{"id":20956424,"url":"https://github.com/bluebrain/brainmolecularatlas","last_synced_at":"2025-06-10T10:34:23.930Z","repository":{"id":41833220,"uuid":"364983202","full_name":"BlueBrain/BrainMolecularAtlas","owner":"BlueBrain","description":"Brain Molecular Atlas","archived":false,"fork":false,"pushed_at":"2022-04-27T11:49:31.000Z","size":7379,"stargazers_count":2,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-03-13T06:11:51.295Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","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/BlueBrain.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2021-05-06T17:10:32.000Z","updated_at":"2023-06-30T19:50:37.000Z","dependencies_parsed_at":"2022-08-11T18:50:52.474Z","dependency_job_id":null,"html_url":"https://github.com/BlueBrain/BrainMolecularAtlas","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%2FBrainMolecularAtlas","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FBrainMolecularAtlas/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FBrainMolecularAtlas/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FBrainMolecularAtlas/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BlueBrain","download_url":"https://codeload.github.com/BlueBrain/BrainMolecularAtlas/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FBrainMolecularAtlas/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":257276834,"owners_count":22519211,"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":"2024-11-19T01:25:53.424Z","updated_at":"2025-06-10T10:34:23.878Z","avatar_url":"https://github.com/BlueBrain.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# BrainMolecularAtlas\n\nThis is the code to reproduce the figures from the manuscript: A Standardized Brain Molecular Atlas: a resource for systems modeling and simulation (under review in Frontiers in Molecular Neuroscience)\nThe data processing toolkit (pipeline) code is available from the accompanying repository https://github.com/BlueBrain/MADIP \n\n## Getting Started\n\nThe Jupyter Notebooks and R scripts provide the details to reproduce the figures and are named according to the figures in the paper.\n\n### Prerequisites\n\nAll libs that are imported in the code needs to be installed. This includes: \n\nPython: Pandas, Numpy, Matplotlib, Seaborn, Altair, Scipy, scikit\\_posthoc \n\nR-script: RISmed, data.table, openxlsx, stringr, adjutant, dplyr, ggplot2, tidytext, Rtsne\n\n### Installing\n\nNo need for specific installation procedure, only prerequisite dependencies need to be installed. Please use Jupyter Lab or Jupyter Notebook to run the ipynb code.\n\n### Structure\n\nNotebooks and scripts are named according to the figures in the paper\n\n# Citation\n\nWhen you use the MADIP for your research, please cite the following publication (this includes poster presentations):\n[provisionally accepted] Shichkova P, Coggan JS, Markram H, Keller D (2021) A Standardized Brain Molecular Atlas: a resource for systems modeling and simulation. DOI: 10.3389/fnmol.2021.604559 \n\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\n\nCopyright (c) 2021-2022 Blue Brain Project/EPFL\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fbrainmolecularatlas","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbluebrain%2Fbrainmolecularatlas","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fbrainmolecularatlas/lists"}