metaCRM_SynCom

Metabolomics-informed consumer-resource modeling of a 15-member synthetic microbial community.

Project Structure

• data/: A folder containing the processed data ready for plotting, generated according to figureX/process_data.py.
• utils.py: Utility Python constants, filepaths, and functions used across data processing and plotting scripts.
• figureX/: Each figure has its own folder containing two files:
  • plot_figures.py: A script that generates plots associated with the given figure and saves them to figures/, including any supplemental figures related to this figure.
  • process_data.py: A script that takes the raw data as input to perform processing and analysis and outputs files in the correct format for plot_figures.py.
• plot_all.sh: A Bash script that runs all figureX/plot_figures.py scripts to generate all figures and place them in figures/.
• environment.yml: A Conda environment file containing software versions used for data processing and figure generation.