4 papers · 1 filter
Using PyBioNetFit to Leverage Qualitative and Quantitative Data in Biological Model Parameterization and Uncertainty Quantification
Ely F. Miller, Abhishek Mallela, Jacob Neumann +3
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…
Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit
Jacob Neumann, Yen Ting Lin, Abhishek Mallela +6
Bayesian inference in biological modeling commonly relies on Markov chain Monte Carlo (MCMC) sampling of a multidimensional and non-Gaussian posterior distribution that is not anal…
PyBioNetFit and the Biological Property Specification Language
Eshan D. Mitra, Ryan Suderman, Joshua Colvin +5
In systems biology modeling, important steps include model parameterization, uncertainty quantification, and evaluation of agreement with experimental observations. To help modeler…
A Step-by-Step Guide to Using BioNetFit
William S. Hlavacek, Jennifer Longo, Lewis R. Baker +9
BioNetFit is a software tool designed for solving parameter identification problems that arise in the development of rule-based models. It solves these problems through curve fitti…