mptool 0.1.4

Enumeration and sampling of minimal pathways in metabolic (sub)networks.

Enumeration and sampling of minimal pathways in metabolic (sub)networks

Minimal pathways (MPs) are minimal sets of reactions that need to be active (have non-zero flux) in a metabolic (sub)network to satisfy all constraints on the network as a whole [1]. They can also be defined as the set of support-minimal flux patterns from elementary flux vectors (EFVs) [2].

An MP can be found by direct minimization of a mixed-integer linear program (MILP) or by iterative minimization of multiple linear programs (LPs). Enumeration of MPs is implemented using both of these approaches, in the iterative case by computing minimal cut sets (MCSs) in a separate binary integer program (BIP) [3]. For iterative minimization, enumeration can be accelerated by using a graph defined by the known MPs to predict unknown MPs, or it can be randomized to allow random sampling of MPs in cases where complete enumeration is inconvenient or infeasible.

Installation

You can install mptool using pip:

pip install mptool

This will also install the minimal requirements cobra, gurobipy, networkx, numpy, and pytest.

The Gurobi Optimizer (tested with versions ≥9.0.1)) needs to be installed separately (free academic licenses).

Citation

If you use mptool for a scientific publication please cite our paper [1].

References

[1] O. Øyås, A. Theorell, and J. Stelling. "Scalable enumeration and sampling of minimal metabolic pathways for organisms and communities". bioRxiv (2024).

[2] S. Klamt et al. "From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints". PLOS Computational Biology 13.4 (2017).

[3] H.S. Song et al. "Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming". Bioinformatics 33.15 (2017).