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drug_database_statistics

https://github.com/research-hyperion/drug_database_statistics

Science Score: 26.0%

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

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    Academic publication links
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (6.5%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: research-hyperion
  • License: gpl-3.0
  • Language: Shell
  • Default Branch: master
  • Size: 2.55 GB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 4 years ago · Last pushed over 3 years ago
Metadata Files
Readme License Citation

README.md

Drug database statistics

Build Docker Image

  • Download all DrugBank versions recorded as XML files, from version 3.0 (January 2011) to version 5.1.9 (January 2022). Access to download the database versions is free with a validated account; an account can be created with an institutional email. The DrugBank versions 5.1.9 to 4.5.0 can be downloaded from https://go.drugbank.com/releases and 4.3 to 3.0 from https://go.drugbank.com/downloads/archived.

  • Each XML file must be saved following a naming convention to avoid file overwriting. Therefore each DrugBank XML file is saved as drugbank_version.xml in the Drugbank directory.

Examples: drugbank_3.0.xml, drugbank_5.1.8.xml, drugbank_5.1.9.xml

  • Build image

docker build --build-arg wolframId=<wolfram account email> --build-arg wolframPass=<wolfram account password> -t hyperion .

  • Running image

docker run -t -i hyperion /bin/bash

Interactive script

  • In docker container run ./execute_scripts.sh [-h]|[-i][-s]. By invoking the script with the -i parameter, it will build and analyze DDI and DTI networks for each DrugBank version; if it is invoked with the -s parameter, it will build the networks and run the robustness analysis. -h option is for showing the help.

Example

root@59ed68e0d3d8:/code# ./execute_scripts.sh -h Usage sh execute_scripts.sh [-i|-s|-h]. -i=Execute jupyter notebooks. -s=Execute robustness tests. -h=help

Owner

  • Login: research-hyperion
  • Kind: user

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Dependencies

Dockerfile docker
  • python 3.10-bullseye build