Using PyBioNetFit to Leverage Qualitative and Quantitative Data in Biological Model Parameterization and Uncertainty Quantification

TL;DR

This paper demonstrates how PyBioNetFit software can systematically incorporate qualitative and quantitative data into biological model parameterization and uncertainty quantification, improving reproducibility and analysis.

Contribution

It introduces a formalized approach to use qualitative data in model fitting and uncertainty analysis, enhancing reproducibility and insights in systems biology modeling.

Findings

PyBioNetFit enables systematic use of qualitative data in model parameterization.

The approach improves uncertainty quantification in biological models.

Qualitative data integration enhances model reliability and reproducibility.

Abstract

Data generated in studies of cellular regulatory systems are often qualitative. For example, measurements of signaling readouts in the presence and absence of mutations may reveal a rank ordering of responses across conditions but not the precise extents of mutation-induced differences. Qualitative data are often ignored by mathematical modelers or are considered in an ad hoc manner, as in the study of Kocieniewski and Lipniacki (2013) [Phys Biol 10: 035006], which was focused on the roles of MEK isoforms in ERK activation. In this earlier study, model parameter values were tuned manually to obtain consistency with a combination of qualitative and quantitative data. This approach is not reproducible, nor does it provide insights into parametric or prediction uncertainties. Here, starting from the same data and the same ordinary differential equation (ODE) model structure, we generate formalized statements of qualitative observations, making these observations more reusable, and we improve the model parameterization procedure by applying a systematic and automated approach enabled by the software package PyBioNetFit. We also demonstrate uncertainty quantification (UQ), which was absent in the original study. Our results show that PyBioNetFit enables qualitative data to be leveraged, together with quantitative data, in parameterization of systems biology models and facilitates UQ. These capabilities are important for reliable estimation of model parameters and model analyses in studies of cellular regulatory systems and reproducibility.