Bioinformatics (Oxford, England) · 2026
COCOA.jl - A Julia package for high-performance anal y sis of concordance and kinetic modules in biochemical networks.
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Schaffranke Anton, Küken Anika, Nikoloski Zoran
Аннотация
MOTIVATION: Recent advances in analysis of biochemical networks have contributed the identification of their modular structure based on the concept of multi reaction dependencies and kinetic coupling of reaction rates (Küken et al., 2022; Langary et al., 2025). Existing implementations of the algorithms to study modular structure do not scale well with the size of the networks, prohibiting their application with genome-scale networks.
RESULTS: Here, we introduce COCOA.jl, a multithreaded Julia package for identification of concordant and kinetic modules, with applications in the study of concentration robustness.
AVAILABILITY: COCOA.jl is implemented in Julia 1.12.6 and is freely available under the MIT license at GitHub (https://github.com/antoniofranky/COCOA.jl) and Zenodo (https://doi.org/10.5281/zenodo.22094185). It runs on Linux, macOS, and Windows; installation is supported via the Julia package manager. COCOA.jl can be called from Python via JuliaCall.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
RESULTS: Here, we introduce COCOA.jl, a multithreaded Julia package for identification of concordant and kinetic modules, with applications in the study of concentration robustness.
AVAILABILITY: COCOA.jl is implemented in Julia 1.12.6 and is freely available under the MIT license at GitHub (https://github.com/antoniofranky/COCOA.jl) and Zenodo (https://doi.org/10.5281/zenodo.22094185). It runs on Linux, macOS, and Windows; installation is supported via the Julia package manager. COCOA.jl can be called from Python via JuliaCall.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.