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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