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 thebio-appsmodule.
Usage
SteadierCom is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the module:
Run the analysis with the steadiercom command, giving the community's genome-scale
models:
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.