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.

• SteadierCom
  • License
  • Available
  • Usage
    • Example batch script
  • Support
  • More information

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

• SteadierCom GitHub repository

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