https://github.com/bluebrain/brainmolecularatlas
Brain Molecular Atlas
https://github.com/bluebrain/brainmolecularatlas
Last synced: about 1 year ago
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Brain Molecular Atlas
- Host: GitHub
- URL: https://github.com/bluebrain/brainmolecularatlas
- Owner: BlueBrain
- License: gpl-3.0
- Created: 2021-05-06T17:10:32.000Z (about 5 years ago)
- Default Branch: main
- Last Pushed: 2022-04-27T11:49:31.000Z (about 4 years ago)
- Last Synced: 2025-03-13T06:11:51.295Z (over 1 year ago)
- Language: Jupyter Notebook
- Size: 7.04 MB
- Stars: 2
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
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README
# BrainMolecularAtlas
This 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)
The data processing toolkit (pipeline) code is available from the accompanying repository https://github.com/BlueBrain/MADIP
## Getting Started
The Jupyter Notebooks and R scripts provide the details to reproduce the figures and are named according to the figures in the paper.
### Prerequisites
All libs that are imported in the code needs to be installed. This includes:
Python: Pandas, Numpy, Matplotlib, Seaborn, Altair, Scipy, scikit\_posthoc
R-script: RISmed, data.table, openxlsx, stringr, adjutant, dplyr, ggplot2, tidytext, Rtsne
### Installing
No need for specific installation procedure, only prerequisite dependencies need to be installed. Please use Jupyter Lab or Jupyter Notebook to run the ipynb code.
### Structure
Notebooks and scripts are named according to the figures in the paper
# Citation
When you use the MADIP for your research, please cite the following publication (this includes poster presentations):
[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
# Funding & Acknowledgment
The 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.
Copyright (c) 2021-2022 Blue Brain Project/EPFL