| Name | coralME JSON |
| Version |
1.1.10
JSON |
| download |
| home_page | https://github.com/jdtibochab/coralme |
| Summary | Comprehensive Reconstruction Algorithm for ME-models (coralME) |
| upload_time | 2024-12-05 00:25:25 |
| maintainer | None |
| docs_url | None |
| author | Juan D. Tibocha-Bonilla and Rodrigo Santibanez-Palominos |
| requires_python | ~=3.0 |
| license | MIT License Copyright (c) 2022 Juan D. Tibocha-Bonilla 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. |
| keywords |
metabolism
biology
constraint-based
linear programming
mixed-integer
optimization
flux-balance analysis
reconstruction
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
cobra
python-libsbml
Biopython
anyconfig
pyranges
xlsxwriter
openpyxl
numpy
scipy
sympy
pandas
jsonschema
tqdm
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
.. image:: https://github.com/jdtibochab/coralme/blob/main/docs/logo.png
.. image:: https://img.shields.io/pypi/v/coralme.svg
:target: https://pypi.org/project/coralme/
:alt: Current PyPI Version
.. image:: https://img.shields.io/pypi/pyversions/coralme.svg
:target: https://pypi.org/project/coralme/
:alt: Supported Python Versions
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.
Installation
------------
Install using pip
=================
1. ``pip install coralme``
Install locally
===============
1. Clone repository and navigate to coralme/.
2. ``pip install -r requirements.txt``
3. ``python3 setup.py clean build install``
Install using docker (tested on Ubuntu 22.04)
=============================================
1. Clone repository and navigate to coralme/
2. ``docker build --file "./Dockerfile-Python3.10" . -t "python3.10-coralme"``
3. ``docker run --detach -p 10000:8888 -v USER/PATH/TO/coralme/:/opt/notebooks/ python3.10-coralme``
4. In your browser, go to ``localhost:10000``
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
Compiled MINOS and quad MINOS are provided here as ``*.so`` files under ``coralme/solver``, and have been compiled using:
- Python3, versions 3.11.9 and 3.12.4
- wheel 0.43.0
- numpy 2.0.0
- cython 3.0.10
Documentation
-------------
You can find the documentation as a combined PDF called coralME_Documentation.pdf
Development
-----------
The coralME package has been tested using the most recent package versions available for each python3 version, except for numpy
========== ============ ============ ============ ============= ============= =============
Package Python 3.7 Python 3.8 Python 3.9 Python 3.10 Python 3.11 Python 3.12
========== ============ ============ ============ ============= ============= =============
cobra 0.28.0 0.29.0 0.29.0 0.29.0 0.29.0 0.29.0
numpy 1.21.6 1.24.4 1.26.4 1.26.4 2.0.1 2.0.1
scipy 1.7.3 1.10.1 1.13.1 1.14.0 1.14.0 1.14.0
pandas 1.3.5 2.0.3 2.2.2 2.2.2 2.2.2 2.2.2
sympy 1.10.1 1.13.1 1.13.1 1.13.1 1.13.1 1.13.1
anyconfig 0.13.0 0.14.0 0.14.0 0.14.0 0.14.0 0.14.0
========== ============ ============ ============ ============= ============= =============
.. 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
Raw data
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