cobra

COBRApy is a package for constraint-based modeling of metabolic networks.

Science Score: 59.0%

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

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 2 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Committers with academic emails
11 of 62 committers (17.7%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (16.3%) to scientific vocabulary

Keywords

biochemistry bioinformatics cell-design cobra computational-biology flux metabolic-models metabolic-network metabolism modeling python sbml sbml-model sbml-simulation strain-engineering systems-biology

Keywords from Contributors

pdb protein-structure

Last synced: 6 months ago · JSON representation

Repository

COBRApy is a package for constraint-based modeling of metabolic networks.

Basic Info

Host: GitHub
Owner: opencobra
License: gpl-2.0
Language: Python
Default Branch: devel
Homepage: http://opencobra.github.io/cobrapy/
Size: 60 MB

Statistics

Stars: 513
Watchers: 36
Forks: 227
Open Issues: 101
Releases: 71

Topics

Created over 13 years ago · Last pushed 6 months ago

Metadata Files

Readme Contributing License Code of conduct Support

README.rst

================================================================
COBRApy - Constraint-Based Reconstruction and Analysis in Python
================================================================

.. image:: https://img.shields.io/pypi/v/cobra.svg
   :target: https://pypi.org/project/cobra/
   :alt: Current PyPI Version

.. image:: https://img.shields.io/pypi/pyversions/cobra.svg
   :target: https://pypi.org/project/cobra/
   :alt: Supported Python Versions

.. image:: https://img.shields.io/pypi/l/cobra.svg
   :target: https://www.gnu.org/licenses/old-licenses/lgpl-2.0.html
   :alt: GNU Lesser General Public License 2 or later

.. image:: https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg
   :target: https://github.com/opencobra/cobrapy/blob/devel/.github/CODE_OF_CONDUCT.md
   :alt: Code of Conduct

.. image:: https://github.com/opencobra/cobrapy/actions/workflows/main.yml/badge.svg
   :target: https://github.com/opencobra/cobrapy/actions/workflows/main.yml
   :alt: GitHub Actions CI/CD Status

.. image:: https://codecov.io/gh/opencobra/cobrapy/branch/master/graph/badge.svg
   :target: https://codecov.io/gh/opencobra/cobrapy
   :alt: Codecov

.. image:: https://readthedocs.org/projects/cobrapy/badge/?version=latest
   :target: https://cobrapy.readthedocs.io/en/latest/?badge=latest
   :alt: Documentation Status

.. image:: https://badges.gitter.im/opencobra/cobrapy.svg
   :target: https://gitter.im/opencobra/cobrapy
   :alt: Gitter Chat Room

.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
   :target: https://github.com/ambv/black
   :alt: Black

.. image:: https://zenodo.org/badge/6510063.svg
   :target: https://zenodo.org/badge/latestdoi/6510063
   :alt: Zenodo DOI

What is COBRApy?
================

COBRA methods are widely used for genome-scale modeling of metabolic networks in
both prokaryotes and eukaryotes. **COBRApy** is a constraint-based modeling
package that is designed to accommodate the biological complexity of the next
generation of COBRA models and provides access to commonly used COBRA methods,
such as flux balance analysis, flux variability analysis, and gene deletion
analyses.

Our aim with COBRApy is to provide useful, efficient infrastructure for:

- creating and managing metabolic models
- accessing popular solvers
- analyzing models with methods such as FVA, FBA, pFBA, MOMA etc.
- inspecting models and drawing conclusions on gene essentiality, testing
  consequences of knock-outs etc.

Our goal with COBRApy is for it to be useful on its own, and for it to be the
natural choice of infrastructure for developers that want to build new COBRA
related python packages for e.g. visualization, strain-design and data driven
analysis. By re-using the same classes and design principles, we can make new
methods both easier to implement and easier to use, thereby bringing the power
of COBRA to more researchers.

The documentation is browseable online at `readthedocs
`_ and can also be `downloaded
`_.

Please use the `Google Group `_ for
help. By writing a well formulated question, with sufficient detail, you are
much more likely to quickly receive a good answer! Please refer to these
`StackOverflow guidelines `_ on how
to ask questions.  Alternatively, you can use `gitter.im
`_ for quick questions and discussions
about COBRApy (faster response times). Please keep in mind that answers are
provided on a volunteer basis.

More information about opencobra is available at the `website
`_.

If you use COBRApy in a scientific publication, please cite
`doi:10.1186/1752-0509-7-74 `_

Installation
============

Use pip to `install COBRApy from PyPI `_ (we
recommend doing this inside a `virtual environment
`_)::

    pip install cobra

If you want to load MATLAB models, you will need additional dependencies. Please
install::

    pip install cobra[array]

For further information, please follow the `detailed installation instructions
`_.

Contributing
============

Contributions are always welcome! Please read the `contributing guidelines
`_ to
get started.

License
=======

The COBRApy source is released under both the GPL and LGPL licenses version 2 or
later. You may choose which license you choose to use the software under.

This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License or the GNU Lesser General Public
License as published by the Free Software Foundation, either version 2 of the
License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU General Public License for more details.

Owner

Name: openCOBRA
Login: opencobra
Kind: organization
Location: Terra

Website: opencobra.github.io
Repositories: 33
Profile: https://github.com/opencobra

Community driven constraint-based reconstruction, analysis and modelling of biology

GitHub Events

Total

Issues event: 34
Watch event: 49
Delete event: 4
Issue comment event: 86
Push event: 14
Pull request review comment event: 10
Pull request review event: 16
Pull request event: 23
Fork event: 9
Create event: 4

Last Year

Issues event: 34
Watch event: 49
Delete event: 4
Issue comment event: 86
Push event: 14
Pull request review comment event: 10
Pull request review event: 16
Pull request event: 23
Fork event: 9
Create event: 4

Committers

Last synced: about 2 years ago

All Time

Total Commits: 2,430
Total Committers: 62
Avg Commits per committer: 39.194
Development Distribution Score (DDS): 0.763

Past Year

Commits: 54
Committers: 8
Avg Commits per committer: 6.75
Development Distribution Score (DDS): 0.37

Top Committers

Name	Email	Commits
Ali Ebrahim	a**m@u**u	575
Synchon Mandal	s**l@g**m	289
Midnighter	m**r@p**t	252
Matthias Koenig	k**t@g**m	225
uri.akavia	u**a@m**a	191
Henning Redestig	h**d@g**m	168
Christian Diener	c**r@g**m	164
danielhyduke	d**e@b**a	116
Moritz E. Beber	m**b@b**k	111
Daniel Robert Hyduke	d**e@g**m	82
Peter St. John	p**n@g**m	42
ali-ebrahim	a**m@b**a	21
akaviaLab	u**a@m**a	20
Ali Ebrahim	a**4@g**m	19
akaviaLab	u**a@g**m	15
HemantYadav	h**9@g**m	14
Zachary King	z**7@g**m	14
Nikolaus Sonnenschein	n**n@g**m	10
Maximilian Greil	m**l@w**e	9
Ali Ebrahim	a****m	6
JuBra	j****a	6
maureencarey	m**y@m**m	6
Benjamin Sanchez	b**b@g**m	5
Ali Kaafarani	a**i@k**o	5
Erik Cederstrand	e**k@c**k	5
gregmedlock	g**o@g**m	4
Teddy Groves	g**y@g**m	4
Daria Komkova	d**a@i**m	4
weilandtd	d**t@e**h	4
Vivek Rai	v**p@g**m	3
and 32 more...

Committer Domains (Top 20 + Academic)

biosustain.dtu.dk: 3 ucsd.edu: 2 mcgill.ca: 2 posteo.net: 1 mac.com: 1 kvikshaug.no: 1 cederstrand.dk: 1 itechart-group.com: 1 epfl.ch: 1 stud.kea.dk: 1 ghraoui.name: 1 hemoshear.com: 1 imperial.ac.uk: 1 steinbiss.name: 1 eng.ucsd.edu: 1 mnt.org: 1 aol.com: 1 mayo.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 142
Total pull requests: 75
Average time to close issues: about 1 year
Average time to close pull requests: 24 days
Total issue authors: 93
Total pull request authors: 27
Average comments per issue: 3.99
Average comments per pull request: 2.12
Merged pull requests: 42
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 31
Pull requests: 29
Average time to close issues: 11 days
Average time to close pull requests: 11 days
Issue authors: 21
Pull request authors: 12
Average comments per issue: 0.97
Average comments per pull request: 0.86
Merged pull requests: 8
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

oxinabox (9)
Midnighter (8)
helehera (5)
achillesrasquinha (5)
amarsh26 (4)
Ilhem36 (4)
cdiener (4)
wshao1 (3)
pstjohn (3)
cjrodriguez98 (3)
kristycyw (2)
freiburgermsu (2)
zakandrewking (2)
axelvonkamp (2)
dengxiao01 (2)

Pull Request Authors

cdiener (21)
Midnighter (10)
akaviaLab (6)
oxinabox (6)
a-detiste (5)
achillesrasquinha (5)
mdziurzynski (5)
ripaul (2)
dagl1 (2)
alexpan00 (2)
Palaract (2)
pascalaldo (2)
jedforrest (2)
djinnome (2)
synchon (2)

Top Labels

Issue Labels

bug (44) enhancement (15) SBML (8) needs information (5) stale (5) JSON (4) docs (3) question (3) cookbook (2) help-wanted (2) WIP (1) optlang (1)

Pull Request Labels

stale (9) enhancement (2) ready (1) WIP (1)

Packages

Total packages: 2
Total downloads:
- pypi 34,262 last-month
Total docker downloads: 808

Total dependent packages: 59
(may contain duplicates)
Total dependent repositories: 242
(may contain duplicates)
Total versions: 107
Total maintainers: 5

pypi.org: cobra

COBRApy is a package for constraint-based modeling of metabolic networks.

Homepage: https://opencobra.github.io/cobrapy
Documentation: https://cobrapy.readthedocs.io
License: LGPL-2.0-or-later OR GPL-2.0-or-later
Latest release: 0.29.1
published over 1 year ago

Versions: 100
Dependent Packages: 56
Dependent Repositories: 240
Downloads: 34,262 Last month
Docker Downloads: 808

Rankings

Dependent packages count: 0.4%

Dependent repos count: 1.0%

Docker downloads count: 1.4%

Average: 2.2%

Stargazers count: 3.2%

Downloads: 3.3%

Forks count: 3.6%

Maintainers (5)

midnighter Nikolaus.Sonnenschein Ali.Ebrahim henred danielhyduke

Last synced: 6 months ago

conda-forge.org: cobra

Constraint-based reconstruction and analysis (COBRA) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes and eukaryotes. COBRApy is a constraint-based modeling package that is designed to accommodate the biological complexity of the next generation of COBRA models and provides access to commonly used COBRA methods, such as flux-balance analysis, flux variability analysis, and gene deletion analyses.

Homepage: https://opencobra.github.io/cobrapy
License: LGPL-2.0-or-later OR GPL-2.0-or-later
Latest release: 0.26.0
published over 3 years ago

Versions: 7
Dependent Packages: 3
Dependent Repositories: 2

Rankings

Forks count: 12.7%

Dependent packages count: 15.6%

Average: 17.0%

Stargazers count: 19.7%

Dependent repos count: 20.0%

Last synced: 6 months ago

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