4 papers
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…
Daily Forecasting of New Cases for Regional Epidemics of Coronavirus Disease 2019 with Bayesian Uncertainty Quantification
Yen Ting Lin, Jacob Neumann, Ely Miller +7
To increase situational awareness and support evidence-based policy-making, we formulated two types of mathematical models for COVID-19 transmission within a regional population. O…
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…