Stoichiometric metabolic modelling

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  • License: GNU General Public License v3 or later (GPLv3+) (GPL-3.0-or-later)
  • Author: Marvin van Aalst
  • Maintainer: Marvin van Aalst
  • Tags modelling, stoichiometric, metacyc, blast
  • Requires: Python >=3.8, <3.11
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Project description

pipeline status coverage report Documentation Status PyPi Code style: black Checked with mypy Downloads

moped

A metabolic object-oriented Python modelling environment.

Installation

You can install moped using pip

pip install moped

However, you will still need to install NCBI Blast if you want to use the genome / proteome reconstruction methods

If you are using conda or mamba, you can install blast from bioconda:

conda install -c bioconda blast==2.12.0
mamba install -c bioconda blast==2.12.0

If you want to install BLAST yourself:

  • download the latest blast version from NCBI
  • Extract the downloaded folder to a path of your liking
  • Add blast to your path e.g. by adding the following line to your .bashrc
    • export PATH="your_blast_directory/bin:$PATH"

Documentation

Check out our tutorial on readthedocs

Contributing

All contributions, bug reports, bug fixes, documentation improvements, enhancements and ideas are welcome. If you want to contribute code to the project, please consider our contribution guide

License

moped is licensed under GPL 3

Issues and support

If you experience issues using the software please contact us through our issues page.

Project details

Verified details

These details have been verified by PyPI
Maintainers
Avatar for marvin.vanaalst from gravatar.com marvin.vanaalst Avatar for qtb from gravatar.com qtb

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License: GNU General Public License v3 or later (GPLv3+) (GPL-3.0-or-later)
  • Author: Marvin van Aalst
  • Maintainer: Marvin van Aalst
  • Tags modelling, stoichiometric, metacyc, blast
  • Requires: Python >=3.8, <3.11
Classifiers

Release history Release notifications | RSS feed

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