ACRE: absolute concentration robustness exploration in module-based combinatorial networks

H. Kuwahara, R. Umarov, I. Almasri, X. Gao
Synth Biol. 2(1): ysx001, (2017)

ACRE: absolute concentration robustness exploration in module-based combinatorial networks

Keywords

Biological design principle, Combinatorial network analysis, Concentration robustness, Chemical reaction network theory

Abstract

​To engineer cells for industrial-scale application, a deep understanding of how to design molecular control mechanisms to tightly maintain functional stability under various fluctuations is crucial. Absolute concentration robustness (ACR) is a category of robustness in reaction network models in which the steady-state concentration of a molecular species is guaranteed to be invariant even with perturbations in the other molecular species in the network. Here, we introduce a software tool, absolute concentration robustness explorer (ACRE), which efficiently explores combinatorial biochemical networks for the ACR property. ACRE has a user-friendly interface, and it can facilitate efficient analysis of key structural features that guarantee the presence and the absence of the ACR property from combinatorial networks. Such analysis is expected to be useful in synthetic biology as it can increase our understanding of how to design molecular mechanisms to tightly control the concentration of molecular species. ACRE is freely available at https://github.com/ramzan1990/ACRE.

Code

DOI: 10.1093/synbio/ysx001

Sources

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