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Using both qualitative and quantitative data in parameter identification for systems biology models
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Journal Article
Using both qualitative and quantitative data in parameter identification for systems biology models
2018
Overview
In systems biology, qualitative data are often generated, but rarely used to parameterize models. We demonstrate an approach in which qualitative and quantitative data can be combined for parameter identification. In this approach, qualitative data are converted into inequality constraints imposed on the outputs of the model. These inequalities are used along with quantitative data points to construct a single scalar objective function that accounts for both datasets. To illustrate the approach, we estimate parameters for a simple model describing Raf activation. We then apply the technique to a more elaborate model characterizing cell cycle regulation in yeast. We incorporate both quantitative time courses (561 data points) and qualitative phenotypes of 119 mutant yeast strains (1647 inequalities) to perform automated identification of 153 model parameters. We quantify parameter uncertainty using a profile likelihood approach. Our results indicate the value of combining qualitative and quantitative data to parameterize systems biology models.
Much of the data generated in biology is qualitative, but exploiting such data to inform models of biological systems remains a challenge. Here, the authors demonstrate an approach that allows use of both quantitative and qualitative data for parameterising dynamical models.
Publisher
Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
Subject
/ Animals
/ Biology
/ Biomedical Research - methods
/ Biomedical Research - statistics & numerical data
/ Humanities and Social Sciences
/ Humans
/ Kinetics
/ Mutation
/ raf Kinases - antagonists & inhibitors
/ Saccharomycetales - genetics
/ Saccharomycetales - metabolism
/ Science
/ Systems Biology - statistics & numerical data
/ Yeast
