Generated Code
The following is python code generated by the CellML API from this CellML file. (Back to language selection)
The raw code is available.
# Size of variable arrays:
sizeAlgebraic = 53
sizeStates = 22
sizeConstants = 83
from math import *
from numpy import *
def createLegends():
legend_states = [""] * sizeStates
legend_rates = [""] * sizeStates
legend_algebraic = [""] * sizeAlgebraic
legend_voi = ""
legend_constants = [""] * sizeConstants
legend_voi = "time in component environment (hour)"
legend_constants[0] = "eps in component E (dimensionless)"
legend_constants[1] = "K1 in component A (per_hour)"
legend_constants[2] = "K1a in component A (per_hour)"
legend_constants[3] = "K2 in component A (per_hour)"
legend_constants[4] = "K2a in component A (per_hour)"
legend_constants[5] = "K2aa in component A (per_hour)"
legend_constants[6] = "K3 in component A (per_hour)"
legend_constants[7] = "K3a in component A (per_hour)"
legend_constants[8] = "K4 in component A (per_hour)"
legend_constants[9] = "J1 in component A (dimensionless)"
legend_constants[10] = "J3 in component A (dimensionless)"
legend_constants[11] = "J4 in component A (dimensionless)"
legend_algebraic[1] = "v_20 in component A (per_hour)"
legend_algebraic[21] = "v_21 in component A (per_hour)"
legend_algebraic[0] = "v_42 in component A (per_hour)"
legend_algebraic[22] = "v_19 in component A (per_hour)"
legend_constants[12] = "GA in component A (dimensionless)"
legend_constants[13] = "GB in component A (dimensionless)"
legend_constants[14] = "GE in component A (dimensionless)"
legend_algebraic[12] = "V_2 in component A (per_hour)"
legend_algebraic[13] = "V_4 in component A (per_hour)"
legend_states[0] = "Cdh1 in component A (dimensionless)"
legend_constants[15] = "Cdc20 in component D (dimensionless)"
legend_states[1] = "CYCA in component D (dimensionless)"
legend_states[2] = "CYCB in component A (dimensionless)"
legend_states[3] = "CYCE in component D (dimensionless)"
legend_constants[16] = "k15 in component B (per_hour)"
legend_constants[17] = "k16 in component B (per_hour)"
legend_constants[18] = "k17 in component B (per_hour)"
legend_constants[19] = "k17a in component B (per_hour)"
legend_constants[20] = "k18 in component B (per_hour)"
legend_constants[21] = "K9 in component B (per_hour)"
legend_constants[22] = "J17 in component B (dimensionless)"
legend_constants[23] = "J15 in component B (dimensionless)"
legend_algebraic[14] = "v_1 in component B (per_hour)"
legend_algebraic[15] = "v_2 in component B (per_hour)"
legend_algebraic[2] = "v_34 in component B (per_hour)"
legend_algebraic[5] = "v_39 in component B (per_hour)"
legend_algebraic[3] = "v_41 in component B (per_hour)"
legend_states[4] = "DRG in component B (dimensionless)"
legend_states[5] = "ERG in component B (dimensionless)"
legend_constants[24] = "K19 in component C (per_hour)"
legend_constants[25] = "K19a in component C (per_hour)"
legend_constants[26] = "K20 in component C (per_hour)"
legend_constants[27] = "K21 in component C (dimensionless)"
legend_constants[28] = "K22 in component C (per_hour)"
legend_constants[29] = "K23a in component C (per_hour)"
legend_constants[30] = "K23 in component C (per_hour)"
legend_constants[31] = "K26 in component C (per_hour)"
legend_constants[32] = "K26R in component C (per_hour)"
legend_algebraic[16] = "v_29 in component C (per_hour)"
legend_algebraic[23] = "v_30 in component C (per_hour)"
legend_algebraic[25] = "v_43 in component C (per_hour)"
legend_algebraic[27] = "v_44 in component C (per_hour)"
legend_algebraic[29] = "v_45 in component C (per_hour)"
legend_algebraic[31] = "v_46 in component C (per_hour)"
legend_algebraic[33] = "v_47 in component C (per_hour)"
legend_algebraic[35] = "v_48 in component C (per_hour)"
legend_algebraic[37] = "v_49 in component C (per_hour)"
legend_algebraic[40] = "v_50 in component C (per_hour)"
legend_algebraic[42] = "v_51 in component C (per_hour)"
legend_algebraic[44] = "v_52 in component C (per_hour)"
legend_constants[33] = "LA in component C (dimensionless)"
legend_constants[34] = "LB in component C (dimensionless)"
legend_constants[35] = "LD in component C (dimensionless)"
legend_constants[36] = "LE in component C (dimensionless)"
legend_constants[37] = "FE in component C (dimensionless)"
legend_constants[38] = "FB in component C (dimensionless)"
legend_states[6] = "Rb in component C (dimensionless)"
legend_states[7] = "PPRb in component C (dimensionless)"
legend_states[8] = "E2F in component C (dimensionless)"
legend_states[9] = "PE2F in component C (dimensionless)"
legend_states[10] = "E2FRb in component C (dimensionless)"
legend_states[11] = "PE2FRb in component C (dimensionless)"
legend_algebraic[4] = "PP1A in component C (dimensionless)"
legend_constants[39] = "PP1T in component C (dimensionless)"
legend_constants[40] = "CYCDT in component C (dimensionless)"
legend_constants[41] = "K5 in component D (per_hour)"
legend_constants[42] = "K6a in component D (per_hour)"
legend_constants[43] = "K6 in component D (per_hour)"
legend_constants[44] = "K7a in component D (per_hour)"
legend_constants[45] = "K7 in component D (per_hour)"
legend_constants[46] = "K8a in component D (per_hour)"
legend_constants[47] = "K8 in component D (per_hour)"
legend_constants[48] = "K10 in component D (per_hour)"
legend_constants[49] = "k24 in component D (per_hour)"
legend_constants[50] = "k24r in component D (per_hour)"
legend_constants[51] = "K25 in component D (per_hour)"
legend_constants[52] = "K25R in component D (per_hour)"
legend_constants[53] = "K29 in component D (per_hour)"
legend_constants[54] = "K30 in component D (per_hour)"
legend_constants[55] = "J8 in component D (dimensionless)"
legend_algebraic[26] = "v_3 in component D (per_hour)"
legend_algebraic[28] = "v_4 in component D (per_hour)"
legend_algebraic[30] = "v_5 in component D (per_hour)"
legend_algebraic[32] = "v_6 in component D (per_hour)"
legend_algebraic[34] = "v_7 in component D (per_hour)"
legend_algebraic[36] = "v_8 in component D (per_hour)"
legend_algebraic[38] = "v_9 in component D (per_hour)"
legend_algebraic[41] = "v_10 in component D (per_hour)"
legend_algebraic[43] = "v_11 in component D (per_hour)"
legend_algebraic[45] = "v_12 in component D (per_hour)"
legend_algebraic[46] = "v_13 in component D (per_hour)"
legend_algebraic[49] = "v_14 in component D (per_hour)"
legend_algebraic[48] = "v_15 in component D (per_hour)"
legend_algebraic[51] = "v_16 in component D (per_hour)"
legend_algebraic[39] = "v_17 in component D (per_hour)"
legend_algebraic[47] = "v_18 in component D (per_hour)"
legend_algebraic[50] = "v_36 in component D (per_hour)"
legend_algebraic[52] = "v_38 in component D (per_hour)"
legend_constants[79] = "v_40 in component D (per_hour)"
legend_constants[56] = "HA in component D (dimensionless)"
legend_constants[57] = "HB in component D (dimensionless)"
legend_constants[58] = "HE in component D (dimensionless)"
legend_constants[59] = "YE in component D (dimensionless)"
legend_constants[60] = "YB in component D (dimensionless)"
legend_states[12] = "p27 in component D (dimensionless)"
legend_algebraic[17] = "V_6 in component D (per_hour)"
legend_algebraic[24] = "V_8 in component D (per_hour)"
legend_states[13] = "MASS in component E (dimensionless)"
legend_states[14] = "CA in component D (dimensionless)"
legend_states[15] = "CD in component D (dimensionless)"
legend_states[16] = "CE in component D (dimensionless)"
legend_states[17] = "CYCD in component D (dimensionless)"
legend_constants[61] = "CYCET in component D (dimensionless)"
legend_constants[62] = "K27 in component E (per_hour)"
legend_constants[63] = "K28 in component E (per_hour)"
legend_algebraic[6] = "v_31 in component E (per_hour)"
legend_algebraic[18] = "v_32 in component E (per_hour)"
legend_algebraic[7] = "v_33 in component E (per_hour)"
legend_constants[64] = "r31switch in component E (dimensionless)"
legend_constants[65] = "MU in component E (per_hour)"
legend_states[18] = "GM in component E (dimensionless)"
legend_constants[66] = "K11a in component F (per_hour)"
legend_constants[67] = "K11 in component F (per_hour)"
legend_constants[68] = "K12 in component F (per_hour)"
legend_constants[69] = "K13 in component F (per_hour)"
legend_constants[70] = "K14 in component F (per_hour)"
legend_constants[71] = "K31 in component F (per_hour)"
legend_constants[72] = "K32 in component F (per_hour)"
legend_constants[73] = "K33 in component F (per_hour)"
legend_constants[74] = "K34 in component F (per_hour)"
legend_constants[75] = "J13 in component F (dimensionless)"
legend_constants[76] = "J14 in component F (dimensionless)"
legend_constants[77] = "J31 in component F (dimensionless)"
legend_constants[78] = "J32 in component F (dimensionless)"
legend_algebraic[8] = "v_22 in component F (per_hour)"
legend_algebraic[9] = "v_23 in component F (per_hour)"
legend_algebraic[19] = "v_24 in component F (per_hour)"
legend_algebraic[11] = "v_25 in component F (per_hour)"
legend_algebraic[10] = "v_26 in component F (per_hour)"
legend_constants[80] = "v_27 in component F (per_hour)"
legend_constants[81] = "v_28 in component F (per_hour)"
legend_algebraic[20] = "v_35 in component F (per_hour)"
legend_constants[82] = "v_37 in component F (per_hour)"
legend_states[19] = "IEP in component F (dimensionless)"
legend_states[20] = "PPX in component F (dimensionless)"
legend_states[21] = "Cdc20T in component F (dimensionless)"
legend_rates[0] = "d/dt Cdh1 in component A (dimensionless)"
legend_rates[2] = "d/dt CYCB in component A (dimensionless)"
legend_rates[4] = "d/dt DRG in component B (dimensionless)"
legend_rates[5] = "d/dt ERG in component B (dimensionless)"
legend_rates[7] = "d/dt PPRb in component C (dimensionless)"
legend_rates[8] = "d/dt E2F in component C (dimensionless)"
legend_rates[9] = "d/dt PE2F in component C (dimensionless)"
legend_rates[6] = "d/dt Rb in component C (dimensionless)"
legend_rates[10] = "d/dt E2FRb in component C (dimensionless)"
legend_rates[11] = "d/dt PE2FRb in component C (dimensionless)"
legend_rates[14] = "d/dt CA in component D (dimensionless)"
legend_rates[15] = "d/dt CD in component D (dimensionless)"
legend_rates[16] = "d/dt CE in component D (dimensionless)"
legend_rates[1] = "d/dt CYCA in component D (dimensionless)"
legend_rates[17] = "d/dt CYCD in component D (dimensionless)"
legend_rates[3] = "d/dt CYCE in component D (dimensionless)"
legend_rates[12] = "d/dt p27 in component D (dimensionless)"
legend_rates[18] = "d/dt GM in component E (dimensionless)"
legend_rates[13] = "d/dt MASS in component E (dimensionless)"
legend_rates[21] = "d/dt Cdc20T in component F (dimensionless)"
legend_rates[19] = "d/dt IEP in component F (dimensionless)"
legend_rates[20] = "d/dt PPX in component F (dimensionless)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 1
constants[1] = 0.6
constants[2] = 0.1
constants[3] = 20
constants[4] = 0.05
constants[5] = 1
constants[6] = 140
constants[7] = 7.5
constants[8] = 40
constants[9] = 0.1
constants[10] = 0.01
constants[11] = 0.04
constants[12] = 0.3
constants[13] = 1
constants[14] = 0
states[0] = 0.000653278
constants[15] = 0.00220177
states[1] = 1.4094
states[2] = 2.72898
states[3] = 0.0229112
constants[16] = 0.25
constants[17] = 0.25
constants[18] = 10
constants[19] = 0.35
constants[20] = 10
constants[21] = 2.5
constants[22] = 0.3
constants[23] = 0.1
states[4] = 0.900533
states[5] = 0.0121809
constants[24] = 20
constants[25] = 0
constants[26] = 10
constants[27] = 1
constants[28] = 1
constants[29] = 0.005
constants[30] = 1
constants[31] = 10000
constants[32] = 200
constants[33] = 3
constants[34] = 5
constants[35] = 3.3
constants[36] = 5
constants[37] = 25
constants[38] = 2
states[6] = 0.000190871
states[7] = 9.97574
states[8] = 0.989986
states[9] = 3.98594
states[10] = 0.00478911
states[11] = 0.0192822
constants[39] = 1
constants[40] = 0.010976
constants[41] = 20
constants[42] = 10
constants[43] = 100
constants[44] = 0
constants[45] = 0.6
constants[46] = 0.1
constants[47] = 2
constants[48] = 5
constants[49] = 1000
constants[50] = 10
constants[51] = 1000
constants[52] = 10
constants[53] = 0.05
constants[54] = 20
constants[55] = 0.1
constants[56] = 0.5
constants[57] = 1
constants[58] = 0.5
constants[59] = 1
constants[60] = 0.05
states[12] = 0.00922806
states[13] = 1.68776
states[14] = 0.0356927
states[15] = 0.010976
states[16] = 0.000542587
states[17] = 0.43929
constants[61] = 0.000542587
constants[62] = 0.2
constants[63] = 0.2
constants[64] = 1
constants[65] = 0.061
states[18] = 1.35565
constants[66] = 0
constants[67] = 1.5
constants[68] = 1.5
constants[69] = 5
constants[70] = 2.5
constants[71] = 0.7
constants[72] = 1.8
constants[73] = 0.05
constants[74] = 0.05
constants[75] = 0.005
constants[76] = 0.005
constants[77] = 0.01
constants[78] = 0.01
states[19] = 0.154655
states[20] = 1
states[21] = 2.36733
constants[79] = constants[0]*constants[41]
constants[80] = (constants[70]*constants[15])/(constants[76]+constants[15])
constants[81] = constants[68]*constants[15]
constants[82] = constants[0]*constants[73]
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[7] = constants[0]*constants[65]*states[18]
rates[13] = algebraic[7]
algebraic[8] = constants[74]*states[20]
rates[20] = constants[82]-algebraic[8]
algebraic[15] = constants[20]*states[4]
algebraic[3] = constants[0]*((constants[18]*(power(states[4]/constants[22], 2.00000)))/(power(states[4]/constants[22], 2.00000)+1.00000)+constants[19]*states[5])
rates[4] = algebraic[3]-algebraic[15]
algebraic[14] = constants[17]*states[5]
algebraic[2] = (constants[0]*constants[16])/(power(states[4]/constants[23], 2.00000)+1.00000)
rates[5] = algebraic[2]-algebraic[14]
algebraic[6] = constants[62]*states[13]*constants[64]
algebraic[18] = constants[63]*states[18]
rates[18] = algebraic[6]-algebraic[18]
algebraic[11] = constants[68]*states[21]
algebraic[20] = constants[0]*constants[66]+constants[67]*states[2]
rates[21] = algebraic[20]-algebraic[11]
algebraic[9] = (constants[71]*states[2]*(1.00000-states[19]))/((constants[77]-states[19])+1.00000)
algebraic[19] = (constants[72]*states[20]*states[19])/(constants[78]+states[19])
rates[19] = algebraic[9]-algebraic[19]
algebraic[1] = ((constants[7]+constants[6]*constants[15])*(1.00000-states[0]))/((constants[10]-states[0])+1.00000)
algebraic[13] = constants[8]*(constants[12]*states[1]+constants[13]*states[2]+constants[14]*states[3])
algebraic[21] = (algebraic[13]*states[0])/(constants[11]+states[0])
rates[0] = algebraic[1]-algebraic[21]
algebraic[0] = constants[0]*((constants[1]*(power(states[2]/constants[9], 2.00000)))/(power(states[2]/constants[9], 2.00000)+1.00000)+constants[2])
algebraic[12] = constants[5]*constants[15]+constants[4]*(1.00000-states[0])+constants[3]*states[0]
algebraic[22] = algebraic[12]*states[2]
rates[2] = algebraic[0]-algebraic[22]
algebraic[16] = states[10]*constants[26]*(constants[40]*constants[35]+constants[33]*states[1]+constants[34]*states[2]+constants[36]*states[3])
algebraic[23] = states[11]*constants[26]*(constants[40]*constants[35]+constants[33]*states[1]+constants[34]*states[2]+constants[36]*states[3])
algebraic[25] = states[6]*constants[26]*(constants[40]*constants[35]+constants[33]*states[1]+constants[34]*states[2]+constants[36]*states[3])
algebraic[4] = constants[39]/(constants[27]*constants[37]*(states[1]+states[3]+constants[38]*states[2])+1.00000)
algebraic[27] = states[7]*(constants[25]*(constants[39]-algebraic[4])+constants[24]*algebraic[4])
rates[7] = (algebraic[16]+algebraic[23]+algebraic[25])-algebraic[27]
algebraic[29] = states[10]*constants[32]
algebraic[31] = states[8]*(constants[29]+constants[30]*(states[1]+states[2]))
algebraic[33] = states[9]*constants[28]
algebraic[35] = states[8]*states[6]*constants[31]
rates[8] = ((algebraic[16]+algebraic[29]+algebraic[33])-algebraic[31])-algebraic[35]
algebraic[26] = constants[48]*states[15]
algebraic[34] = constants[49]*states[12]*states[17]
algebraic[36] = constants[50]*states[15]
algebraic[17] = constants[42]+constants[43]*(constants[56]*states[1]+constants[57]*states[2]+constants[58]*states[3])
algebraic[39] = algebraic[17]*states[15]
rates[15] = ((algebraic[34]-algebraic[36])-algebraic[39])-algebraic[26]
algebraic[5] = constants[0]*constants[21]*states[4]
algebraic[28] = constants[48]*states[17]
rates[17] = ((algebraic[5]+algebraic[39]+algebraic[36])-algebraic[34])-algebraic[28]
algebraic[37] = states[11]*constants[32]
algebraic[40] = states[6]*states[9]*constants[31]
rates[9] = ((algebraic[23]+algebraic[37]+algebraic[31])-algebraic[33])-algebraic[40]
rates[6] = (((algebraic[27]+algebraic[29]+algebraic[37])-algebraic[35])-algebraic[40])-algebraic[25]
algebraic[42] = states[11]*constants[28]
algebraic[44] = states[10]*(constants[29]+constants[30]*(states[1]+states[2]))
rates[10] = (((algebraic[42]+algebraic[35])-algebraic[44])-algebraic[16])-algebraic[29]
rates[11] = (((algebraic[44]+algebraic[40])-algebraic[42])-algebraic[23])-algebraic[37]
algebraic[32] = constants[51]*states[12]*states[1]
algebraic[41] = constants[54]*constants[15]*states[14]
algebraic[45] = constants[52]*states[14]
algebraic[47] = algebraic[17]*states[14]
rates[14] = ((algebraic[32]-algebraic[45])-algebraic[47])-algebraic[41]
algebraic[38] = constants[54]*constants[15]*states[1]
algebraic[50] = constants[0]*constants[53]*states[8]*states[13]
rates[1] = ((algebraic[50]-algebraic[38])-algebraic[32])+algebraic[45]+algebraic[47]
algebraic[30] = constants[51]*states[12]*states[3]
algebraic[43] = constants[52]*states[16]
algebraic[24] = (constants[47]*(constants[59]*(states[1]+states[3])+constants[60]*states[2]))/(constants[61]+constants[55])+constants[46]
algebraic[46] = algebraic[24]*states[16]
algebraic[48] = algebraic[17]*states[12]
rates[12] = (((((constants[79]+algebraic[26]+algebraic[36])-algebraic[48])-algebraic[30])-algebraic[32])-algebraic[34])+algebraic[43]+algebraic[45]+algebraic[46]+algebraic[41]
algebraic[51] = algebraic[17]*states[16]
rates[16] = ((algebraic[30]-algebraic[43])-algebraic[46])-algebraic[51]
algebraic[49] = algebraic[24]*states[3]
algebraic[52] = constants[0]*(constants[44]+constants[45]*states[8])
rates[3] = ((algebraic[52]-algebraic[49])-algebraic[30])+algebraic[43]+algebraic[51]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[7] = constants[0]*constants[65]*states[18]
algebraic[8] = constants[74]*states[20]
algebraic[15] = constants[20]*states[4]
algebraic[3] = constants[0]*((constants[18]*(power(states[4]/constants[22], 2.00000)))/(power(states[4]/constants[22], 2.00000)+1.00000)+constants[19]*states[5])
algebraic[14] = constants[17]*states[5]
algebraic[2] = (constants[0]*constants[16])/(power(states[4]/constants[23], 2.00000)+1.00000)
algebraic[6] = constants[62]*states[13]*constants[64]
algebraic[18] = constants[63]*states[18]
algebraic[11] = constants[68]*states[21]
algebraic[20] = constants[0]*constants[66]+constants[67]*states[2]
algebraic[9] = (constants[71]*states[2]*(1.00000-states[19]))/((constants[77]-states[19])+1.00000)
algebraic[19] = (constants[72]*states[20]*states[19])/(constants[78]+states[19])
algebraic[1] = ((constants[7]+constants[6]*constants[15])*(1.00000-states[0]))/((constants[10]-states[0])+1.00000)
algebraic[13] = constants[8]*(constants[12]*states[1]+constants[13]*states[2]+constants[14]*states[3])
algebraic[21] = (algebraic[13]*states[0])/(constants[11]+states[0])
algebraic[0] = constants[0]*((constants[1]*(power(states[2]/constants[9], 2.00000)))/(power(states[2]/constants[9], 2.00000)+1.00000)+constants[2])
algebraic[12] = constants[5]*constants[15]+constants[4]*(1.00000-states[0])+constants[3]*states[0]
algebraic[22] = algebraic[12]*states[2]
algebraic[16] = states[10]*constants[26]*(constants[40]*constants[35]+constants[33]*states[1]+constants[34]*states[2]+constants[36]*states[3])
algebraic[23] = states[11]*constants[26]*(constants[40]*constants[35]+constants[33]*states[1]+constants[34]*states[2]+constants[36]*states[3])
algebraic[25] = states[6]*constants[26]*(constants[40]*constants[35]+constants[33]*states[1]+constants[34]*states[2]+constants[36]*states[3])
algebraic[4] = constants[39]/(constants[27]*constants[37]*(states[1]+states[3]+constants[38]*states[2])+1.00000)
algebraic[27] = states[7]*(constants[25]*(constants[39]-algebraic[4])+constants[24]*algebraic[4])
algebraic[29] = states[10]*constants[32]
algebraic[31] = states[8]*(constants[29]+constants[30]*(states[1]+states[2]))
algebraic[33] = states[9]*constants[28]
algebraic[35] = states[8]*states[6]*constants[31]
algebraic[26] = constants[48]*states[15]
algebraic[34] = constants[49]*states[12]*states[17]
algebraic[36] = constants[50]*states[15]
algebraic[17] = constants[42]+constants[43]*(constants[56]*states[1]+constants[57]*states[2]+constants[58]*states[3])
algebraic[39] = algebraic[17]*states[15]
algebraic[5] = constants[0]*constants[21]*states[4]
algebraic[28] = constants[48]*states[17]
algebraic[37] = states[11]*constants[32]
algebraic[40] = states[6]*states[9]*constants[31]
algebraic[42] = states[11]*constants[28]
algebraic[44] = states[10]*(constants[29]+constants[30]*(states[1]+states[2]))
algebraic[32] = constants[51]*states[12]*states[1]
algebraic[41] = constants[54]*constants[15]*states[14]
algebraic[45] = constants[52]*states[14]
algebraic[47] = algebraic[17]*states[14]
algebraic[38] = constants[54]*constants[15]*states[1]
algebraic[50] = constants[0]*constants[53]*states[8]*states[13]
algebraic[30] = constants[51]*states[12]*states[3]
algebraic[43] = constants[52]*states[16]
algebraic[24] = (constants[47]*(constants[59]*(states[1]+states[3])+constants[60]*states[2]))/(constants[61]+constants[55])+constants[46]
algebraic[46] = algebraic[24]*states[16]
algebraic[48] = algebraic[17]*states[12]
algebraic[51] = algebraic[17]*states[16]
algebraic[49] = algebraic[24]*states[3]
algebraic[52] = constants[0]*(constants[44]+constants[45]*states[8])
algebraic[10] = (constants[69]*states[19]*(states[21]-constants[15]))/((constants[75]-constants[15])+states[21])
return algebraic
def solve_model():
"""Solve model with ODE solver"""
from scipy.integrate import ode
# Initialise constants and state variables
(init_states, constants) = initConsts()
# Set timespan to solve over
voi = linspace(0, 10, 500)
# Construct ODE object to solve
r = ode(computeRates)
r.set_integrator('vode', method='bdf', atol=1e-06, rtol=1e-06, max_step=1)
r.set_initial_value(init_states, voi[0])
r.set_f_params(constants)
# Solve model
states = array([[0.0] * len(voi)] * sizeStates)
states[:,0] = init_states
for (i,t) in enumerate(voi[1:]):
if r.successful():
r.integrate(t)
states[:,i+1] = r.y
else:
break
# Compute algebraic variables
algebraic = computeAlgebraic(constants, states, voi)
return (voi, states, algebraic)
def plot_model(voi, states, algebraic):
"""Plot variables against variable of integration"""
import pylab
(legend_states, legend_algebraic, legend_voi, legend_constants) = createLegends()
pylab.figure(1)
pylab.plot(voi,vstack((states,algebraic)).T)
pylab.xlabel(legend_voi)
pylab.legend(legend_states + legend_algebraic, loc='best')
pylab.show()
if __name__ == "__main__":
(voi, states, algebraic) = solve_model()
plot_model(voi, states, algebraic)