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From 2013.igem.org

title = "FNR simulator";
//declare the molecules and metabolite
molecule fnr_on, fnr_off, fnr_on_pair;
molecule prom_fnr, prom_fnr_binded;
molecule protein;
metabolite o2;
//declare the size of molecule
size (fnr_on) = 0.1; size (fnr_on_pair) = 0.2; size (fnr_off) = 0.1;
speed (fnr_on) = 0.1; speed (fnr_on_pair) = 0.05; speed (fnr_off) = 0.1;
size (prom_fnr) = 2.0; speed (prom_fnr) = 0.05; size (prom_fnr_binded) = 2.0;
speed (prom_fnr_binded) = 0.05; size (protein) = 0.2; speed (protein) = 0.1;
//syntax of reaction rules
fnr_on + o2 -> fnr_off + o2 [0.7];// probability for this rule take place is 0.7
fnr_off -> fnr_on [0.001];
fnr_on + fnr_on -> fnr_on_pair [0.5];
fnr_on_pair -> fnr_on + fnr_on [0.001];
prom_fnr + fnr_on_pair -> prom_fnr_binded [0.6];
prom_fnr_binded -> prom_fnr + fnr_on_pair [0.03];
prom_fnr_binded -> prom_fnr_binded + protein [0.01];
//Initial concentrations
init (10000, fnr_on);
init (3, prom_fnr);
init (2, o2); //oxy

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