Community Dynamic Flux Balance Analysis using process-bigraph.
Release version 0.0.1 is available from PyPI. Requires python>=3.9
To install use:
pip install cdFBA
cdFBA uses the cobrapy repository to perform FBA analysis.
Static FBA optimizations are used to dynamically change the substrate concentrations in the environment at each time-step, based on substrate exchange reaction kinetics. The subsatrate concentrations are then used to set flux boundaries for the FBA optimization in the following time-step.
cdFBA includes some basic utility functions to create the model specification dictionaries automatically. Just provide a list of model files and exchange reaction IDs. The functions can be found here.
!!CAUTION!!: The utility functions work only for metabolic models with the same annotation systems - i.e. same reaction name and IDs. If you need to use models from different sources with different annotation systems, you will need to manually map the substrate/metabolite names.
Demo Jupyter notebooks can be found here. The primary demo using the process-bigraph interface can be found here. We will be adding more notebooks to demonstrate usage reproduction of results from the literature.