BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts

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Title BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts
Authors William Poole, Ayush Pandey, Zoltan Tuza, Andrey Shur, Richard M Murray
Source 2020 IWBDA
Abstract 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.
Type Conference paper
URL https://www.biorxiv.org/content/biorxiv/early/2020/08/03/2020.08.02.233478.full.pdf
Tag whp+20-iwbda
ID 2020c
Funding DARPA BioCon, NSF Cell Free
Flags Biocircuits