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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

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.

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