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:
- Synchronize input files to remove contradictory entries.
- Complement input files from homology with a template organism to complete the E-matrix.
- Reconstruct a ME-model.
- Troubleshoot the ME-model to make it functional.
For more information on coralME's inputs, architecture and usage, see coralME's documentation.
pip install -r requirements.txtpython3 setup.py clean build install
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. Alternatively, Windows users can install 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
You can find the documentation as a combined PDF called coralME_Documentation.pdf