Discrete stochastic simulation of cell signaling: comparison of computational tools

@article{Manninen2006DiscreteSS,
  title={Discrete stochastic simulation of cell signaling: comparison of computational tools},
  author={Tiina Manninen and E. Makiraatikka and Antti Ylipaa and Antti Pettinen and Kalle Leinonen and M Linne},
  journal={2006 International Conference of the IEEE Engineering in Medicine and Biology Society},
  year={2006},
  pages={2013-2016}
}
Several stochastic simulation tools have been developed recently for cell signaling. A comparative evaluation of the stochastic simulation tools is needed to highlight the current state of the development. In our study, we have chosen to evaluate three stochastic simulation tools: Dizzy, Systems Biology Toolbox, and Copasi, using our own MATLABreg implementation as a benchmark. The Gillespie stochastic simulation algorithm is used in all tests. With all the tools, we are able to simulate… CONTINUE READING