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The Tenth q-bio Summer School - Albuquerque: Computer Lab 1

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Introduction to biochemical modeling with BioNetGen

James R. Faeder, University of Pittsburgh School of Medicine

In this tutorial participant will learn how to construct, simulate, and analyze detailed models of biochemical systems using RuleBender, which provides a unified interface to the popular rule-based modeling software BioNetGen. Participants will learn the structure of a model input file, and how to run simulations using a variety of simulation engines, including ODE’s, SSA, and network-free stochastic simulation. Participants will work with a range of models that cover commonly-modeled features of signaling networks.

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