coralME 1.2.2

Comprehensive Reconstruction Algorithm for ME-models (coralME)

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.

Getting started

With an existing M-model file (JSON or XML) and a corresponding genome GenBank file, run (only v1.2.0+)

coralme --m-model-path PATH_TO_M_MODEL --genbank-path PATH_TO_GENBANK_FILE

To get help:

coralme --help

For more usage information, go to Tutorials.

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

Install using docker (to run MINOS and quad MINOS for Apple Silicon)

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

Requirements

• Python3, version 3.8, 3.9, 3.10, 3.11, 3.12, or 3.13

• COBRApy

• GUROBIpy (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, 3.8.20, 3.9.21, and 3.10.16

• wheel 0.38.4

• cython 0.29.32

• numpy 1.21.6

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

• Python3, versions 3.11.11, 3.12.9, and 3.13.2

• wheel 0.43.0

• cython 3.0.10

• numpy 2.0.0

• meson 1.8.0

• ninja 1.11.1.4

Documentation

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

Development

The coralME package has been tested using the following package versions:

Package	Python 3.8	Python 3.9	Python 3.10	Python 3.11	Python 3.12	Python 3.13
cobra	0.29.0	0.29.0	0.29.0	0.29.0	0.29.0	0.29.0
numpy	1.24.4	1.26.4	1.26.4	2.2.5	2.2.5	2.2.5
scipy	1.10.1	1.13.1	1.14.0	1.14.0	1.14.0	1.14.1
pandas	2.0.3	2.2.3	2.2.3	2.2.3	2.2.3	2.2.3
sympy	1.12.1	1.12.1	1.12.1	1.12.1	1.12.1	1.12.1
pint	0.21.1	0.24.4	0.24.4	0.24.4	0.24.4	0.24.4
anyconfig	0.14.0	0.14.0	0.14.0	0.14.0	0.14.0	0.14.0
gurobipy	11.0.0	11.0.0	11.0.0	11.0.0	11.0.0	12.0.0