giFBA: Greedy Interaction Flux Balance Analysis

This is a COBRApy extension for modeling community interaction.

Installation

pip install "git+https://github.com/m-3-lab/giFBA.git@main#subdirectory=package"

Directory Description

📦giFBA
 ┣ 📂Examples
 ┃ ┣ 📂Model_Diagrams
 ┃ ┣ 📂Results
 ┃ ┃ ┣ 📂cFBA
 ┃ ┃ ┣ 📂giFBA_AGORA
 ┃ ┃ ┣ 📂giFBA_Simple
 ┃ ┃ ┣ 📂cFBA_Models
 ┃ ┃ ┗ micom_results.csv
 ┃ ┣ create_simple_fba.ipynb
 ┃ ┣ gifba_comparisons.ipynb
 ┃ ┗ gifba_utilization.ipynb
 ┣ 📂package
 ┃ ┣ 📂gifba
 ┃ ┃ ┣ 📂Simple_Models
 ┃ ┃ ┣ __init__.py
 ┃ ┃ ┣ config.py
 ┃ ┃ ┣ gifba_object.py
 ┃ ┃ ┣ summary.py
 ┃ ┃ ┗ utils.py
 ┃ ┣ README.md
 ┃ ┗ pyproject.toml
 ┣ .gitignore
 ┗ README.md

Description of Directory Tree

• package/ : contains all package code for gifba package
  • package/gifba/ : contains source code (objects, methods, validation models, etc.)
  • package/gifba/Simple_Models : All simple models used for validation of methods
• Examples : contains all validation, results, & figure generation
  • Examples/gifba_comparisons.ipynb : Contains validation code for the following:
    • Generating compartmentalized FBA (cFBA) models (stored in Examples/Results/cFBA_Models)
    • Solving cFBA models & finding solution space
    • Creating & solving MICOM communities
  • Examples/gifba_utilization.ipynb : Contains walkthrough code for the following:
    • All 12 Simple Modesl for validation with:
      • Initialization & giFBA usage
      • Plotting/Comparison to individualized FBA, cFBA, MICOM, & giFBA
    • 2 simulations of real AGORA2 communities (not included in repository) with:
      • Summary Display
      • Cytoscape-ready files
  • Examples/create_simple_fba.ipynb : Notebook to create each unique "organism" for simple model validation. Some models are exact duplicates or similar (internal rxn bounds changed), thus not shown.
  • Examples/Model_Diagrams/ : Contains all Validation model diagrams (corresponding to simple models in package/gifba/Simple_Models)
  • Examples/Results/ : Contains the following:
    • cFBA/ : csv files of each simulation and the solution space
    • giFBA_AGORA/ : Cytoscape-ready files of nodes & edges for AGORA2 model examples
    • giFBA_Simple/ : Saved images of the simulated growth of each simple, validation model
    • micom_results.csv : MICOM simulation results for each simulation (each simulation has 5 tradeoff parameter values stored)