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An automated model reduction tool to guide the design and analysis of synthetic biological circuits

Pandey, Ayush and Murray, Richard M. (2019) An automated model reduction tool to guide the design and analysis of synthetic biological circuits. . (Unpublished) http://resolver.caltech.edu/CaltechAUTHORS:20190517-100226134

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Abstract

We present an automated model reduction algorithm that uses quasi-steady state approximation based reduction to minimize the error between the desired outputs. Additionally, the algorithm minimizes the sensitivity of the error with respect to parameters to ensure robust performance of the reduced model in the presence of parametric uncertainties. We develop the theory for this model reduction algorithm and present the implementation of the algorithm that can be used to perform model reduction of given SBML models. To demonstrate the utility of this algorithm, we consider the design of a synthetic biological circuit to control the population density and composition of a consortium consisting of two different cell strains. We show how the model reduction algorithm can be used to guide the design and analysis of this circuit.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/640276DOIDiscussion Paper
https://www.biorxiv.org/content/10.1101/640276v1OrganizationDiscussion Paper
ORCID:
AuthorORCID
Pandey, Ayush0000-0003-3590-4459
Murray, Richard M.0000-0002-5785-7481
Additional Information:We would like to thank Chelsea Hu, Reed McCardell, and Shailja for insightful discussions. We would also like to thank Samuel Clamons for helping with sensitivity analysis computations. The author A.P. is supported by the Defense Advanced Research Projects Agency (Agreement HR0011-17-2-0008). The content of the information does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred.
Funders:
Funding AgencyGrant Number
Defense Advanced Research Projects Agency (DARPA)HR0011-17-2-0008
Record Number:CaltechAUTHORS:20190517-100226134
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20190517-100226134
Official Citation:An automated model reduction tool to guide the design and analysis of synthetic biological circuits. Ayush Pandey, Richard M Murray. bioRxiv 640276; doi: https://doi.org/10.1101/640276
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:95561
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:17 May 2019 17:08
Last Modified:17 May 2019 17:08

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