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Title
A protocol for dynamic model calibration
Authors
Keywords
-
Journal
BRIEFINGS IN BIOINFORMATICS
Volume 23, Issue 1, Pages -
Publisher
Oxford University Press (OUP)
Online
2021-09-08
DOI
10.1093/bib/bbab387
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- (2018) Alejandro F Villaverde et al. BIOINFORMATICS
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- (2016) Mark Bruno et al. JOURNAL OF EXPERIMENTAL BOTANY
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- Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems: Fig. 1.
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- A consensus approach for estimating the predictive accuracy of dynamic models in biology
- (2015) Alejandro F. Villaverde et al. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
- Nonlinear ill-posed problem analysis in model-based parameter estimation and experimental design
- (2015) Diana C. López C. et al. COMPUTERS & CHEMICAL ENGINEERING
- Higher-order Lie symmetries in identifiability and predictability analysis of dynamic models
- (2015) Benjamin Merkt et al. PHYSICAL REVIEW E
- A Novel Protocol for Model Calibration in Biological Wastewater Treatment
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