Dynamic Community FBA

Welcome to Dynamic Community FBA (dcFBA): The Python package that makes modeling Microbial Communities dynamically a breeze!

This project is licensed under the MIT License - please refer to the LICENSE file for more details.

About

Dynamic Community FBA (dcFBA) is a versatile tool designed for modeling microbial communities as single organisms using Genome Scale Metabolic Models (GSMMs). This package builds upon the solid foundation of cbmpy and seamlessly integrates with SBML and COBRApy models. dcFBA empowers users with three distinct dynamic modeling methods:

1. Dynamic Joint FBA - Incrementally updates the concentrations of biomass and metabolites within the combined stoichiometric matrix of the provided models.

2. Dynamic Parallel FBA - Simultaneously updates the concentrations of biomass and metabolites while performing FBA on individual models.

3. EndPointFBA - Duplicates the CommunityMatrix N times and performs FBA on the community's time-dependent stoichiometric matrix.

For a comprehensive understanding of these methods and their underlying mathematics, please consult ¹.

Whether you're exploring parasitic interactions or investigating costly cross-feeding behaviors in microbial communities, dcFBA offers an elegant and efficient solution.

Installation

Prerequisites

Before installing dcFBA, make sure you have the following prerequisites in place:

• Python >= 3.8, < 3.11
• cbmpy
• cplex

Installation Steps

To install dcFBA, follow these simple steps:

1. Install using pip:

   pip install dcFBA
   

Usage

For basic usage examples and detailed documentation on both cbmpy and dcFBA, please refer to their respective documentation pages.