Optimal Experimental Design for Systems and Synthetic Biology Using AMIGO2

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Abstract / Description of output

Dynamic modeling in systems and synthetic biology is still quite a challenge-the complex nature of the interactions results in nonlinear models, which include unknown parameters (or functions). Ideally, time-series data support the estimation of model unknowns through data fitting. Goodness-of-fit measures would lead to the best model among a set of candidates. However, even when state-of-the-art measuring techniques allow for an unprecedented amount of data, not all data suit dynamic modeling.Model-based optimal experimental design (OED) is intended to improve model predictive capabilities. OED can be used to define the set of experiments that would (a) identify the best model or (b) improve the identifiability of unknown parameters. In this chapter, we present a detailed practical procedure to compute optimal experiments using the AMIGO2 toolbox.

Original languageEnglish
Title of host publicationSynthetic Gene Circuits
Subtitle of host publicationMethods and Protocols
EditorsFilippo Menolascina
Number of pages19
ISBN (Electronic)978-1-0716-1032-9
ISBN (Print)978-1-0716-1031-2, 978-1-0716-1034-3
Publication statusPublished - 7 Jan 2021

Publication series

NameMethods in molecular biology (Clifton, N.J.)
PublisherHumana Press
ISSN (Print)1064-3745

Keywords / Materials (for Non-textual outputs)

  • Biological systems
  • dynamic models
  • Optimal experimental design
  • practical identifiability


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