Metadata-Version: 2.1
Name: coralME
Version: 1.0.0.post2
Summary: Comprehensive Reconstruction Algorithm for ME-models (coralME)
Home-page: https://github.com/jdtibochab/coralme
Author: Juan D. Tibocha-Bonilla and Rodrigo Santibanez-Palominos
Author-email: jdtibochab@users.noreply.github.com
License: MIT
Project-URL: Manual, https://coralme.readthedocs.io
Project-URL: Bug Reports, https://github.com/jdtibochab/coralme/issues
Project-URL: Source, https://github.com/jdtibochab/coralme
Keywords: metabolism,biology,constraint-based,linear programming,mixed-integer,optimization,flux-balance analysis,reconstruction
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Environment :: Console
Classifier: Operating System :: Unix
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: MacOS
Requires-Python: ~=3.0
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: cobra==0.26.3
Requires-Dist: python-libsbml
Requires-Dist: Biopython==1.80
Requires-Dist: anyconfig
Requires-Dist: pyranges
Requires-Dist: xlsxwriter
Requires-Dist: openpyxl
Requires-Dist: numpy==1.23.5
Requires-Dist: scipy
Requires-Dist: sympy
Requires-Dist: pandas==1.5.1
Requires-Dist: jsonschema
Requires-Dist: tqdm

.. image:: https://github.com/jdtibochab/coralme/blob/main/docs/logo.png

The **COmprehensive Reconstruction ALgorithm for ME-models (coralME)** is an automatic pipeline for the reconstruction of ME-models. coralME integrates existing ME-modeling packages `COBRAme`_, `ECOLIme`_, and `solveME`_, generalizes their functions for implementation on any prokaryote, and processes readily available organism-specific inputs for the automatic generation of a working ME-model.

coralME has four main objectives:

1. **Synchronize** input files to remove contradictory entries.
2. **Complement** input files from homology with a template organism to complete the E-matrix.
3. **Reconstruct** a ME-model.
4. **Troubleshoot** the ME-model to make it functional.

For more information on coralME's inputs, architecture and usage, see coralME's documentation.

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

1. ``pip install -r requirements.txt``
2. ``python3 setup.py clean build install``


Requirements
------------

coralME was tested with the following package versions:

- Python3, versions 3.7, 3.8, 3.9, and 3.10
- COBRApy version 0.26.3
- GUROBIpy version 9.5.2 (license is required)
- Ubuntu 22.04 is recommended (libgfortran.so.5 is required to execute MINOS and quad MINOS)
- Windows and MacOS users need to install `Gurobi`_ or `IBM CPLEX Optimizer <cplex_>`_. Alternatively, Windows users can install `WSL <wsl_>`_ and Ubuntu. Windows and MacOS users can use as well Docker Desktop to install it. We recommend the installation of Jupyter in the guest and its access through a browser from the host.

Compiled MINOS and quad MINOS are provided here as ``*.so`` files under ``coralme/solver``, and have been compiled using:

- Python3, versions 3.7.17, 3.8.17, 3.9.17, and 3.10.12
- wheel 0.38.4
- numpy 1.21.6
- scipy 1.7.3
- cython 0.29.32
- cpython 0.0.6

Documentation
-------------

You can find the documentation as a combined PDF called coralME_Documentation.pdf

.. refs
.. _COBRAme: https://github.com/SBRG/cobrame
.. _ECOLIme: https://github.com/SBRG/ecolime
.. _solveME: https://github.com/SBRG/solvemepy
.. _readthedocs: https://coralme.readthedocs.io/
.. _Gurobi: https://www.gurobi.com/
.. _cplex: https://www.ibm.com/products/ilog-cplex-optimization-studio/cplex-optimizer
.. _wsl: https://learn.microsoft.com/en-us/windows/wsl/install
