COBREXA.jl: constraint-based reconstruction and exascale analysis#
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, and Wei Gu
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.
COBREXA.jl source code is available from GitHub.
SBML.jl source code is available from GitHub.
DistributedData.jl source code is available from GitHub.
The documentation of COBREXA.jl is available from GitHub.
The benchmark scripts are available from GitHub.
A comparison of CPU performance used for the difference estimate in supplementary section 3.3 is available at cpubenchmark.net.