4 papers · 1 filter
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…
Using RuleBuilder to graphically define and visualize BioNetGen-language patterns and reaction rules
Ryan Suderman, G. Matthew Fricke, William S. Hlavacek
RuleBuilder is a tool for drawing graphs that can be represented by the BioNetGen language (BNGL), which is used to formulate mathematical, rule-based models of biochemical systems…
Generalizing Gillespie's direct method to enable network-free simulations
Ryan Suderman, Eshan D. Mitra, Yen Ting Lin +3
Gillespie's direct method for stochastic simulation of chemical kinetics is a staple of computational systems biology research. However, the algorithm requires explicit enumeration…