mptool 0.1.2

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 minimzation, 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

The minimal requirements (cobra, gurobipy, networkx, numpy, and pytest) are installed automatically when mptool is installed through pip:

pip install mptool

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 and J. Stelling. "Scalable metabolic pathway analysis". biorXiv (2020).

[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).

[4] Z.A. King et al. "BiGG Models: A platform for integrating, standardizing, and sharing genome-scale models" Nucleic Acids Research 44.D1 (2016).

[5] A. Noronha et al. "The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease" Nucleic Acids Research 47.D1 (2018).