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 the resource usage. Parameter lumping and the reduced order modeling are used to maintain computational tractability and to avoid illconditioning. The toolbox allows for most applications to be implemented with standard set of commands for ease of use. Due to the breadboarding nature of the underlying cell-free system, the toolbox provides a general framework for experiment planning and predictive modeling for synthetic biomolecular circuits cell-free systems, accelerating our capacity to rationally design circuits from well characterized parts.