dingo : a Python package for metabolic flux sampling

Apostolos Chalkis (1) , Vissarion Fisikopoulos (1, 2) , Elias Tsigaridas (3) , Haris Zafeiropoulos (4)

1 GeomScale Org.
2 NKUA - National and Kapodistrian University of Athens
3 OURAGAN - OUtils de Résolution Algébriques pour la Géométrie et ses ApplicatioNs
4 Laboratory of Molecular Bacteriology [KU Leuven]

We present dingo, a Python package that supports a variety of methods to sample from the flux space of metabolic models, based on state-of-the-art random walks and rounding methods. For uniform sampling, dingo’s sampling methods provide significant speed-ups and outperform existing software. Indicatively, dingo can sample from the flux space of the largest metabolic model up to now (Recon3D) in less than a day using a personal computer, under several statistical guarantees; this computation is out of reach for other similar software. In addition, dingo supports common analysis methods, such as flux balance analysis and flux variability analysis, and visualization components. dingo contributes to the arsenal of tools in metabolic modelling by enabling flux sampling in high dimensions (in the order of thousands).

Mots clés: Metabolic networks; Python Library; Sampling; Flux model

Domaines: Biologie moléculaire

Apostolos Chalkis, Vissarion Fisikopoulos, Elias Tsigaridas, Haris Zafeiropoulos. dingo : a Python package for metabolic flux sampling. Bioinformatics Advances, 2024, 4 (1), ⟨10.1093/bioadv/vbae037⟩. ⟨hal-04549128⟩