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. 2022 Jan 27;38(4):1171-1172.
doi: 10.1093/bioinformatics/btab782.

COBREXA.jl: constraint-based reconstruction and exascale analysis

Miroslav Kratochvíl  1 , Laurent Heirendt  1   2 , St Elmo Wilken  3 , Taneli Pusa  1   4 , Sylvain Arreckx  1 , Alberto Noronha  4 , Marvin van Aalst  3 , Venkata P Satagopam  1   2 , Oliver Ebenhöh  3 , Reinhard Schneider  1   2 , Christophe Trefois  1   2 , Wei Gu  1   2
Affiliations

COBREXA.jl: constraint-based reconstruction and exascale analysis

Miroslav Kratochvíl et al. Bioinformatics. .

Abstract

Summary: COBREXA.jl is a Julia package for scalable, high-performance constraint-based reconstruction and analysis of very large-scale biological models. Its primary purpose is to facilitate the integration of modern high performance computing environments with the processing and analysis of large-scale metabolic models of challenging complexity. We report the architecture of the package, and demonstrate how the design promotes analysis scalability on several use-cases with multi-organism community models.

Availability and implementation: https://doi.org/10.17881/ZKCR-BT30.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
Schema of an example custom analysis construction that examines flux variability in many variants of a model, its distributed execution with COBREXA.jl, and collection of many results in a multi-dimensional array
See this image and copyright information in PMC

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