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To cite Alchemist in publications, please use:

Pianini, D., Montagna, S., & Viroli, M. (2013). Chemical-oriented simulation of computational systems with ALCHEMIST.
Journal of Simulation, 7(3), 202–215. https://doi.org/10.1057/jos.2012.27

A BibTeX entry for LaTeX users is

@article{Pianini2013,
  doi = {10.1057/jos.2012.27},
  url = {https://doi.org/10.1057/jos.2012.27},
  year = {2013},
  month = aug,
  publisher = {Informa {UK} Limited},
  volume = {7},
  number = {3},
  pages = {202--215},
  author = {D Pianini and S Montagna and M Viroli},
  title = {Chemical-oriented simulation of computational systems with {ALCHEMIST}},
  journal = {Journal of Simulation}
}