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brendapyrser

A Python parser for the BRENDA database

https://github.com/robaina/brendapyrser

Science Score: 77.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 4 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.4%) to scientific vocabulary

Keywords

biochemistry bioinformatics brenda computational-biology enzyme enzyme-kinetics metabolism python
Last synced: 6 months ago · JSON representation ·

Repository

A Python parser for the BRENDA database

Basic Info
  • Host: GitHub
  • Owner: Robaina
  • License: apache-2.0
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 702 KB
Statistics
  • Stars: 32
  • Watchers: 1
  • Forks: 7
  • Open Issues: 2
  • Releases: 3
Topics
biochemistry bioinformatics brenda computational-biology enzyme enzyme-kinetics metabolism python
Created over 5 years ago · Last pushed over 2 years ago
Metadata Files
Readme Contributing License Code of conduct Citation

README.md

logo

a Python package to parse and manipulate the BRENDA database

tests codecov PyPI GitHub release (latest by date) GitHub license Contributor Covenant DOI

What is Brendapyrser?

This project provides python classes and functions to parse the text file containing the entire BRENDA enzyme database (https://www.brenda-enzymes.org)

This is an ongoing project!

Installation

  1. pip install brendapyrser

or

  1. Git clone project to local directory.

In terminal navigate to directory and enter: python setup.py install

Usage

Due to BRENDA's license, BRENDA's database cannot be downloaded directly by the parser, instead, the user is asked to download the database as a text file after accepting usage conditions here.

You can find a jupyter notebook with usage examples here.

Contribute

Contributions are always more than welcome! Feel free to fork, make changes and pull requests. If you don't know where to start, you can always browse open issues. Thanks!

Citation

If you use this software, please cite it as below:

Robaina-Estévez, S. (2022). BRENDApyrser: a Python package to parse and manipulate the BRENDA database (Version 0.0.3)[Computer software]. https://doi.org/10.5281/zenodo.7026555

Owner

  • Name: Semidán Robaina
  • Login: Robaina
  • Kind: user
  • Location: Atlantic Ocean
  • Company: Hapdera

Computational Biology | Data Science | Python Dev. | Ph.D. Systems Biology

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: "Robaina-Estévez"
    given-names: "Semidán"
    orcid: "https://orcid.org/0000-0003-0781-1677"
title: "BRENDApyrser: a Python package to parse and manipulate the BRENDA database"
version: 0.0.3
doi: 10.5281/zenodo.7026555
date-released: 2022-08-26
url: "https://github.com/Robaina/BRENDApyrser"

GitHub Events

Total
  • Watch event: 7
  • Fork event: 3
Last Year
  • Watch event: 7
  • Fork event: 3

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 91
  • Total Committers: 4
  • Avg Commits per committer: 22.75
  • Development Distribution Score (DDS): 0.308
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Semidán Robaina Estévez s****a@g****m 63
Semidán Robaina-Estévez t****e@g****m 15
Semidán Robaina Estévez h****o@s****m 9
Zhiyue Chen 2****8@f****n 4
Committer Domains (Top 20 + Academic)
fudan.edu.cn: 1 semidanrobaina.com: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 8
  • Total pull requests: 3
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 18 days
  • Total issue authors: 5
  • Total pull request authors: 2
  • Average comments per issue: 1.75
  • Average comments per pull request: 3.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Robaina (3)
  • PolinaShichkova (2)
  • MistyField (1)
  • TheOnlylight (1)
  • daheym (1)
Pull Request Authors
  • Robaina (2)
  • MistyField (1)
Top Labels
Issue Labels
enhancement (3)
Pull Request Labels
enhancement (2)

Dependencies

.github/workflows/ci.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
.github/workflows/docker.yml actions
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  • docker/metadata-action 98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 composite
.github/workflows/docs.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v2 composite
.github/workflows/joss.yml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v1 composite
  • openjournals/openjournals-draft-action master composite
.github/workflows/tests.yml actions
  • actions/checkout v3 composite
  • codecov/codecov-action v3 composite
  • conda-incubator/setup-miniconda v2 composite
pyproject.toml pypi
  • importlib-metadata ^4.0.1
  • numpy ^1.20.2
  • pandas ^1.2.4
  • python ^3.8