cdFBA 0.0.4

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cdFBA

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

FBA Implementation

cdFBA uses the cobrapy repository to perform FBA analysis.

Dynamics

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.

Utility Functions

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 Notebooks

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.

!!This project is a work in progress!!