“…While this paper has shown that the Beacon Calculus can easily produce flexible and concise models of biological systems from the current literature, it is not appropriate for every task. Section S2 compares the Beacon Calculus with the stochastic π-calculus [15,16,18], Kappa [47][48][49], Bio-PEPA [9], BioNetGen [44,45], PySB [46], ML-Rules [50,51], and Simmune [52,53]. For each of these tools, examples are described where they may be more appropriate than the Beaocn Calculus.…”