MarkovWeightedEFMs.jl

MarkovWeightedEFMs.jl is a package to decompose steady state metabolic fluxes onto elementary flux mode (EFM) weights and atomic elementary flux mode (AEFM) weights. EFM flux decomposition works only for closed-loop networks of unimolecular reactions. AEFM flux decomposition works on metabolic flux networks with known metabolite structures and integer-based stoichiometries.

Usage

See Getting started for package installation and Python dependencies (RXNMapper) for AEFM enumeration and flux decomposition. Once installed, the package is loaded in a julia session by typing:

julia> using MarkovWeightedEFMs

See the tutorial sections for EFM or AEFM enumeration and flux decomposition.

Citing MarkovWeightedEFMs.jl

Please cite the following papers if you use our method for (A)EFM enumeration and flux decomposition.

Justin G. Chitpin and Theodore J. Perkins, Atomic elementary flux modes explain the steady state flow of metabolites in flux networks. biorXiv preprint doi: 10.1101/2024.11.13.623484.

Justin G. Chitpin and Theodore J. Perkins, A Markov constraint to uniquely identify elementary flux mode weights in unimolecular metabolic networks. J Theor Biol. 2023 Nov 7;575:111632. doi: 10.1016/j.jtbi.2023.111632.

License

This software is released under the MIT license.

Contact information

Justin G. Chitpin at jchit069@uottawa.ca for questions.