An In Silico Modeling Toolbox for Rapid Prototyping of Circuits in a Biomolecular “Breadboard” System

Title	An In Silico Modeling Toolbox for Rapid Prototyping of Circuits in a Biomolecular “Breadboard” System
Authors	Zoltan A. Tuza, Vipul Singhal, Jongmin Kim and Richard M. Murray
Source	2013 Conference on Decision and Control (CDC)
Abstract	In this paper, we develop an experimentally val- idated 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 ill-conditioning. 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 sys- tem, 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.
Type	Conference paper
URL	http://www.cds.caltech.edu/~murray/preprints/tskm13-cdc s.pdf
DOI
Tag	tskm13-cdc
ID	2013b
Funding
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