ArticlePLoS computational biology2022
BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts.
Article in PLoS computational biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Nucleotide-Level Chemical Reaction Network Modeling Enables Quantitative Prediction of Reconstituted Cell-Free Expression Systems.ACS synthetic biology · 2026Article
- GCAD: A Computational Framework for Mammalian Genetic Program Computer-Aided Design.ACS synthetic biology · 2026Article
- Resolving emergent transient oscillations in gene circuits with a growth-coupled model.Science advances · 2026Article
- Gene Expression Across Growth Stages (GEAGS): Modeling Circuit Dynamics in Batch Cultures.Methods in molecular biology (Clifton, N.J.) · 2026Article
- MobsPy: A programming language for biochemical reaction networks.PLoS computational biology · 2025Article
- A mathematical model of cell-free transcription-translation with plasmid crosstalk.Synthetic biology (Oxford, England) · 2025Article
- Fine-tuned protein-lipid interactions in biological membranes: exploration and implications of the ORMDL-ceramide negative feedback loop in the endoplasmic reticulum.Frontiers in cell and developmental biology · 2024Article
- Catalyst: Fast and flexible modeling of reaction networks.PLoS computational biology · 2023Article
- Vivarium: an interface and engine for integrative multiscale modeling in computational biology.Bioinformatics (Oxford, England) · 2022Article
- Rapid modeling of experimental molecular kinetics with simple electronic circuits instead of with complex differential equations.Frontiers in bioengineering and biotechnology · 2022Article
- Competitive dCas9 binding as a mechanism for transcriptional control.Molecular systems biology · 2021Article
- Towards understanding the messengers of extracellular space: Computational models of outside-in integrin reaction networks.Computational and structural biotechnology journal · 2021Review
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Authors and funding
5 authors.
Funding
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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 represented succinctly with design choices propagated 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. 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. By using BioCRNpyler, users ranging from expert modelers to novice script-writers can easily build, manage, and explore sophisticated biochemical models using diverse biochemical implementations, environments, and modeling assumptions.
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Registered trials
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