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