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micom

Python package to study microbial communities using metabolic modeling.

https://github.com/micom-dev/micom

Science Score: 39.0%

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
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.7%) to scientific vocabulary

Keywords

biochemistry cobra cobrapy community flux hacktoberfest metabolic-models microbiome microbiota modeling python systems-biology

Keywords from Contributors

interactive serializer packaging network-simulation shellcodes hacking autograding observability embedded optim
Last synced: 6 months ago · JSON representation

Repository

Python package to study microbial communities using metabolic modeling.

Basic Info
Statistics
  • Stars: 106
  • Watchers: 4
  • Forks: 20
  • Open Issues: 14
  • Releases: 59
Topics
biochemistry cobra cobrapy community flux hacktoberfest metabolic-models microbiome microbiota modeling python systems-biology
Created about 9 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License Code of conduct

README.rst 

.. image:: https://github.com/micom-dev/micom/raw/main/docs/source/micom.png
    :width: 640 px

|actions status| |coverage| |pypi status| |mastodon|

Welcome
-------

`MICOM` is a Python package for metabolic modeling of microbial
communities currently developed in the `Diener Lab `_ at the 
`Medical University of Graz `_. Previous development took place in
the `Gibbons Lab `_ at the `Institute for Systems
Biology `_ and the
`Human Systems Biology Group `_ of
Prof. Osbaldo Resendis Antonio at the `National Institute of Genomic
Medicine Mexico `_.

`MICOM` allows you to construct a community model from a list on input
COBRA models and manages exchange fluxes between individuals and individuals
with the environment. It explicitly accounts for different abundances of
individuals in the community and can thus incorporate data from biomass quantification,
cytometry, amplicon sequencing, or metagenomic shotgun sequencing.

It identifies a relevant flux space by incorporating an ecological model for the trade-off
between individual taxa growth and community-wide growth that shows good agreement with
experimental data.

Attribution
-----------

MICOM is published in

::

      MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota
      Christian Diener, Sean M. Gibbons, Osbaldo Resendis-Antonio
      mSystems 5:e00606-19
      https://doi.org/10.1128/mSystems.00606-19

Please cite this publication when referencing MICOM. Thanks :smile:

Installation
------------

`MICOM` is available on PyPi and can be installed via

.. code:: bash

    pip install micom

For more info on the installation or setting up the solvers please see the `documentation `_ .

Getting started
---------------

Documentation can be found at https://micom-dev.github.io/micom .

Getting help
------------

General questions on usage can be asked in Github Discussions
    https://github.com/micom-dev/micom/discussions

We are also available on the cobrapy Gitter channel
    https://gitter.im/opencobra/cobrapy

Questions specific to the MICOM Qiime2 plugin (q2-micom) can also be asked on the Qiime2 forum
    https://forum.qiime2.org/c/community-plugin-support/

.. |actions status| image:: https://github.com/micom-dev/micom/actions/workflows/pythonpackage.yml/badge.svg
   :target: https://github.com/micom-dev/micom/actions/workflows/pythonpackage.yml
.. |coverage| image:: https://codecov.io/gh/micom-dev/micom/branch/main/graph/badge.svg
   :target: https://codecov.io/gh/micom-dev/micom
.. |pypi status| image:: https://img.shields.io/pypi/v/micom.svg
   :target: https://pypi.org/project/micom/
.. |mastodon| image:: https://img.shields.io/mastodon/follow/109960852316221526?domain=https%3A%2F%2Fmstdn.science&style=social
   :target: https://mstdn.science/@micom

Owner

  • Name: micom-dev
  • Login: micom-dev
  • Kind: organization

Developers of the microbial community modeling package micom.

GitHub Events

Total
  • Create event: 18
  • Release event: 1
  • Issues event: 2
  • Watch event: 18
  • Delete event: 11
  • Issue comment event: 5
  • Push event: 34
  • Pull request review event: 5
  • Pull request event: 28
  • Fork event: 2
Last Year
  • Create event: 18
  • Release event: 1
  • Issues event: 2
  • Watch event: 18
  • Delete event: 11
  • Issue comment event: 5
  • Push event: 34
  • Pull request review event: 5
  • Pull request event: 28
  • Fork event: 2

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 716
  • Total Committers: 4
  • Avg Commits per committer: 179.0
  • Development Distribution Score (DDS): 0.043
Past Year
  • Commits: 39
  • Committers: 2
  • Avg Commits per committer: 19.5
  • Development Distribution Score (DDS): 0.282
Top Committers
Name Email Commits
Christian Diener c****r@g****m 685
dependabot[bot] 4****] 28
Christian Diener m****l@c****m 2
Nils Giordano n****d 1
Committer Domains (Top 20 + Academic)
cdiener.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 45
  • Total pull requests: 81
  • Average time to close issues: 4 months
  • Average time to close pull requests: 11 days
  • Total issue authors: 22
  • Total pull request authors: 4
  • Average comments per issue: 2.6
  • Average comments per pull request: 0.68
  • Merged pull requests: 72
  • Bot issues: 0
  • Bot pull requests: 62
Past Year
  • Issues: 2
  • Pull requests: 24
  • Average time to close issues: N/A
  • Average time to close pull requests: 22 days
  • Issue authors: 2
  • Pull request authors: 3
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.29
  • Merged pull requests: 18
  • Bot issues: 0
  • Bot pull requests: 21
View more stats
Top Authors
Issue Authors
  • cdiener (12)
  • arianccbasile (4)
  • mmp3 (3)
  • krcurtis (3)
  • zoey-rw (3)
  • nigiord (2)
  • PathogeNish (2)
  • mmundy42 (2)
  • Ilhem36 (1)
  • shalabs (1)
  • wtscott31 (1)
  • wintermute221 (1)
  • nick-youngblut (1)
  • vicru93 (1)
  • dorarinyo88 (1)
Pull Request Authors
  • dependabot[bot] (79)
  • cdiener (22)
  • nickp60 (2)
  • nigiord (1)
Top Labels
Issue Labels
feature (2) numeric (2) question (2) bug (1) done (1)
Pull Request Labels
dependencies (79) github_actions (9) hacktoberfest-accepted (2) numeric (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 1,221 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 1
  • Total versions: 113
  • Total maintainers: 1
pypi.org: micom

Microbial community modeling based on cobrapy.

  • Versions: 113
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 1,221 Last month
Rankings
Dependent packages count: 4.8%
Stargazers count: 8.0%
Forks count: 9.3%
Downloads: 9.7%
Average: 10.7%
Dependent repos count: 21.5%
Maintainers (1)
cdiener
Last synced: 6 months ago

Dependencies

.github/workflows/docs.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4.5.0 composite
  • peaceiris/actions-gh-pages v3 composite
.github/workflows/pythonpackage.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4.5.0 composite
  • actions/upload-artifact v3 composite
  • codecov/codecov-action v3.1.1 composite
  • ncipollo/release-action v1 composite
requirements.txt pypi
  • cobra >=0.17.1
  • coverage *
  • jinja2 >=2.10.0
  • nbsphinx *
  • osqp >=0.6.2
  • pytest *
  • pytest-cov *
  • recommonmark *
  • scikit-learn >=0.22.0
  • scipy >=1.0.0
  • sphinx *
  • sphinx-autoapi *
  • sphinx-book-theme *
  • symengine >=0.6.1
pyproject.toml pypi
setup.py pypi