COBREXA.jl: constraint-based reconstruction and exascale analysis

• DOI: 10.1093/bioinformatics/btab782
• Publication Date: 2021-11-10T12:31:17Z
• Authors: Miroslav Kratochvíl; Laurent Heirendt; St Elmo Wilken; Taneli Pusa; Sylvain Arreckx; Alberto Noronha; Marvin van Aalst; Venkata P Satagopam; Oliver Ebenhöh; Reinhard Schneider; Christophe Trefois; Wei Gu
• Keywords: 0301 basic medicine; 03 medical and health sciences; Applications Notes; Computing Methodologies; Models, Biological; Software

AbstractSummaryCOBREXA.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 implementationhttps://doi.org/10.17881/ZKCR-BT30.Supplementary informationSupplementary data are available at Bioinformatics online.