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

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 compiles high-level design specifications represented using a modular library of biochemical parts, mechanisms, and contexts to CRN implementations. This compilation process offers four 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 be represente

SUBMITTER: Poole W 

PROVIDER: S-EPMC9060376 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature