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BioCRNpyler: Compiling Chemical Reaction Networks from Biomolecular Parts in Diverse Contexts

By William Poole, Ayush Pandey, Andrey Shur, Zoltan A. Tuza, Richard M. Murray

Posted 03 Aug 2020
bioRxiv DOI: 10.1101/2020.08.02.233478

Biochemical interactions in systems and synthetic biology are often modeled with Chemical Reaction Networks (CRNs). CRNs provide a principled modeling environment capable of expressing a huge range of biochemical processes. In this paper, we present a software toolbox, written in python, that complies high-level design specifications to CRN representations. This compilation process offers three advantages. First, the building of the actual CRN representation is automatic and outputs Systems Biology Markup Language (SBML) models compatible with numerous simulators. Second, a library of modular biochemical components allows for different architectures and implementations of biochemical circuits to represented succinctly with design choices propogated throughout the underlying CRN automatically. This prevents the often occurring mismatch between high-level designs and model dynamics. Third, high-level design specification can be embedded into diverse biomolecular environments, such as cell-free extracts and in vivo milieus. With these advantages offered by BioCRNpyler, users can quickly build and test multitude of models in different environments. Finally, our software toolbox has a parameter database, which allows users to rapidly prototype large models using very few parameters which can be customized later. ### Competing Interest Statement The authors have declared no competing interest.

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