
Open access
Date
2013-08Type
- Conference Paper
ETH Bibliography
yes
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Abstract
With recent improvements of protocols for the assembly of transcriptional parts, synthetic biological devices can now more reliably be assembled according to a given design. The standardization of parts open up the way for in silico design tools that improve the construct and optimize devices with respect to given formal design specifications. The simplest such optimization is the selection of kinetic parameters and protein abundances such that the specified design constraints are robustly satisfied. In this work we address the problem of determining parameter values that fulfill specifications expressed in terms of a functional on the trajectories of a dynamical model. We solve this inverse problem by linearizing the forward operator that maps parameter sets to specifications, and then inverting it locally. This approach has two advantages over brute-force random sampling. First, the linearization approach allows us to map back intervals instead of points and second, every obtained value in the parameter region is satisfying the specifications by construction. The method is general and can hence be incorporated in a pipeline for the rational forward design of arbitrary devices in synthetic biology. Show more
Permanent link
https://doi.org/10.3929/ethz-b-000071966Publication status
publishedExternal links
Journal / series
BMC BioinformaticsVolume
Pages / Article No.
Publisher
BioMed CentralEvent
Subject
Synthetic Biology; Parameter Region; Linear Temporal Logic; Behavioral Specification; Reaction Rate EquationFunding
128503 - Advanced algorithms and design principles for bio-molecular circuit analysis (SNF)
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ETH Bibliography
yes
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