BioNetFit

BioNetFit performs parameter estimation for rule-based biochemical network models by fitting simulations from BioNetGen and NFsim to experimental data.

Key Features:

• Compatibility: Supports models and simulation output from BioNetGen and NFsim.
• Distributed computing: Uses distributed computing to distribute simulation and optimization tasks across multiple nodes to handle computationally intensive parameter searches.
• Platform versatility: Runs on macOS, Windows/Cygwin, and Linux, and is optimized for Linux clusters using SLURM, Torque/PBS, or SGE job schedulers.
• Implementation: Source code is implemented in Perl.

Scientific Applications:

• Parameter estimation: Optimizes model parameter values to align rule-based model simulations with empirical experimental data.
• Rule-based biochemical network modeling: Enables refinement and quantitative analysis of complex biochemical networks represented in BioNetGen rule-based formalisms.

Methodology:

Optimization of model parameters via fitting procedures to reconcile simulated outputs with empirical data, leveraging distributed computing to explore large parameter spaces.