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electrum

Visualization platform for exploring MIDAS protein-small molecule interaction data

https://github.com/electrum-app/electrum

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: science.org
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    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (8.2%) to scientific vocabulary

Keywords

django interaction metabolism metabolomics network protein-metabolite python visualization-platform
Last synced: 6 months ago · JSON representation ·

Repository

Visualization platform for exploring MIDAS protein-small molecule interaction data

Basic Info
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 0
  • Open Issues: 3
  • Releases: 1
Topics
django interaction metabolism metabolomics network protein-metabolite python visualization-platform
Created almost 6 years ago · Last pushed 11 months ago
Metadata Files
Readme License Citation

README.md

Electrum

MIDAS publication

What does Electrum do?

Electrum is a visualization platform for exploring MIDAS protein-metabolite interaction data.

Testing

  • python manage.py runserver
  • In Chrome:
  • Navigate to: http://127.0.0.1:8000/
  • Ctrl+F5 to clear cache

Deploy instructions

  • Update latest MIDAS database and store at: static/Electrum/data/MIDAS-latest.txt
  • python electrum-utils.py buildSubstructureReference --output ..\..\data
  • buildEntityDatabase is a util for name mapping metabolites from MIDAS datasets

  • In settings.py, set DEBUG = False and SECURE_SSL_REDIRECT = True

  • In virtual environment with Python installed and activated:

  • conda create --name electron-deploy

  • conda activate electron-deploy

  • conda install python=3.8

  • pip install -r requirements.txt

Licensing

  • Electrum is available via a GPL-3.0 License
  • D3 is provided under an ISC License
  • d3-ForceEdgeBundling is provided under a GPL-2.0 License
  • jQuery is provided under an MIT License
  • saveSvgAsPng is provided under an MIT License
  • streamsaver is provided under an MIT License

Notes

  • Copy settings.py to Electrum directory
  • Change path to find config
  • Run /uufs/chpc.utah.edu/common/home/rutter-website/html/Electrum-django/electrum-deploy-env/bin/gunicorn Electrum-admin.wsgi:application

Owner

  • Name: Electrum-app
  • Login: Electrum-app
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 0.0.1
message: "If you use this software, please cite it as below."
authors:
  - family-names: Berg
    given-names: Jordan A.
    orcid: https://orcid.org/0000-0002-5096-0558
title: "Electrum"
version: 0.0.1
doi: N/A
date-released: N/A

GitHub Events

Total
  • Push event: 1
Last Year
  • Push event: 1

Dependencies

Electrum/static/Electrum/python/electrum-utils/requirements.txt pypi
  • matplotlib *
  • numpy *
  • pandas *
  • plotly *
  • requests *
  • scikit-learn *
Electrum/static/Electrum/python/substructure_enrich/requirements.txt pypi
  • fisher *
  • numpy *
  • pandas *
  • statsmodels *
requirements.txt pypi
  • Django *
  • fisher *
  • gunicorn *
  • matplotlib *
  • numpy *
  • pandas *
  • plotly *
  • requests *
  • requests-toolbelt *
  • scikit-learn *
  • scipy *
  • statsmodels *