Metadata-Version: 2.1
Name: ModelSEEDpy
Version: 0.4.0
Summary: Python package for building and analyzing models using ModelSEED
Home-page: https://github.com/ModelSEED/ModelSEEDpy
Author: Christopher Henry
Author-email: chenry@anl.gov
License: MIT License
        
        Copyright (c) 2021 ModelSEED
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        
Project-URL: Documentation, https://modelseedpy.readthedocs.io/en/latest/
Project-URL: Issues, https://github.com/ModelSEED/ModelSEEDpy/issues
Classifier: Development Status :: 3 - Alpha
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Natural Language :: English
Description-Content-Type: text/x-rst
License-File: LICENSE
Requires-Dist: networkx>=2.4
Requires-Dist: cobra>=0.29.0
Requires-Dist: scikit-learn==1.2.0
Requires-Dist: scipy>=1.5.4
Requires-Dist: chemicals>=1.0.13
Requires-Dist: chemw>=0.3.2
Requires-Dist: matplotlib>=3.0.0
Requires-Dist: Jinja2>=3.1.4
Requires-Dist: sympy>=1.12.0

.. image:: https://raw.githubusercontent.com/modelseed/modelseedpy/main/examples/ms-logo-horizontal.png?sanitize=true

Metabolic modeling with the ModelSEED Database
________________________________________________________________________

|PyPI version| |docs| |Downloads| |License|

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

.. |PyPI version| image:: https://img.shields.io/pypi/v/modelseedpy.svg?logo=PyPI&logoColor=brightgreen
   :target: https://pypi.org/project/modelseedpy/
   :alt: PyPI version

.. |Actions Status| image:: https://github.com/modelseed/modelseedpy/workflows/Test%20modelseedpy/badge.svg
   :target: https://github.com/modelseed/modelseedpy/actions
   :alt: Actions Status

.. |License| image:: https://img.shields.io/badge/License-MIT-blue.svg
   :target: https://opensource.org/licenses/MIT
   :alt: License

.. |Downloads| image:: https://pepy.tech/badge/modelseedpy
   :target: https://pepy.tech/project/modelseedpy
   :alt: Downloads


Metabolic modeling is an pivotal method for computational research in synthetic biology and precision medicine. The metabolic models, such as the constrint-based flux balance analysis (FBA) algorithm, are improved with comprehensive datasets that capture more metabolic chemistry in the model and improve the accuracy of simulation predictions. We therefore developed ModelSEEDpy as a comprehensive suite of packages that bootstrap metabolic modeling with the ModelSEED Database (`Seaver et al., 2021 <https://academic.oup.com/nar/article/49/D1/D575/5912569?login=true>`_ ). These packages parse and manipulate (e.g. gapfill missing reactions or calculated chemical properties of metabolites), constrain (with kinetic, thermodynamics, and nutrient uptake), and simulate cobrakbase models (both individual models and communities). This is achieved by standardizing COBRA models through the   ``cobrakbase`` module into a form that is amenable with the KBase/ModelSEED ecosystem. These functionalities are exemplified in `Python Notebooks <https://github.com/ModelSEED/ModelSEEDpy/examples>`_ . Please submit errors, inquiries, or suggestions as `GitHub issues <https://github.com/ModelSEED/ModelSEEDpy/issues>`_ where they can be addressed by our developers.


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

ModelSEEDpy will soon be installable via the ``PyPI`` channel::

 pip install modelseedpy

but, until then, the repository must cloned::

 git clone https://github.com/ModelSEED/ModelSEEDpy.git

and then locally installed with ``pip``::

 cd path/to/modelseedpy
 pip install .

The associated ModelSEED Database, which is required for a few packages, is simply downloaded by cloning the GitHub repository::

 git clone https://github.com/ModelSEED/ModelSEEDDatabase.git

and the path to this repository is passed as an argument to the corresponding packages.
