LAPSE:2019.0458
Published Article
LAPSE:2019.0458
On-Line Optimal Input Design Increases the Efficiency and Accuracy of the Modelling of an Inducible Synthetic Promoter
Lucia Bandiera, Zhaozheng Hou, Varun B. Kothamachu, Eva Balsa-Canto, Peter S. Swain, Filippo Menolascina
April 8, 2019
Synthetic biology seeks to design biological parts and circuits that implement new functions in cells. Major accomplishments have been reported in this field, yet predicting a priori the in vivo behaviour of synthetic gene circuits is major a challenge. Mathematical models offer a means to address this bottleneck. However, in biology, modelling is perceived as an expensive, time-consuming task. Indeed, the quality of predictions depends on the accuracy of parameters, which are traditionally inferred from poorly informative data. How much can parameter accuracy be improved by using model-based optimal experimental design (MBOED)? To tackle this question, we considered an inducible promoter in the yeast S. cerevisiae. Using in vivo data, we re-fit a dynamic model for this component and then compared the performance of standard (e.g., step inputs) and optimally designed experiments for parameter inference. We found that MBOED improves the quality of model calibration by ∼60%. Results further improve up to 84 % when considering on-line optimal experimental design (OED). Our in silico results suggest that MBOED provides a significant advantage in the identification of models of biological parts and should thus be integrated into their characterisation.
Keywords
model calibration, model-based optimal experimental design, optimal inputs, synthetic biology, system identification
Suggested Citation
Bandiera L, Hou Z, Kothamachu VB, Balsa-Canto E, Swain PS, Menolascina F. On-Line Optimal Input Design Increases the Efficiency and Accuracy of the Modelling of an Inducible Synthetic Promoter. (2019). LAPSE:2019.0458
Author Affiliations
Bandiera L: School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EG9 3DW, UK; Synthsys—Centre for Synthetic and Systems Biology, The University of Edinburgh, Edinburgh EH9 3BF, UK
Hou Z: School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EG9 3DW, UK
Kothamachu VB: School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EG9 3DW, UK
Balsa-Canto E: (Bio)Process Engineering Group, IIM-CSIC Spanish Reasearch Council, 36208 Vigo, Spain
Swain PS: Synthsys—Centre for Synthetic and Systems Biology, The University of Edinburgh, Edinburgh EH9 3BF, UK
Menolascina F: School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EG9 3DW, UK; Synthsys—Centre for Synthetic and Systems Biology, The University of Edinburgh, Edinburgh EH9 3BF, UK
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Journal Name
Processes
Volume
6
Issue
9
Article Number
E148
Year
2018
Publication Date
2018-09-01
Published Version
ISSN
2227-9717
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PII: pr6090148, Publication Type: Journal Article
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LAPSE:2019.0458
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doi:10.3390/pr6090148
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Apr 8, 2019
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Calvin Tsay
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