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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.

SteadierCom

SteadierCom is a tool for microbial community simulation using genome-scale metabolic models. It predicts steady-state growth and cross-feeding interactions within microbial communities and provides the steadiercom command-line tool.

License

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

Available

  • Roihu: 0.1.5 (module py-steadiercom), via the bio-apps module.

Usage

SteadierCom 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-steadiercom/0.1.5

Run the analysis with the steadiercom command, giving the community's genome-scale models:

steadiercom models/*.xml --output community_results

Example batch script

#!/bin/bash
#SBATCH --job-name=steadiercom
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=04:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=4G

module load bio-apps/v202603
module load py-steadiercom/0.1.5

steadiercom models/*.xml --output community_results

Replace <project> with your CSC project (for example project_2001234).

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

Support

CSC Service Desk

More information