https://github.com/carrascomj/mmodes

MMODES (Metabolic Models based Ordinary Differential Equations Simulation)
https://github.com/carrascomj/mmodes

bioinformatics metabolic-models modelling python3 systems-biology

Last synced: 3 months ago
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MMODES (Metabolic Models based Ordinary Differential Equations Simulation)

• Host: GitHub
• URL: https://github.com/carrascomj/mmodes
• Owner: carrascomj
• License: mit
• Created: 2019-01-14T18:08:24.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2020-08-22T09:00:26.000Z (about 5 years ago)
• Last Synced: 2025-04-08T23:57:08.736Z (6 months ago)
• Topics: bioinformatics, metabolic-models, modelling, python3, systems-biology
• Language: Python
• Homepage: https://mmodes.readthedocs.io/
• Size: 761 KB
• Stars: 4
• Watchers: 0
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE.txt

Awesome Lists containing this project

README

          

.. image:: build_the_docks/logo_f.svg

   :width: 500px

   :alt: MMDOES logotype

   :align: center

.. image:: https://img.shields.io/pypi/v/mmodes.svg

   :target:  https://pypi.org/project/mmodes/

   :alt: Current PyPI Version

.. image:: https://img.shields.io/badge/code%20style-black-000000.svg

   :target: https://github.com/ambv/black

   :alt: Black

What is MMODES?

===============

MMODES (Metabolic Models based Ordinary Differential Equations Simulation) provides

an straight-forward framework to run dynamic simulations of metabolic models communities

using `COBRApy `_ and `Scipy `_.

It implements a version of dFBA. The scipy ODE

implementation of the script was inspired by `DAPHNE `__,

although this code was built for a general case. It also provides I/O utilities

to generate and parse COMETS-like files and to manage "languages" of GEM models.

Documentation

~~~~~~~~~~~~~

User documentation can be found on https://mmodes.readthedocs.io/.

Installation

~~~~~~~~~~~~

Working on a **virtualenv** is highly recommended since the package uses the latest python3 versions of the modules required.

More information about Python virtualenv's `here `_.

MMODES is on PyPi, therefore, given that **pip** in installed:

.. code:: bash

    pip upgrade pip --user

    pip3 install mmodes --user

Another option is **building from source**. Clone this repository and install it via *setup.py*:

.. code:: bash

    git clone https://github.com/carrascomj/mmodes.git # or ssh

    cd path_to_mmodes/mmodes

    sudo python3 setup.py install

On both cases, **uninstalling** can be accomplished via pip:

.. code:: bash

    pip3 uninstall mmodes --user # if user install

    sudo pip3 uninstall mmodes # if superuser install (from source)

Docker

~~~~~~

A `Docker `_ container is under development.

Example script simulation

~~~~~~~~~~~~~~~~~~~~~~~~~

An example with one strain can be found on "example.py".