# Efficient modeling, simulation and coarse-graining of biological complexity with NFsim

@article{Sneddon2011EfficientMS, title={Efficient modeling, simulation and coarse-graining of biological complexity with NFsim}, author={Michael W. Sneddon and James R. Faeder and Thierry Emonet}, journal={Nature Methods}, year={2011}, volume={8}, pages={177-183} }

Managing the overwhelming numbers of molecular states and interactions is a fundamental obstacle to building predictive models of biological systems. Here we introduce the Network-Free Stochastic Simulator (NFsim), a general-purpose modeling platform that overcomes the combinatorial nature of molecular interactions. Unlike standard simulators that represent molecular species as variables in equations, NFsim uses a biologically intuitive representation: objects with binding and modification…

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