// Dizzy model generated by the BioPEPA Workbench #model "Neurospora_CIRCADIAN_CLOCK003"; a1 = 8.3450; a2 = 3.7925; a3 = 0.3154; a4 = 0.6787; a5 = 10.0718; a6 = 6.6644; a7 = 2.4695; b1 = 4.1472; b2 = 0.1560; b3 = 0.7149; b4 = 2.9415; b5 = 4.1075; b7 = 3.5676; b8 = 0.5805; b9 = 7.0233; b10 = 0.8218; d1 = 7.4608; d2 = 0.4405; d3 = 2.1710; d4 = 3.0883; d5 = 23.3120; f1 = 0.1962; f2 = 0.1317; gamma1 = 0.0422; gamma2 = 0.0244; r1 = 5.1759; r2 = 5.0326; n = 1.0168; m = 2.8134; k = 1.4135; g = 1.2730; h = 3.6978; b6 = 0.4715; amp = 1; period = 24; tdawn = 6; tdusk = 18; s= 1000;//scaling factor MF = 0.2053*s; PF = 1.2210*s; E1F = 0.7839*s; E2F = 1.2629*s; MW = 0.2640*s; PW = 5.6253*s; E1W = 16.6588*s; E2W = 14.1157*s; PWL = 0.0000*s; res = 1; LD = [amp*theta( ((time - period*floor(time/period)) - tdawn)*(tdusk - (time - period*floor(time/period))) )]; PW_tot = [PW + PWL + E1W + E2W]; PF_tot = [PF + E1F + E2F]; PW_ = [PW_tot/s]; PF_ = [PF_tot/s]; MW_ = [MW/s]; MF_ = [MF/s]; "transcription_MF_1", -> MF, [(s*a1*PWL^n)/((1+(PF/(s*b1))^g)*(PWL^n + (s*b2)^n))] ; "transcription_MF_2", -> MF, [(s*a2*PW^m)/((1+(PF/(s*b3))^h)*(PW^m + (s*b4)^m))] ; "degradation_MF", MF -> , [s*d1*(MF/(MF + s*b5))] ; "translation_E1F", -> E1F, [a3*MF] ; "transformation_E1F_E2F", E1F -> E2F, [f1*E1F] ; "degradation_E1F", E1F -> , [gamma1*E1F] ; "degradation_E2F", E2F -> , [gamma1*E2F] ; "transformation_E2F_PF", E2F -> PF, [f1*E2F] ; "degradation_PF", PF -> , [s*d2*(PF/(PF + s*b6))] ; "transcription_MW_1", -> MW, [s*a4] ; "transcription_MW_2", -> MW, [(s*a5*PWL^k)/(PWL^k + (s*b7)^k)] ; "degradation_MW", MW -> , [s*d3*(MW/(MW + s*b8))] ; "translation_E1W", -> E1W, [a6*MW] ; "translation_E1W_2", -> E1W, [(a7/s)*PF*MW] ; "transformation_E1W_E2W", E1W -> E2W, [f2*E1W] ; "degradation_E1W", E1W -> , [gamma2*E1W] ; "degradation_E2W", E2W -> , [gamma2*E2W] ; "transformation_E2W_PW", E2W -> PW, [f2*E2W] ; "transformation", PW -> PWL, [amp*theta( ((time - period*floor(time/period)) - tdawn)*(tdusk - (time - period*floor(time/period))) )*r1*PW] ; "transformation_inverse", PWL -> PW, [r2*PWL] ; "degradation_PW", PW -> , [s*d4*(PW/(PW + s*b9))] ; "degradation_PWL", PWL -> , [s*d5*(PWL/(PWL + s*b10))] ;