MICOM

MICOM is a Python package for the metabolic modelling of microbial communities. It builds and simulates community-scale metabolic models from taxon abundances and genome-scale reconstructions.

• MICOM
  • License
  • Available
  • Usage
  • Support
  • More information

License

Free to use and open source under the Apache 2.0 license.

Available

• Roihu: 0.39.0 (module py-micom), via the bio-apps module.

Usage

MICOM is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the module:

module load bio-apps/v202603
module load py-micom/0.39.0

MICOM is used as a Python library. Write your analysis in a Python script and run it, for example within a batch job:

#!/bin/bash
#SBATCH --job-name=micom
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=08:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=4G

module load bio-apps/v202603
module load py-micom/0.39.0

python my_micom_analysis.py

Replace <project> with your CSC project (for example project_2001234). MICOM can use multiple threads; set the number of workers in your script to match --cpus-per-task.

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information

• MICOM documentation
• MICOM GitHub repository

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