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carveme

CarveMe: genome-scale metabolic model reconstruction

https://github.com/cdanielmachado/carveme

Science Score: 36.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 7 committers (14.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.0%) to scientific vocabulary

Keywords

genome-scale metabolism modeling python reconstruction

Keywords from Contributors

biochemistry bioinformatics cell-design cobra computational-biology flux metabolic-models metabolic-network sbml sbml-model
Last synced: 6 months ago · JSON representation

Repository

CarveMe: genome-scale metabolic model reconstruction

Basic Info
  • Host: GitHub
  • Owner: cdanielmachado
  • License: other
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 121 MB
Statistics
  • Stars: 178
  • Watchers: 9
  • Forks: 58
  • Open Issues: 51
  • Releases: 11
Topics
genome-scale metabolism modeling python reconstruction
Created over 8 years ago · Last pushed 10 months ago
Metadata Files
Readme License

README.md

License PyPI version Documentation Status

CarveMe

Genome-scale metabolic model reconstruction with CarveMe

CarveMe is a python-based tool for genome-scale metabolic model reconstruction.

Documentation

For instructions on installation and usage please check: http://carveme.readthedocs.io/

Credits and License

For citation purposes please refer to our paper:

D. Machado et al, "Fast automated reconstruction of genome-scale metabolic models for microbial species and communities", Nucleic Acids Research, gky537, 2018. doi: https://doi.org/10.1093/nar/gky537

Developed at: - European Molecular Biology Laboratory (2017-2019). - Norwegian University of Science and Technology (Since 2020)

CarveMe is now an official service of ELIXIR Norway.

ELIXIR

Owner

  • Name: Daniel Machado
  • Login: cdanielmachado
  • Kind: user
  • Company: NTNU

Computational Biologist

GitHub Events

Total
  • Issues event: 9
  • Watch event: 20
  • Issue comment event: 16
  • Push event: 3
  • Pull request event: 1
  • Fork event: 6
Last Year
  • Issues event: 9
  • Watch event: 20
  • Issue comment event: 16
  • Push event: 3
  • Pull request event: 1
  • Fork event: 6

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 131
  • Total Committers: 7
  • Avg Commits per committer: 18.714
  • Development Distribution Score (DDS): 0.046
Past Year
  • Commits: 8
  • Committers: 1
  • Avg Commits per committer: 8.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Daniel c****o@g****m 125
Benjamin Sanchez b****b@g****m 1
Matthias König k****t@g****m 1
Mike Mundy m****l@m****u 1
Filip Rotnes f****s@N****O 1
Silvia Talavera Marcos s****s@g****m 1
Daniel Machado c****o 1
Committer Domains (Top 20 + Academic)
nmbu.no: 1 mayo.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 132
  • Total pull requests: 7
  • Average time to close issues: 4 months
  • Average time to close pull requests: 1 day
  • Total issue authors: 104
  • Total pull request authors: 5
  • Average comments per issue: 2.92
  • Average comments per pull request: 0.29
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 12
  • Pull requests: 1
  • Average time to close issues: about 1 month
  • Average time to close pull requests: N/A
  • Issue authors: 11
  • Pull request authors: 1
  • Average comments per issue: 1.5
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • franciscozorrilla (5)
  • iuliachiciudean (3)
  • jolespin (3)
  • NatashaJorge (3)
  • shumantov (2)
  • rcolpo (2)
  • wupeng1998 (2)
  • microbial-cookie (2)
  • cdanielmachado (2)
  • SilasK (2)
  • Brunokemon (2)
  • lazzarigioele (2)
  • NantiaL (2)
  • lcottret (2)
  • SPD20 (2)
Pull Request Authors
  • cdanielmachado (3)
  • nickp60 (2)
  • djinnome (1)
  • silvtal (1)
  • filrot (1)
  • BenjaSanchez (1)
Top Labels
Issue Labels
enhancement (3)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 543 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 10
  • Total versions: 17
  • Total maintainers: 1
pypi.org: carveme

CarveMe: automated metabolic model reconstruction

  • Versions: 17
  • Dependent Packages: 0
  • Dependent Repositories: 10
  • Downloads: 543 Last month
  • Docker Downloads: 0
Rankings
Docker downloads count: 3.7%
Dependent repos count: 4.6%
Forks count: 5.9%
Average: 6.4%
Stargazers count: 6.7%
Downloads: 7.5%
Dependent packages count: 10.1%
Maintainers (1)
dmachado
Last synced: 6 months ago