https://github.com/bluebrain/madip
MADIP: Molecular Atlas Data Integration Pipeline
Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 1 DOI reference(s) in README -
○Academic publication links
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.2%) to scientific vocabulary
Repository
MADIP: Molecular Atlas Data Integration Pipeline
Basic Info
- Host: GitHub
- Owner: BlueBrain
- License: apache-2.0
- Language: Jupyter Notebook
- Default Branch: main
- Size: 513 KB
Statistics
- Stars: 1
- Watchers: 3
- Forks: 2
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
MADIP
MADIP: Molecular Atlas Data Integration Pipeline
This is the code to use the data integration and processing pipeline from the manuscript: A Standardized Brain Molecular Atlas: a resource for systems modeling and simulation (under review in Frontiers in Molecular Neuroscience) The figures reproducing code is available from the accompanying repository https://github.com/BlueBrain/BrainMolecularAtlas
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
Owner
- Name: The Blue Brain Project
- Login: BlueBrain
- Kind: organization
- Email: bbp.opensource@epfl.ch
- Location: Geneva, Switzerland
- Website: https://portal.bluebrain.epfl.ch/
- Repositories: 226
- Profile: https://github.com/BlueBrain
Open Source Software produced and used by the Blue Brain Project
GitHub Events
Total
- Fork event: 1
Last Year
- Fork event: 1
Issues and Pull Requests
Last synced: over 1 year ago
All Time
- Total issues: 0
- Total pull requests: 3
- Average time to close issues: N/A
- Average time to close pull requests: about 6 hours
- Total issue authors: 0
- Total pull request authors: 2
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
- alex4200 (2)
- bbpgithubaudit (1)