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.

中文翻译：

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BioCRNpyler：从不同环境中的生物分子部分编译化学反应网络

系统和合成生物学中的生化相互作用通常使用化学反应网络 (CRN) 进行建模。CRN 提供了一个有原则的建模环境，能够表达大量的生化过程。在本文中，我们提出了一个用 Python 编写的软件工具箱，它编译使用 CRN 实现的生化部件、机制和上下文的模块化库表示的高级设计规范。这种编译过程提供了四个优点。首先，实际 CRN 表示的构建是自动的，并输出与众多模拟器兼容的系统生物学标记语言 (SBML) 模型。第二，模块化生化组件库允许通过在底层 CRN 中自动传播的设计选择来简洁地表示生化电路的不同架构和实现。这可以防止高层设计和模型动力学之间经常发生的不匹配。第三，高级设计规范可以嵌​​入到不同的生物分子环境中，例如无细胞提取物和体内环境。最后，我们的软件工具箱有一个参数数据库，它允许用户使用很少的参数快速制作大型模型原型，这些参数可以在以后进行定制。通过使用 BioCRNpyler，从专家建模者到新手脚本编写者的用户都可以使用不同的生化实施、环境和建模假设轻松构建、管理和探索复杂的生化模型。