n### Step 2: Extract features (optional)\nGo into the `feature_extraction` directory and run first `python efeatures_extractor.py` \nand then `python mfeatures_extractor.py`.\n\n### Step 3: Select common features\nGo into the `feature_selection` directory and run first `python feature_selector.py`. It should create two directories named\n`figures` and `filtered_datasets`. Then run `python compute_dataset_labels.py`.\n\n### Step 4: Mapping\nGo into the `mapping` directory and run `python clustering.py` to reproduce the main results of the paper \n(https://www.biorxiv.org/content/10.1101/2021.11.24.469815v1). To reproduce \nthe other figures run `python dataset_overlap_validation.py` for figure 2, `python alpha_optimization_validation.py` for\nfigure 3 and `python pipeline_validation.py` for Table 1.\n\n##  Funding \u0026 Acknowledgment:\n\nThe development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.\n\nCopyright (c) 2022-2022 Blue Brain Project/EPFL\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fme-features-to-mo-id-mapping","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbluebrain%2Fme-features-to-mo-id-mapping","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fme-features-to-mo-id-mapping/lists"}