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.

1. pip install coralme

1. Clone repository and navigate to coralme/.
2. pip install -r requirements.txt
3. python3 setup.py clean build install

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

1. Install OrbStack (Docker Desktop alternative - recommended because it automatically uses Rosetta for AMD images).
2. Clone repository and navigate to coralme/.
3. docker buildx create --name multiarch --use
4. docker buildx build --platform linux/amd64 --file "./Dockerfile-Python3.10" . -t "python3.10-coralme:amd64" --load
5. docker run --detach -p 10000:8888 -v USER/PATH/TO/coralme/:/opt/notebooks/ python3.10-coralme:amd64
6. In your browser, go to localhost:10000

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 2 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. Windows users using WSL 2 should install python3-dev and gcc before installing coralme.

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

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

The coralME package has been tested using the most recent package versions available for each python3 version, except for numpy