An in silico modeling toolbox for rapid prototyping of circuits in a biomolecular “breadboard” system

In this paper, we develop an experimentally validated MATLAB software toolbox as an accompaniment to an in vitro cell-free biomolecular “breadboard” system. The toolbox gives insight into the dynamics of unmeasured states in the cell-free system, accounting especially for resource usage. Parameter lumping and the reduced order modeling are used to maintain computational tractability and to avoid ill-conditioning. The toolbox provides a general framework for experiment planning and predictive modeling for synthetic biomolecular circuits in cell-free systems, accelerating our capacity to rationally design circuits from well characterized parts.