BioNetFit

BioNetFit is a general-purpose fitting program for rule-based models written in the BioNetGen language.

Features

• BioNetFit implements a genetic algorithm for optimization
• BioNetFit can be used on a stand-alone computer or a Linux-based cluster
• BioNetFit is compatible with the various simulation capabilities provided by BioNetGen (generate-first deterministic, stochastic and hybrid methods and network-free stochastic methods) can be used with BioNetFit.
• BioNetFit can perform a global fit, meaning that it can consider multiple datasets in the course of a fitting run. Preprocessing of data (for example, normalization of the average of the measurement values in each dataset) is advised when considering multiple datasets.
• BioNetFit can consider steady-state dose-response data and/or time-series data.
• BioNetFit supports bootstrapping to characterize parameter confidence intervals (not fully tested, use at your own peril)
  • the parameter bootstrap_chi is the maximum objective function value (numeric) required for accepting a particular bootstrapped fitting run
  • the parameter bootstrap takes an integer defining the number of bootstrapped fitting runs to perform

Support

A user manual is present in the repository

Additional support is generally available by contacting the BioNetGen developers