We introduce a MATLAB based simulation toolbox, called txtlsim, for an E. coli based Transcription-Translation (TX- TL) system. This toolbox accounts for several cell-free related phenomena, such as resource loading, consumption, and degradation, and in doing so, models the dynamics of TX-TL reactions for the entire duration of batch-mode experiments. We use a Bayesian parameter inference approach to characterize the reaction rate parameters associated with the core transcription, translation and mRNA degradation mechanics of the toolbox, allowing it to reproduce constitutive mRNA and protien expression trajectories. We demonstrate the use of this characterized toolbox in a circuit behavior prediction case study for an incoherent feed-forward loop.

中文翻译：

---

用于无细胞系统中遗传电路建模的MATLAB工具箱

我们为基于大肠杆菌的转录翻译（TX-TL）系统引入了一个基于MATLAB的仿真工具箱，称为txtlsim。该工具箱解决了几种与无单元格相关的现象，例如资源装载，消耗和降解，并且在此过程中，在批处理模式实验的整个过程中对TX-TL反应的动力学进行了建模。我们使用贝叶斯参数推断方法来表征与工具箱的核心转录，翻译和mRNA降解机理相关的反应速率参数，从而使其能够再现组成型mRNA和蛋白质表达轨迹。我们演示了在不相干前馈回路的电路行为预测案例研究中使用此功能强大的工具箱。