dingo: a Python']Python package for metabolic flux sampling

被引:1
|
作者
Chalkis, Apostolos [1 ,6 ]
Fisikopoulos, Vissarion [1 ,2 ]
Tsigaridas, Elias [1 ,3 ,4 ,5 ]
Zafeiropoulos, Haris [1 ,6 ]
机构
[1] GeomScale Org, Athens, Greece
[2] Natl & Kapodistrian Univ Athens, Dept Informat & Telecommun, Athens 16122, Greece
[3] Sorbonne Univ, Inria Paris, Paris, France
[4] Sorbonne Univ, IMJ PRG, Paris, France
[5] Paris Univ, Paris, France
[6] Katholieke Univ Leuven, Lab Mol Bacteriol, Dept Microbiol Immunol & Transplantat, Rega Inst Med Res, B-3000 Leuven, Belgium
来源
BIOINFORMATICS ADVANCES | 2024年 / 4卷 / 01期
关键词
D O I
10.1093/bioadv/vbae037
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
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).
引用
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页数:3
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