createODEs.py

import numpy as np
import sys
# from RunPrep import *
import csv

from numba import jit, njit

from scipy.integrate import odeint



# NOTE - this file is just used for debugging the ODEs, and is not actually called by the model (which calls nc_createODEs.py)

# @jit(nopython=True)
def createODEs(x,t,data0,data1,data2,data3,data4,data5,data6):

    # returns [ydot,flag,newdata,v]

    # data = RunPrep()[0]



    # # unpacking
    # kS=data.kS;
    # VvPARCDL=data.VvPARCDL;
    # VxPARCDL=data.VxPARCDL;
    # S_PARCDL=data.S_PARCDL;
    # mExp_nM=data.mExp_nM;
    # mMod=data.mMod;
    # flagE=data.flagE;





    # NOTE
    kS=data0;
    VvPARCDL=data1;
    VxPARCDL=data2;
    S_PARCDL=data3;
    mExp_nM=data4;
    mMod=data5;
    flagE=data6;


    # k
    a=0;
    u=1;Rt=kS[a:a+u];a=a+u;
    u=1;EIF4Efree=kS[a:a+u];a=a+u;
    u=1;Vc=kS[a:a+u];a=a+u;
    u=1;Ve=kS[a:a+u];a=a+u;
    u=1;Vm=kS[a:a+u];a=a+u;
    u=1;Vn=kS[a:a+u];a=a+u;
    u=1;kT1=kS[a:a+u];a=a+u;
    u=1;kT2=kS[a:a+u];a=a+u;
    u=1;kT3=kS[a:a+u];a=a+u;
    u=1;kT4=kS[a:a+u];a=a+u;
    u=1;k50E=kS[a:a+u];a=a+u;
    u=1;kbR0=kS[a:a+u];a=a+u;
    u=1;kbRi=kS[a:a+u];a=a+u;
    u=1;kdR0=kS[a:a+u];a=a+u;
    u=1;nR=kS[a:a+u];a=a+u;
    u=1;k50R=kS[a:a+u];a=a+u;
    u=141;kTL=kS[a:a+u];a=a+u;
    u=141;kTLd=kS[a:a+u];a=a+u;
    u=102;kTLCd=kS[a:a+u];a=a+u;
    u=59;kD=kS[a:a+u];a=a+u;
    u=173;kC=kS[a:a+u];a=a+u;


    u=87;kA=kS[a:a+u];a=a+u;



    u=158;kR=kS[a:a+u];a=a+u;
    u=190;kP=kS[a:a+u];a=a+u;
    u=29;kRP1=kS[a:a+u];a=a+u;
    u=29;kRP2=kS[a:a+u];a=a+u;
    u=29;kRP3=kS[a:a+u];a=a+u;
    u=29;kRP4=kS[a:a+u];a=a+u;
    u=29;kRP5=kS[a:a+u];a=a+u;
    u=29;kRP6=kS[a:a+u];a=a+u;
    u=29;kRP7=kS[a:a+u];a=a+u;
    u=29;kRP8=kS[a:a+u];a=a+u;
    u=29;kRP9=kS[a:a+u];a=a+u;
    u=29;kRP10=kS[a:a+u];a=a+u;
    u=29;kRP11=kS[a:a+u];a=a+u;
    u=29;kRP12=kS[a:a+u];a=a+u;
    u=29;kRP13=kS[a:a+u];a=a+u;
    u=29;kRP14=kS[a:a+u];a=a+u;
    u=29;kRP15=kS[a:a+u];a=a+u;
    u=29;kRP16=kS[a:a+u];a=a+u;
    u=29;kRP17=kS[a:a+u];a=a+u;
    u=29;kRP18=kS[a:a+u];a=a+u;
    u=29;kRP19=kS[a:a+u];a=a+u;
    u=29;kRP20=kS[a:a+u];a=a+u;
    u=29;kRP21=kS[a:a+u];a=a+u;
    u=29;kRP22=kS[a:a+u];a=a+u;
    u=29;kRP23=kS[a:a+u];a=a+u;
    u=29;kRP24=kS[a:a+u];a=a+u;
    u=29;kRP25=kS[a:a+u];a=a+u;
    u=29;kRP26=kS[a:a+u];a=a+u;
    u=29;kRP27=kS[a:a+u];a=a+u;
    u=29;kRP28=kS[a:a+u];a=a+u;
    u=29;kRP29=kS[a:a+u];a=a+u;
    u=29;kRP30=kS[a:a+u];a=a+u;
    u=29;kRP31=kS[a:a+u];a=a+u;
    u=29;kRP32=kS[a:a+u];a=a+u;
    u=29;kRP33=kS[a:a+u];a=a+u;
    u=16;kRP34=kS[a:a+u];a=a+u;
    u=4;kDP=kS[a:a+u];a=a+u;
    u=11;kPA=kS[a:a+u];a=a+u;
    u=606;kXd=kS[a:a+u];a=a+u;




    u=3;kE=kS[a-1:a+u];
    # fixed kE bug here




    # ## Defining Entities
    a=0;
    xRibosome=x[a];a=a+1;
    xD=x[a:a+38];a=a+38;
    xC=x[a:a+44];a=a+44;
    xA=x[a:a+72];a=a+72;
    xR=x[a:a+73];a=a+73;
    xRP=x[a:a+414];a=a+414;
    xP=x[a:a+130];a=a+130;
    xE=x[a:a+2];


    # ## xD **
    p53inac =xD[1-1];
    p53ac =xD[2-1];
    Mdm2 =xD[3-1];
    Wip1 =xD[4-1];
    ATMP =xD[5-1];
    ATRac =xD[6-1];
    Mdm2product1=xD[7-1];
    Mdm2product2=xD[8-1];
    Mdm2product3=xD[9-1];
    Mdm2product4=xD[10-1];
    Mdm2product5=xD[11-1];
    Mdm2product6=xD[12-1];
    Mdm2product7=xD[13-1];
    Mdm2product8=xD[14-1];
    Mdm2product9=xD[15-1];
    Mdm2pro =xD[16-1];
    Wip1product1=xD[17-1];
    Wip1product2=xD[18-1];
    Wip1product3=xD[19-1];
    Wip1product4=xD[20-1];
    Wip1product5=xD[21-1];
    Wip1product6=xD[22-1];
    Wip1product7=xD[23-1];
    Wip1product8=xD[24-1];
    Wip1product9=xD[25-1];
    Wip1pro =xD[26-1];
    BRCA2=xD[27-1];
    MSH6=xD[28-1];
    MGMT=xD[29-1];
    damageDSB=xD[30-1];
    damageSSB=xD[31-1];
    ppAKT_Mdm2=xD[32-1];
    pMdm2=xD[33-1];
    ARF=xD[34-1];
    MDM4=xD[35-1];
    p53ac_MDM4=xD[36-1];
    ATMinac=xD[37-1];
    ATRinac=xD[38-1];



    # ## xC **
    pRB=xC[1-1];
    pRBp=xC[2-1];
    pRBpp=xC[3-1];
    E2F=xC[4-1];
    Cd=xC[5-1];
    Mdi=xC[6-1];
    Md=xC[7-1];
    Mdp27=xC[8-1];
    Ce=xC[9-1];
    Mei=xC[10-1];
    Me=xC[11-1];
    Skp2=xC[12-1];
    Mep27=xC[13-1];
    Pe=xC[14-1];
    Pai=xC[15-1];
    Pei=xC[16-1];
    Pbi=xC[17-1];
    Ca=xC[18-1];
    Mai=xC[19-1];
    Ma=xC[20-1];
    Map27=xC[21-1];
    p27=xC[22-1];
    Cdh1i=xC[23-1];
    Cdh1a=xC[24-1];
    E2Fp=xC[25-1];
    p27p=xC[26-1];
    Pa=xC[27-1];
    Cb=xC[28-1];
    Mbi=xC[29-1];
    Mb=xC[30-1];
    Cdc20i=xC[31-1];
    Cdc20a=xC[32-1];
    Pb=xC[33-1];
    Wee1=xC[34-1];
    Wee1p=xC[35-1];
    Mbp27=xC[36-1];
    Chk1=xC[37-1];
    pRBc1=xC[38-1];
    pRBc2=xC[39-1];
    p21=xC[40-1];
    Mdp21=xC[41-1];
    Mep21=xC[42-1];
    Map21=xC[43-1];
    Mbp21=xC[44-1];



    # ## xA **
    L =xA[1-1];
    R =xA[2-1];
    L_R =xA[3-1];
    Ractive =xA[4-1];
    flip =xA[5-1];
    Ractive_flip =xA[6-1];
    pC8 =xA[7-1];
    Ractive_pC8 =xA[8-1];
    C8 =xA[9-1];
    Bar =xA[10-1];
    C8_Bar =xA[11-1];
    pC3 =xA[12-1];
    C8_pC3 =xA[13-1];
    C3 =xA[14-1];
    pC6 =xA[15-1];
    C3_pC6 =xA[16-1];
    C6 =xA[17-1];
    C6_C8 =xA[18-1];
    XIAP =xA[19-1];
    C3_XIAP =xA[20-1];
    PARP =xA[21-1];
    C3_PARP =xA[22-1];
    cPARP =xA[23-1];
    Bid =xA[24-1];
    C8_Bid =xA[25-1];
    tBid =xA[26-1];
    Bcl2c =xA[27-1];
    tBid_Bcl2c =xA[28-1];
    Bax =xA[29-1];
    tBid_Bax =xA[30-1];
    Baxactive =xA[31-1];
    Baxm =xA[32-1];
    Bcl2 =xA[33-1];
    Baxm_Bcl2 =xA[34-1];
    Bax2 =xA[35-1];
    Bax2_Bcl2 =xA[36-1];
    Bax4 =xA[37-1];
    Bax4_Bcl2 =xA[38-1];
    M =xA[39-1];
    Bax4_M =xA[40-1];
    Mactive =xA[41-1];
    CytoCm =xA[42-1];
    Mactive_CytoCm =xA[43-1];
    CytoCr =xA[44-1];
    Smacm =xA[45-1];
    Mactive_Smacm =xA[46-1];
    Smacr =xA[47-1];
    CytoC =xA[48-1];
    Apaf =xA[49-1];
    CytoC_Apaf =xA[50-1];
    Apafactive =xA[51-1];
    pC9 =xA[52-1];
    Apop =xA[53-1];
    Apop_C3 =xA[54-1];
    Smac =xA[55-1];
    Apop_XIAP =xA[56-1];
    Smac_XIAP =xA[57-1];
    C3_Ub =xA[58-1];
    BAD=xA[59-1];
    PUMA=xA[60-1];
    NOXA=xA[61-1];
    Bcl2c_BAD=xA[62-1];
    Bcl2c_PUMA=xA[63-1];
    Bcl2c_NOXA=xA[64-1];
    BIM=xA[65-1];
    BIM_Bax=xA[66-1];
    Bcl2c_BIM=xA[67-1];
    ppERK_BIM=xA[68-1];
    pBIM=xA[69-1];
    ppAKT_BAD=xA[70-1];
    pBAD=xA[71-1];
    ppERK_BAD=xA[72-1]


    ### xR **
    E=xR[1-1];
    H=xR[2-1];
    HGF=xR[3-1];
    P=xR[4-1];
    F=xR[5-1];
    I=xR[6-1];
    IN=xR[7-1];
    E1=xR[8-1];
    pE1=xR[9-1];
    E2=xR[10-1];
    pE2=xR[11-1];
    E3=xR[12-1];
    E4=xR[13-1];
    pE4=xR[14-1];
    Ev3=xR[15-1];
    Met=xR[16-1];
    Pr=xR[17-1];
    Fr=xR[18-1];
    Ir=xR[19-1];
    Isr =xR[20-1];
    E1E1=xR[21-1];
    E1E2=xR[22-1];
    E1E3=xR[23-1];
    E1E4=xR[24-1];
    E2E2=xR[25-1];
    E2E3=xR[26-1];
    E2E4=xR[27-1];
    E3E4=xR[28-1];
    E4E4=xR[29-1];
    Met_Met=xR[30-1];
    FrFr=xR[31-1];
    IrIr=xR[32-1];
    Isr_Isr=xR[33-1];
    EE1=xR[34-1];
    HE3=xR[35-1];
    HE4=xR[36-1];
    HGF_Met=xR[37-1];
    PPr=xR[38-1];
    FFr=xR[39-1];
    EE1E2=xR[40-1];
    EE1Ev3=xR[41-1];
    EE1E1=xR[42-1];
    EE1E3=xR[43-1];
    EE1E4=xR[44-1];
    E2HE3=xR[45-1];
    E1HE3=xR[46-1];
    HE3E3=xR[47-1];
    HE3Ev3=xR[48-1];
    HE3E4=xR[49-1];
    E2HE4=xR[50-1];
    HE4Ev3=xR[51-1];
    E1HE4=xR[52-1];
    E3HE4=xR[53-1];
    HE4E4=xR[54-1];
    HGF_Met_Met=xR[55-1];
    PPrPr=xR[56-1];
    FFrFr=xR[57-1];
    IIrIr=xR[58-1];
    IN_Isr_Isr=xR[59-1];
    EE1EE1=xR[60-1];
    EE1HE3=xR[61-1];
    EE1HE4=xR[62-1];
    HE3HE3=xR[63-1];
    HE3HE4=xR[64-1];
    HE4HE4=xR[65-1];
    HGF_Met_HGF_Met=xR[66-1];
    PPrPPr=xR[67-1];
    FFrFFr=xR[68-1];
    IIrIrI=xR[69-1];
    IN_Isr_Isr_IN=xR[70-1];
    E1_ppERK=xR[71-1];
    E2_ppERK=xR[72-1];
    E4_ppERK=xR[73-1];


    # ## xRP **
    a=0;
    SCD = [EE1E2,EE1Ev3,EE1E1,EE1EE1,EE1E3,EE1HE3,EE1E4,EE1HE4,E2HE3,HE3Ev3,E1HE3,HE3E4,HE3HE4,E2HE4,HE4Ev3,E1HE4,E3HE4,HE4E4,HE4HE4,HGF_Met_Met,HGF_Met_HGF_Met,PPrPPr,PPrPr,FFrFFr,FFrFr,IIrIr,IN_Isr_Isr,IIrIrI,IN_Isr_Isr_IN];
    SCD = np.array(SCD)




    pSCD = xRP[a:a+29]; a=a+33;


    Sp_SCD = xRP[a:a+29]; a=a+29;#[Sp_EE1E2,Sp_EE1Ev3,Sp_EE1E1,Sp_EE1EE1,Sp_EE1E3,Sp_EE1HE3,Sp_EE1E4,Sp_EE1HE4,Sp_E2HE3,Sp_HE3Ev3,Sp_E1HE3,Sp_HE3E4,Sp_HE3HE4,Sp_E2HE4,Sp_HE4Ev3,Sp_E1HE4,Sp_E3HE4,Sp_HE4E4,Sp_HE4HE4,Sp_HGF_Met_Met,Sp_HGF_Met_HGF_Met,Sp_PPrPPr,Sp_PPrPr,Sp_FFrFFr,Sp_FFrFr,Sp_IIrIr,Sp_IIrIIr];


    SCDint = xRP[a:a+29]; a=a+29;#[EE1E2int,EE1Ev3int,EE1E1int,EE1EE1int,EE1E3int,EE1HE3int,EE1E4int,EE1HE4int,E2HE3int,HE3Ev3int,E1HE3int,HE3E4int,HE3HE4int,E2HE4int,HE4Ev3int,E1HE4int,E3HE4int,HE4E4int,HE4HE4int,HGF_Met_Metint,HGF_Met_HGF_Metint,PPrPPrint,PPrPrint,FFrFFrint,FFrFrint,IIrIrint,IIrIIrint];


    pSCDint = xRP[a:a+29]; a=a+33;#[pEE1E2int,pEE1Ev3int,pEE1E1int,pEE1EE1int,pEE1E3int,pEE1HE3int,pEE1E4int,pEE1HE4int,pE2HE3int,pHE3Ev3int,pE1HE3int,pHE3E4int,pHE3HE4int,pE2HE4int,pHE4Ev3int,pE1HE4int,pE3HE4int,pHE4E4int,pHE4HE4int,pHGF_Met_Metint,pHGF_Met_HGF_Metint,pPPrPPrint,pPPrPrint,pFFrFFrint,pFFrFrint,pIIrIrint,pIIrIIrint];


    # pSCD_bind = np.append(xRP[0:25],xRP[29:33]); #[pEE1E2,pEE1Ev3,pEE1E1,pEE1EE1,pEE1E3,pEE1HE3,pEE1E4,pEE1HE4,pE2HE3,pHE3Ev3,pE1HE3,pHE3E4,pHE3HE4,pE2HE4,pHE4Ev3,pE1HE4,pE3HE4,pHE4E4,pHE4HE4,pHGF_Met_Met,pHGF_Met_HGF_Met,pPPrPPr,pPPrPr,pFFrFFr,pFFrFr,pIIrIr_IRS,pIIrIIr_IRS]; #Same as pSCD but with the IRS on the IGF1R. Had to do this because it has an extra step (binding of IRS)



    # NOTE
    # trying to fix append problem
    array1 = xRP[0:25]
    array2 = xRP[29:33]
    pSCD_bind = np.zeros(shape=(array1.shape[0]+array2.shape[0]))

    count = 0

    for itema in array1:
        pSCD_bind[count] = itema
        count = count+1

    for itema in array2:
        pSCD_bind[count] = itema
        count = count+1


    # pSCDint_bind = np.append(xRP[91:116],xRP[120:124]); #[pEE1E2int,pEE1Ev3int,pEE1E1int,pEE1EE1int,pEE1E3int,pEE1HE3int,pEE1E4int,pEE1HE4int,pE2HE3int,pHE3Ev3int,pE1HE3int,pHE3E4int,pHE3HE4int,pE2HE4int,pHE4Ev3int,pE1HE4int,pE3HE4int,pHE4E4int,pHE4HE4int,pHGF_Met_Metint,pHGF_Met_HGF_Metint,pPPrPPrint,pPPrPrint,pFFrFFrint,pFFrFrint,pIIrIrint_IRS,pIIrIIrint_IRS];

    array3 = xRP[91:116]
    array4 = xRP[120:124]
    pSCDint_bind = np.zeros(shape=(array3.shape[0]+array4.shape[0]))

    count = 0

    for itemy in array3:
        pSCDint_bind[count] = itemy
        count = count+1

    for itemz in array4:
        pSCDint_bind[count] = itemz
        count = count+1

    ##########




    pSCD_G2_SOS = xRP[a:a+29]; a=a+29; #[pEE1E2_G2_SOS,pEE1Ev3_G2_SOS,pEE1E1_G2_SOS,pEE1EE1_G2_SOS,pEE1E3_G2_SOS,pEE1HE3_G2_SOS,pEE1E4_G2_SOS,pEE1HE4_G2_SOS,pE2HE3_G2_SOS,pHE3Ev3_G2_SOS,pE1HE3_G2_SOS,pHE3E4_G2_SOS,pHE3HE4_G2_SOS,pE2HE4_G2_SOS,pHE4Ev3_G2_SOS,pE1HE4_G2_SOS,pE3HE4_G2_SOS,pHE4E4_G2_SOS,pHE4HE4_G2_SOS,pHGF_Met_Met_G2_SOS,pHGF_Met_HGF_Met_G2_SOS,pPPrPPr_G2_SOS,pPPrPr_G2_SOS,pFFrFFr_G2_SOS,pFFrFr_G2_SOS,pIIrIr_IRS_G2_SOS,pIIrIIr_IRS_G2_SOS];
    pSCDint_G2_SOS = xRP[a:a+29]; a=a+29; #[pEE1E2int_G2_SOS,pEE1Ev3int_G2_SOS,pEE1E1int_G2_SOS,pEE1EE1int_G2_SOS,pEE1E3int_G2_SOS,pEE1HE3int_G2_SOS,pEE1E4int_G2_SOS,pEE1HE4int_G2_SOS,pE2HE3int_G2_SOS,pHE3Ev3int_G2_SOS,pE1HE3int_G2_SOS,pHE3E4int_G2_SOS,pHE3HE4int_G2_SOS,pE2HE4int_G2_SOS,pHE4Ev3int_G2_SOS,pE1HE4int_G2_SOS,pE3HE4int_G2_SOS,pHE4E4int_G2_SOS,pHE4HE4int_G2_SOS,pHGF_Met_Metint_G2_SOS,pHGF_Met_HGF_Metint_G2_SOS,pPPrPPrint_G2_SOS,pPPrPrint_G2_SOS,pFFrFFrint_G2_SOS,pFFrFrint_G2_SOS,pIIrIrint_IRS_G2_SOS,pIIrIIrint_IRS_G2_SOS];




    pSCD_PLCg = xRP[a:a+29]; a=a+29; #[pEE1E2_PLCg,pEE1Ev3_PLCg,pEE1E1_PLCg,pEE1EE1_PLCg,pEE1E3_PLCg,pEE1HE3_PLCg,pEE1E4_PLCg,pEE1HE4_PLCg,pE2HE3_PLCg,pHE3Ev3_PLCg,pE1HE3_PLCg,pHE3E4_PLCg,pHE3HE4_PLCg,pE2HE4_PLCg,pHE4Ev3_PLCg,pE1HE4_PLCg,pE3HE4_PLCg,pHE4E4_PLCg,pHE4HE4_PLCg,pHGF_Met_Met_PLCg,pHGF_Met_HGF_Met_PLCg,pPPrPPr_PLCg,pPPrPr_PLCg,pFFrFFr_PLCg,pFFrFr_PLCg,pIIrIr_IRS_PLCg,pIIrIIr_IRS_PLCg];
    pSCD_PI3K1 = xRP[a:a+29]; a=a+29; #[pEE1E2_PI3K1,pEE1Ev3_PI3K1,pEE1E1_PI3K1,pEE1EE1_PI3K1,pEE1E3_PI3K1,pEE1HE3_PI3K1,pEE1E4_PI3K1,pEE1HE4_PI3K1,pE2HE3_PI3K1,pHE3Ev3_PI3K1,pE1HE3_PI3K1,pHE3E4_PI3K1,pHE3HE4_PI3K1,pE2HE4_PI3K1,pHE4Ev3_PI3K1,pE1HE4_PI3K1,pE3HE4_PI3K1,pHE4E4_PI3K1,pHE4HE4_PI3K1,pHGF_Met_Met_PI3K1,pHGF_Met_HGF_Met_PI3K1,pPPrPPr_PI3K1,pPPrPr_PI3K1,pFFrFFr_PI3K1,pFFrFr_PI3K1,pIIrIr_IRS_PI3K1,pIIrIIr_IRS_PI3K1];
    pSCD_PI3K2 = xRP[a:a+29]; a=a+29; #[pEE1E2_PI3K2,pEE1Ev3_PI3K2,pEE1E1_PI3K2,pEE1EE1_PI3K2,pEE1E3_PI3K2,pEE1HE3_PI3K2,pEE1E4_PI3K2,pEE1HE4_PI3K2,pE2HE3_PI3K2,pHE3Ev3_PI3K2,pE1HE3_PI3K2,pHE3E4_PI3K2,pHE3HE4_PI3K2,pE2HE4_PI3K2,pHE4Ev3_PI3K2,pE1HE4_PI3K2,pE3HE4_PI3K2,pHE4E4_PI3K2,pHE4HE4_PI3K2,pHGF_Met_Met_PI3K2,pHGF_Met_HGF_Met_PI3K2,pPPrPPr_PI3K2,pPPrPr_PI3K2,pFFrFFr_PI3K2,pFFrFr_PI3K2,pIIrIr_IRS_PI3K2,pIIrIIr_IRS_PI3K2];




    pSCDint_G2_SOS_RasD = xRP[a:a+29]; a=a+29; #[pEE1E2int_G2_SOS_RasDint,pEE1Ev3int_G2_SOS_RasDint,pEE1E1int_G2_SOS_RasDint,pEE1EE1int_G2_SOS_RasDint,pEE1E3int_G2_SOS_RasDint,pEE1HE3int_G2_SOS_RasDint,pEE1E4int_G2_SOS_RasDint,pEE1HE4int_G2_SOS_RasDint,pE2HE3int_G2_SOS_RasDint,pHE3Ev3int_G2_SOS_RasDint,pE1HE3int_G2_SOS_RasDint,pHE3E4int_G2_SOS_RasDint,pHE3HE4int_G2_SOS_RasDint,pE2HE4int_G2_SOS_RasDint,pHE4Ev3int_G2_SOS_RasDint,pE1HE4int_G2_SOS_RasDint,pE3HE4int_G2_SOS_RasDint,pHE4E4int_G2_SOS_RasDint,pHE4HE4int_G2_SOS_RasDint,pHGF_Met_Metint_G2_SOS_RasDint,pHGF_Met_HGF_Metint_G2_SOS_RasDint,pPPrPPrint_G2_SOS_RasDint,pPPrPrint_G2_SOS_RasDint,pFFrFFrint_G2_SOS_RasDint,pFFrFrint_G2_SOS_RasDint,pIIrIrint_IRS_G2_SOS_RasDint,pIIrIIrint_IRS_G2_SOS_RasDint];
    pSCD_G2_SOS_RasD = xRP[a:a+29]; a=a+29; #[pEE1E2_G2_SOS_RasD,pEE1Ev3_G2_SOS_RasD,pEE1E1_G2_SOS_RasD,pEE1EE1_G2_SOS_RasD,pEE1E3_G2_SOS_RasD,pEE1HE3_G2_SOS_RasD,pEE1E4_G2_SOS_RasD,pEE1HE4_G2_SOS_RasD,pE2HE3_G2_SOS_RasD,pHE3Ev3_G2_SOS_RasD,pE1HE3_G2_SOS_RasD,pHE3E4_G2_SOS_RasD,pHE3HE4_G2_SOS_RasD,pE2HE4_G2_SOS_RasD,pHE4Ev3_G2_SOS_RasD,pE1HE4_G2_SOS_RasD,pE3HE4_G2_SOS_RasD,pHE4E4_G2_SOS_RasD,pHE4HE4_G2_SOS_RasD,pHGF_Met_Met_G2_SOS_RasD,pHGF_Met_HGF_Met_G2_SOS_RasD,pPPrPPr_G2_SOS_RasD,pPPrPr_G2_SOS_RasD,pFFrFFr_G2_SOS_RasD,pFFrFr_G2_SOS_RasD,pIIrIr_IRS_G2_SOS_RasD,pIIrIIr_IRS_G2_SOS_RasD];
    pSCD_PLCg_PIP2 = xRP[a:a+29]; a=a+29; #[pEE1E2_PLCg_PIP2,pEE1Ev3_PLCg_PIP2,pEE1E1_PLCg_PIP2,pEE1EE1_PLCg_PIP2,pEE1E3_PLCg_PIP2,pEE1HE3_PLCg_PIP2,pEE1E4_PLCg_PIP2,pEE1HE4_PLCg_PIP2,pE2HE3_PLCg_PIP2,pHE3Ev3_PLCg_PIP2,pE1HE3_PLCg_PIP2,pHE3E4_PLCg_PIP2,pHE3HE4_PLCg_PIP2,pE2HE4_PLCg_PIP2,pHE4Ev3_PLCg_PIP2,pE1HE4_PLCg_PIP2,pE3HE4_PLCg_PIP2,pHE4E4_PLCg_PIP2,pHE4HE4_PLCg_PIP2,pHGF_Met_Met_PLCg_PIP2,pHGF_Met_HGF_Met_PLCg_PIP2,pPPrPPr_PLCg_PIP2,pPPrPr_PLCg_PIP2,pFFrFFr_PLCg_PIP2,pFFrFr_PLCg_PIP2,pIIrIr_IRS_PLCg_PIP2,pIIrIIr_IRS_PLCg_PIP2];
    pSCD_PI3K1_PIP2 = xRP[a:a+29]; a=a+29; #[pEE1E2_PI3K1_PIP2,pEE1Ev3_PI3K1_PIP2,pEE1E1_PI3K1_PIP2,pEE1EE1_PI3K1_PIP2,pEE1E3_PI3K1_PIP2,pEE1HE3_PI3K1_PIP2,pEE1E4_PI3K1_PIP2,pEE1HE4_PI3K1_PIP2,pE2HE3_PI3K1_PIP2,pHE3Ev3_PI3K1_PIP2,pE1HE3_PI3K1_PIP2,pHE3E4_PI3K1_PIP2,pHE3HE4_PI3K1_PIP2,pE2HE4_PI3K1_PIP2,pHE4Ev3_PI3K1_PIP2,pE1HE4_PI3K1_PIP2,pE3HE4_PI3K1_PIP2,pHE4E4_PI3K1_PIP2,pHE4HE4_PI3K1_PIP2,pHGF_Met_Met_PI3K1_PIP2,pHGF_Met_HGF_Met_PI3K1_PIP2,pPPrPPr_PI3K1_PIP2,pPPrPr_PI3K1_PIP2,pFFrFFr_PI3K1_PIP2,pFFrFr_PI3K1_PIP2,pIIrIr_IRS_PI3K1_PIP2,pIIrIIr_IRS_PI3K1_PIP2];
    pSCD_PI3K2_PIP = xRP[a:a+29]; #[pEE1E2_PI3K2_PIP,pEE1Ev3_PI3K2_PIP,pEE1E1_PI3K2_PIP,pEE1EE1_PI3K2_PIP,pEE1E3_PI3K2_PIP,pEE1HE3_PI3K2_PIP,pEE1E4_PI3K2_PIP,pEE1HE4_PI3K2_PIP,pE2HE3_PI3K2_PIP,pHE3Ev3_PI3K2_PIP,pE1HE3_PI3K2_PIP,pHE3E4_PI3K2_PIP,pHE3HE4_PI3K2_PIP,pE2HE4_PI3K2_PIP,pHE4Ev3_PI3K2_PIP,pE1HE4_PI3K2_PIP,pE3HE4_PI3K2_PIP,pHE4E4_PI3K2_PIP,pHE4HE4_PI3K2_PIP,pHGF_Met_Met_PI3K2_PIP,pHGF_Met_HGF_Met_PI3K2_PIP,pPPrPPr_PI3K2_PIP,pPPrPr_PI3K2_PIP,pFFrFFr_PI3K2_PIP,pFFrFr_PI3K2_PIP,pIIrIr_IRS_PI3K2_PIP,pIIrIIr_IRS_PI3K2_PIP];




    # # Need these independently because of binding to IRS
    pIIrIr=xRP[26-1];
    pIN_Isr_Isr=xRP[27-1];
    pIIrIrI=xRP[28-1];
    pIN_Isr_Isr_IN=xRP[29-1];
    pIIrIr_IRS=xRP[30-1];
    pIN_Isr_Isr_IRS=xRP[31-1];
    pIIrIrI_IRS=xRP[32-1];
    pIN_Isr_Isr_IN_IRS=xRP[33-1];



    pIIrIr_int=xRP[117-1];
    pIN_Isr_Isr_int=xRP[118-1];
    pIIrIrI_int=xRP[119-1];
    pIN_Isr_Isr_IN_int=xRP[120-1];
    pIIrIr_int_IRS=xRP[121-1];
    pIN_Isr_Isr_int_IRS=xRP[122-1];
    pIIrIrI_int_IRS=xRP[123-1];
    pIN_Isr_Isr_IN_int_IRS=xRP[124-1];



    # ## xP **
    IRS=xP[1-1];
    Sp=xP[2-1];
    Cbl=xP[3-1];
    G2=xP[4-1];
    G2_SOS=xP[5-1];
    G2_pSOS=xP[6-1];
    PLCg=xP[7-1];
    PI3KC1=xP[8-1];
    PI3KR1=xP[9-1];
    PI3K1=xP[10-1];
    pPI3K1=xP[11-1];
    PI3K2=xP[12-1];
    mTORC1=xP[13-1];
    mTORC1active=xP[14-1];
    PIP=xP[15-1];




    PI3P=xP[16-1];
    DAG=xP[17-1];
    GRP=xP[18-1];
    DAG_GRP=xP[19-1];
    RasT=xP[20-1];
    RasD=xP[21-1];
    NF1=xP[22-1];
    pNF1=xP[23-1];
    pCRaf=xP[24-1];
    CRaf=xP[25-1];
    RasT_CRaf=xP[26-1];
    BRaf=xP[27-1];
    RasT_CRaf_BRaf=xP[28-1];
    MEK=xP[29-1];
    pMEK=xP[30-1];
    ppMEK=xP[31-1];
    MKP3=xP[32-1];
    ERKnuc=xP[33-1];
    ppERKnuc=xP[34-1];
    RSK=xP[35-1];
    pRSK=xP[36-1];
    pRSKnuc=xP[37-1];
    MKP1=xP[38-1];
    pMKP1=xP[39-1];
    cFos=xP[40-1];
    pcFos=xP[41-1];
    cJun=xP[42-1];
    pcFos_cJun=xP[43-1];
    cMyc=xP[44-1];
    bCATENINnuc=xP[45-1];
    bCATENIN=xP[46-1];
    pbCATENIN=xP[47-1];
    IP3=xP[48-1];
    PIP2=xP[49-1];
    PIP3=xP[50-1];
    PTEN=xP[51-1];
    PIP3_AKT=xP[52-1];
    AKT=xP[53-1];


    pAKT=xP[54-1];
    ppAKT=xP[55-1];
    PDK1=xP[56-1];
    PIP3_PDK1=xP[57-1];
    PIP3_pAKT=xP[58-1];
    Rictor=xP[59-1];
    mTOR=xP[60-1];
    mTORC2=xP[61-1];
    PIP3_ppAKT=xP[62-1];
    GSK3b=xP[63-1];
    pGSK3b=xP[64-1];
    TSC1=xP[65-1];
    TSC2=xP[66-1];
    pTSC2=xP[67-1];
    TSC=xP[68-1];
    PKC=xP[69-1];
    DAG_PKC=xP[70-1];
    pRKIP=xP[71-1];
    RKIP=xP[72-1];
    RKIP_CRaf=xP[73-1];
    ERK=xP[74-1];
    pERK=xP[75-1];
    ppERK=xP[76-1];
    FOXO=xP[77-1];
    pFOXO=xP[78-1];
    RhebD=xP[79-1];
    RhebT=xP[80-1];
    Raptor=xP[81-1];
    S6K=xP[82-1];
    pS6K=xP[83-1];
    EIF4EBP1=xP[84-1];
    pEIF4EBP1=xP[85-1];
    SOS=xP[86-1];
    G2_SOS_ppERK=xP[87-1];
    CRaf_ppERK=xP[88-1];
    RasD_DAG_GRP=xP[89-1];
    RasT_NF1=xP[90-1];
    NF1_ppERK=xP[91-1];
    MEK_RasT_CRaf_BRaf=xP[92-1];
    pMEK_RasT_CRaf_BRaf=xP[93-1];
    ERK_ppMEK=xP[94-1];
    pERK_ppMEK=xP[95-1];
    RSK_ppERK=xP[96-1];
    pRSKnuc_MKP1=xP[97-1];
    ppERKnuc_MKP1=xP[98-1];
    cFos_pRSKnuc=xP[99-1];
    cFos_ppERKnuc=xP[100-1];
    RKIP_DAG_PKC=xP[101-1];
    PIP3_PTEN=xP[102-1];
    PIP3_AKT_PIP3_PDK1=xP[103-1];
    PIP3_pAKT_mTORC2=xP[104-1];
    GSK3b_ppAKT=xP[105-1];
    bCATENIN_GSK3b=xP[106-1];
    TSC2_ppAKT=xP[107-1];
    TSC2_ppERK=xP[108-1];
    RhebT_TSC=xP[109-1];
    EIF4EBP1_mTORC1active=xP[110-1];
    S6K_mTORC1active=xP[111-1];
    FOXO_ppAKT=xP[112-1];
    PI3K1_mTORC1active=xP[113-1];
    pERK_MKP3=xP[114-1];
    ppERK_MKP3=xP[115-1];
    ppERKnuc_pMKP1=xP[116-1];
    RasT_BRaf=xP[117-1];
    RasT_BRaf_BRaf=xP[118-1];
    MEK_RasT_BRaf_BRaf=xP[119-1];
    pMEK_RasT_BRaf_BRaf=xP[120-1];
    EIF4E=xP[121-1];
    EIF4EBP1_EIF4E=xP[122-1];
    RasT_CRaf_CRaf=xP[123-1];
    MEK_RasT_CRaf_CRaf=xP[124-1];
    pMEK_RasT_CRaf_CRaf=xP[125-1];
    FOXOnuc=xP[126-1];

    MEKi=xP[127-1];
    MEKi_ppMEK=xP[128-1];
    AKTi=xP[129-1];
    AKTi_AKT=xP[130-1];



    # ###### RATE CONSTANTS ASSIGNMENT

    # ###DNA Damage Rate Constants
    bp=kD[1-1];
    ampi=kD[2-1];
    api=kD[3-1];
    bsp=kD[4-1];
    ns=kD[5-1];
    Ts=kD[6-1];
    ampa=kD[7-1];
    awpa=kD[8-1];
    bm=kD[9-1];
    bmi=kD[10-1];
    am=kD[11-1];
    asm=kD[12-1];
    bw=kD[13-1];
    aw=kD[14-1];
    asm2=kD[15-1];
    aws=kD[16-1];
    nw=kD[17-1];
    Tw=kD[18-1];



    as_=kD[19-1];
    # NOTE - had to change name of this variable because "as" is a reserved word in python


    bs=kD[20-1];
    bs2=kD[21-1];
    tau1=kD[22-1];
    tau2=kD[23-1];
    tau3=kD[24-1];
    tau4=kD[25-1];
    tau5=kD[26-1];
    tau6=kD[27-1];
    tau7=kD[28-1];
    tau8=kD[29-1];
    tau9=kD[30-1];
    tau10=kD[31-1];
    tau11=kD[32-1];
    tau12=kD[33-1];
    tau13=kD[34-1];
    tau14=kD[35-1];
    tau15=kD[36-1];
    tau16=kD[37-1];
    tau17=kD[38-1];
    tau18=kD[39-1];
    tau19=kD[40-1];
    tau20=kD[41-1];



    kD[42-1]=kD[42-1];
    kD[43-1]=kD[43-1];
    kD[44-1]=kD[44-1];
    kD[45-1]=kD[45-1];
    fixdsb1 =kD[46-1];
    fixmsh =kD[47-1];
    fixmgmt =kD[48-1];
    basalp53act=kD[49-1];
    kDDbasal=kD[50-1];
    kDDE=kD[51-1];
    kDEtop=kD[52-1];
    Etop=kD[53-1];
    kDnSP=kD[54-1];
    kDkmSP=kD[55-1];
    kDnSS=kD[56-1];
    kDnDS=kD[57-1];
    kDkmSS=kD[58-1];
    kDkmDS=kD[59-1];




    # ### Cell Cycle Rate Constants
    aa=kC[1-1];
    ab=kC[2-1];
    ae=kC[3-1];
    cdk1tot=kC[4-1];
    cdk2tot=kC[5-1];
    cdk4tot=kC[6-1];
    Chk1tot=kC[7-1];
    eps=kC[8-1];
    ib=kC[9-1];
    ib1=kC[10-1];
    ib2=kC[11-1];
    ib3=kC[12-1];
    K1=kC[13-1];
    K1a=kC[14-1];
    K1b=kC[15-1];
    K1cdh1=kC[16-1];
    K1chk=kC[17-1];
    K1d=kC[18-1];
    K1e=kC[19-1];
    K1e2f=kC[20-1];
    K1p27=kC[21-1];
    K2=kC[22-1];
    K2a=kC[23-1];
    K2b=kC[24-1];
    K2cdh1=kC[25-1];
    K2chk=kC[26-1];
    K2d=kC[27-1];
    K2e=kC[28-1];
    K2e2f=kC[29-1];
    K2p27=kC[30-1];
    K3=kC[31-1];
    K3b=kC[32-1];
    K4=kC[33-1];
    K4b=kC[34-1];
    K5a=kC[35-1];
    K5b=kC[36-1];
    K5e=kC[37-1];
    K6a=kC[38-1];
    K6b=kC[39-1];
    K6e=kC[40-1];
    K7b=kC[41-1];
    K8b=kC[42-1];
    Kacdc20=kC[43-1];
    kc1=kC[44-1];
    kc10=kC[45-1];
    kc11=kC[46-1];
    kc12=kC[47-1];
    kc13=kC[48-1];
    kc14=kC[49-1];
    kc15=kC[50-1];



    kc16=kC[51-1];
    kc2=kC[52-1];
    kc3=kC[53-1];
    kc4=kC[54-1];
    kc5=kC[55-1];
    kc6=kC[56-1];
    kc7=kC[57-1];
    kc8=kC[58-1];
    kc9=kC[59-1];
    kca=kC[60-1];
    kcd2=kC[61-1];
    Kcdh1=kC[62-1];
    kce=kC[63-1];
    kcom1=kC[64-1];
    kcom2=kC[65-1];
    kcom3=kC[66-1];
    kcom4=kC[67-1];
    Kda=kC[68-1];
    Kdb=kC[69-1];
    Kdbcdc20=kC[70-1];
    Kdbcdh1=kC[71-1];
    kdcdc20a=kC[72-1];
    kdcdc20i=kC[73-1];
    kdcdh1a=kC[74-1];
    kdcdh1i=kC[75-1];
    Kdceskp2=kC[76-1];
    Kdd=kC[77-1];
    kdda=kC[78-1];
    kddb=kC[79-1];
    kddd=kC[80-1];
    kdde=kC[81-1];
    kddp21=kC[82-1];
    kddp27=kC[83-1];
    kddp27p=kC[84-1];
    kddskp2=kC[85-1];
    Kde=kC[86-1];
    kde2f=kC[87-1];
    kde2fp=kC[88-1];
    kdecom1=kC[89-1];
    kdecom2=kC[90-1];
    kdecom3=kC[91-1];
    kdecom4=kC[92-1];
    Kdp27p=kC[93-1];
    Kdp27skp2=kC[94-1];
    kdpa=kC[95-1];
    kdpai=kC[96-1];
    kdpb=kC[97-1];
    kdpbi=kC[98-1];
    kdpe=kC[99-1];
    kdpei=kC[100-1];
    kdprb=kC[101-1];
    kdprbp=kC[102-1];
    kdprbpp=kC[103-1];
    Kdskp2=kC[104-1];
    kdWee1=kC[105-1];
    kdWee1p=kC[106-1];
    Ki10=kC[107-1];
    Ki11=kC[108-1];
    Ki12=kC[109-1];
    Ki13=kC[110-1];
    Ki14=kC[111-1];
    Ki7=kC[112-1];
    Ki8=kC[113-1];
    Ki9=kC[114-1];
    kpc1=kC[115-1];
    kpc2=kC[116-1];
    kpc3=kC[117-1];
    kpc4=kC[118-1];
    V1=kC[119-1];
    V1cdh1=kC[120-1];
    V1chk=kC[121-1];
    V1e2f=kC[122-1];
    V1p27=kC[123-1];
    V2=kC[124-1];
    V2cdh1=kC[125-1];
    V2chk=kC[126-1];
    V2e2f=kC[127-1];
    V2p27=kC[128-1];
    V3=kC[129-1];
    V4=kC[130-1];
    V6a=kC[131-1];
    V6b=kC[132-1];
    V6e=kC[133-1];
    vcb=kC[134-1];
    Vda=kC[135-1];
    Vdb=kC[136-1];
    Vdd=kC[137-1];
    Vde=kC[138-1];
    Vdp27p=kC[139-1];
    Vdskp2=kC[140-1];
    Vm1a=kC[141-1];
    Vm1b=kC[142-1];
    Vm1d=kC[143-1];
    Vm1e=kC[144-1];
    Vm2a=kC[145-1];
    Vm2b=kC[146-1];





    Vm2d=kC[147-1];
    Vm2e=kC[148-1];
    Vm3b=kC[149-1];
    Vm4b=kC[150-1];
    Vm5a=kC[151-1];
    Vm5b=kC[152-1];
    Vm5e=kC[153-1];
    Vm7b=kC[154-1];
    Vm8b=kC[155-1];
    vs1p27=kC[156-1];
    vs2p27=kC[157-1];
    vscdc20i=kC[158-1];
    vscdh1a=kC[159-1];
    vse2f=kC[160-1];
    vspai=kC[161-1];
    vspbi=kC[162-1];
    vspei=kC[163-1];
    vsprb=kC[164-1];
    vsskp2=kC[165-1];
    vswee1=kC[166-1];
    xa1=kC[167-1];
    xa2=kC[168-1];
    xb1=kC[169-1];
    xb2=kC[170-1];
    xe1=kC[171-1];
    xe2=kC[172-1];
    kcd1=kC[173-1];




    # #### RATE LAWS

    # ## EIF4E sequestration by total mRNA in cell
    mT=xE[0];




    EIF4E_mT=xE[1];
    ksynth_mT=kE[0];
    kdeg_mT=kE[1];
    kdeg_EIF4E_mT=kE[2];



    # NOTE
    vE = np.zeros(shape=(5))
    vE[0]=kT1[0]*EIF4E*mT;

    vE[1]=kT2[0]*EIF4E_mT;

    vE[2]=ksynth_mT;
    vE[3]=kdeg_mT*mT;
    vE[4]=kdeg_EIF4E_mT*EIF4E_mT;

    #########


    # ## vRIBOSOME **
    f1=((pS6K**nR)/(k50R**nR+pS6K**nR));
    vbR=kbR0+(kbRi*f1);
    vdR=kdR0*xRibosome;

    # ## vTL **
    rhs=(1/((EIF4Efree/(k50E+EIF4Efree))))*(Vn/Vc);


    # # # DNA Damage Mods
    # NOTE
    kTL[0]=bp/mExp_nM[0]*rhs[0];
    kTL[1]=(bmi+bm*Mdm2pro)/mExp_nM[1]*rhs[0];
    kTL[2]=(bw*Wip1pro)/mExp_nM[2]*rhs[0];



    # # Cell Cycle Mods
    # NOTE
    kTL[5]=vsprb/mExp_nM[5]*rhs[0]*eps;
    kTL[6:9]=vse2f/np.sum(mExp_nM[6:9])*rhs[0]*eps;
    kTL[9:12]=(kcd1+kcd2*E2F*(Ki7/(Ki7+pRB))*(Ki8/(Ki8+pRBp)))/np.sum(mExp_nM[9:12])*rhs[0]*eps;
    kTL[12:14]=kce*E2F*(Ki9/(Ki9+pRB))*(Ki10/(Ki10+pRBp))/np.sum(mExp_nM[12:14])*rhs[0]*eps;
    kTL[14]=vsskp2/mExp_nM[14]*rhs[0]*eps;
    kTL[15]=vspei/mExp_nM[15]*rhs[0]*eps;
    kTL[16]=vspai/mExp_nM[16]*rhs[0]*eps;
    kTL[17]=vspbi/mExp_nM[17]*rhs[0]*eps;
    kTL[18]=kca*E2F*(Ki11/(Ki11+pRB))*(Ki12/(Ki12+pRBp))/mExp_nM[18]*rhs[0]*eps;
    kTL[19]=(vs1p27+(vs2p27*E2F*(Ki13/(Ki13+pRB))*(Ki14/(Ki14+pRBp))))/mExp_nM[19]*rhs[0]*eps;
    kTL[20]=vscdh1a/mExp_nM[20]*rhs[0]*eps;
    kTL[21]=vcb/mExp_nM[21]*rhs[0]*eps;
    kTL[22]=vscdc20i/mExp_nM[22]*rhs[0]*eps;
    kTL[23]=vswee1/mExp_nM[23]*rhs[0]*eps;


    kTLcdk1tot=(cdk1tot/mExp_nM[26])*kTLd[26];
    cdk1tot=(kTLcdk1tot*mExp_nM[26])/kTLd[26];
    kTLcdk2tot=(cdk2tot/mExp_nM[27])*kTLd[27];
    cdk2tot=(kTLcdk2tot*mExp_nM[27])/kTLd[27];


    avgktl=np.mean(kTLd[28:30]);

    # NOTE
    summExp=np.sum(mExp_nM[28:30]);

    kTLcdk4tot=(cdk4tot/summExp)*avgktl;
    cdk4tot=(kTLcdk4tot*summExp)/avgktl;



    kTLChk1tot=(kTLd[24]*Chk1tot)/mExp_nM[24];
    Chk1tot=(kTLChk1tot*mExp_nM[24])/kTLd[24];


    # syntax for flattening stuff

    # NOTE
    mMod_new = np.zeros(shape=(141))
    count = 0

    for itemx in mMod[:,0]:
        mMod_new[count] = itemx
        count = count+1



    if flagE:
        vTL=np.multiply(kTL,mMod_new)*(EIF4E/(k50E+EIF4E));
    else:

        vTL= np.multiply(kTL,mMod_new) * (EIF4Efree/(k50E+EIF4Efree));





    # # Cell cycle proteins should not be affected by EIF4E, nor SGE.
    vTL[5:9]=np.multiply(kTL[5:9],mMod_new[5:9])*(EIF4Efree/(k50E+EIF4Efree));
    vTL[12:30]=np.multiply(kTL[12:30],mMod_new[12:30])*(EIF4Efree/(k50E+EIF4Efree));



    # ## vTLCd Protein Conglomerates Degradation Reactions
    vTLCd = np.zeros(shape=(102))
    vTLCd[1-1]=kTLCd[1-1]*p53inac;
    vTLCd[2-1]=kTLCd[2-1]*Mdm2 ;
    vTLCd[3-1]=kTLCd[3-1]*Wip1 ;
    vTLCd[4-1]=kTLCd[4-1]*BRCA2;
    vTLCd[5-1]=kTLCd[5-1]*MSH6;
    vTLCd[6-1]=kTLCd[6-1]*MGMT;
    vTLCd[7-1]=kTLCd[7-1]*ARF;
    vTLCd[8-1]=kTLCd[8-1]*MDM4;
    vTLCd[9-1]=kTLCd[9-1]*ATMinac;
    vTLCd[10-1]=kTLCd[10-1]*ATRinac;
    vTLCd[11-1]=0;#kTLCd[11-1]*pRB;
    vTLCd[12-1]=0;#kTLCd[12-1]*E2F;
    vTLCd[13-1]=0;#kTLCd[13-1]*Cd;
    vTLCd[14-1]=0;#kTLCd[14-1]*Ce;
    vTLCd[15-1]=0;#kTLCd[15-1]*Skp2;
    vTLCd[16-1]=0;#kTLCd[16-1]*Pai;
    vTLCd[17-1]=0;#kTLCd[17-1]*Pei;
    vTLCd[18-1]=0;#kTLCd[18-1]*Pbi;
    vTLCd[19-1]=0;#kTLCd[19-1]*Ca;
    vTLCd[20-1]=0;#kTLCd[20-1]*p27;
    vTLCd[21-1]=0;#kTLCd[21-1]*Cdh1a;
    vTLCd[22-1]=0;#kTLCd[22-1]*Cb;
    vTLCd[23-1]=0;#kTLCd[23-1]*Cdc20i;
    vTLCd[24-1]=0;#kTLCd[24-1]*Wee1;
    vTLCd[25-1]=0;#kTLCd[25-1]*Chk1;
    vTLCd[26-1]=0;#kTLCd[26-1]*p21;
    vTLCd[27-1]=kTLCd[27-1]*L ;
    vTLCd[28-1]=kTLCd[28-1]*R ;
    vTLCd[29-1]=kTLCd[29-1]*flip ;
    vTLCd[30-1]=kTLCd[30-1]*pC8 ;
    vTLCd[31-1]=kTLCd[31-1]*Bar ;
    vTLCd[32-1]=kTLCd[32-1]*pC3 ;
    vTLCd[33-1]=kTLCd[33-1]*pC6 ;
    vTLCd[34-1]=kTLCd[34-1]*XIAP ;
    vTLCd[35-1]=kTLCd[35-1]*PARP ;
    vTLCd[36-1]=kTLCd[36-1]*Bid ;
    vTLCd[37-1]=kTLCd[37-1]*Bcl2c ;
    vTLCd[38-1]=kTLCd[38-1]*Bax ;
    vTLCd[39-1]=kTLCd[39-1]*CytoCm ;
    vTLCd[40-1]=kTLCd[40-1]*Smacm ;
    vTLCd[41-1]=kTLCd[41-1]*Apaf ;
    vTLCd[42-1]=kTLCd[42-1]*pC9 ;
    vTLCd[43-1]=kTLCd[43-1]*BAD;
    vTLCd[44-1]=kTLCd[44-1]*PUMA;
    vTLCd[45-1]=kTLCd[45-1]*NOXA;
    vTLCd[46-1]=kTLCd[46-1]*BIM;
    vTLCd[47-1]=kTLCd[47-1]*E;
    vTLCd[48-1]=kTLCd[48-1]*H;
    vTLCd[49-1]=kTLCd[49-1]*HGF;
    vTLCd[50-1]=kTLCd[50-1]*P;
    vTLCd[51-1]=kTLCd[51-1]*F;
    vTLCd[52-1]=kTLCd[52-1]*I;
    vTLCd[53-1]=kTLCd[53-1]*IN;
    vTLCd[54-1]=kTLCd[54-1]*E1;
    vTLCd[55-1]=kTLCd[55-1]*E2;
    vTLCd[56-1]=kTLCd[56-1]*E3;
    vTLCd[57-1]=kTLCd[57-1]*E4;
    vTLCd[58-1]=kTLCd[58-1]*Ev3;
    vTLCd[59-1]=kTLCd[59-1]*Met;
    vTLCd[60-1]=kTLCd[60-1]*Pr;
    vTLCd[61-1]=kTLCd[61-1]*Fr;
    vTLCd[62-1]=kTLCd[62-1]*Ir;
    vTLCd[63-1]=kTLCd[63-1]*Isr;
    vTLCd[64-1]=kTLCd[64-1]*IRS;
    vTLCd[65-1]=kTLCd[65-1]*Sp;
    vTLCd[66-1]=kTLCd[66-1]*Cbl;
    vTLCd[67-1]=kTLCd[67-1]*G2;
    vTLCd[68-1]=kTLCd[68-1]*PLCg;
    vTLCd[69-1]=kTLCd[69-1]*PI3KC1;
    vTLCd[70-1]=kTLCd[70-1]*PI3KR1;
    vTLCd[71-1]=kTLCd[71-1]*PI3K2;
    vTLCd[72-1]=kTLCd[72-1]*GRP;
    vTLCd[73-1]=kTLCd[73-1]*RasD;
    vTLCd[74-1]=kTLCd[74-1]*NF1;
    vTLCd[75-1]=kTLCd[75-1]*CRaf;
    vTLCd[76-1]=kTLCd[76-1]*BRaf;
    vTLCd[77-1]=kTLCd[77-1]*MEK;
    vTLCd[78-1]=kTLCd[78-1]*MKP3;
    vTLCd[79-1]=kTLCd[79-1]*RSK;
    vTLCd[80-1]=kTLCd[80-1]*MKP1;
    vTLCd[81-1]=kTLCd[81-1]*cFos;
    vTLCd[82-1]=kTLCd[82-1]*cJun;
    vTLCd[83-1]=kTLCd[83-1]*cMyc;
    vTLCd[84-1]=kTLCd[84-1]*bCATENIN;
    vTLCd[85-1]=kTLCd[85-1]*PTEN;
    vTLCd[86-1]=kTLCd[86-1]*AKT;
    vTLCd[87-1]=kTLCd[87-1]*PDK1;
    vTLCd[88-1]=kTLCd[88-1]*Rictor;
    vTLCd[89-1]=kTLCd[89-1]*mTOR;
    vTLCd[90-1]=kTLCd[90-1]*GSK3b;
    vTLCd[91-1]=kTLCd[91-1]*TSC1;
    vTLCd[92-1]=kTLCd[92-1]*TSC2;
    vTLCd[93-1]=kTLCd[93-1]*PKC;
    vTLCd[94-1]=kTLCd[94-1]*RKIP;
    vTLCd[95-1]=kTLCd[95-1]*ERK;
    vTLCd[96-1]=kTLCd[96-1]*FOXO;
    vTLCd[97-1]=kTLCd[97-1]*RhebD;
    vTLCd[98-1]=kTLCd[98-1]*Raptor;
    vTLCd[99-1]=kTLCd[99-1]*S6K;
    vTLCd[100-1]=kTLCd[100-1]*EIF4EBP1;
    vTLCd[101-1]=kTLCd[101-1]*SOS;
    vTLCd[102-1]=kTLCd[102-1]*EIF4E;




    # ## vD **
    # some of these were commented out in the original matlab file, so i kept them commented out
    vD = np.zeros(shape=(66))
    #vD[1-1]= bp;
    vD[2-1]= ampi*Mdm2*p53inac;
    vD[3-1]= basalp53act + bsp*p53inac*(ATMP**ns/(ATMP**ns+Ts**ns)+ATRac**ns/(ATRac**ns+Ts**ns));
    vD[4-1]= awpa*Wip1*p53ac;
    vD[5-1]= api*p53inac;
    vD[6-1]= ampa*Mdm2*p53ac;
    #vD[7-1]= bm*Mdm2pro;
    #vD[8-1]= bmi;
    vD[9-1]= asm*Mdm2*ATMP;
    vD[10-1]= asm2*Mdm2*ATRac;
    vD[11-1]= am*Mdm2;
    #vD[12-1]= bw*Wip1pro;
    vD[13-1]= aw*Wip1;


    vD[14-1]= bs*((damageDSB**kDnDS)/((kDkmDS**kDnDS)+(damageDSB**kDnDS)));
    vD[15-1]= aws*ATMP*Wip1**nw/(Wip1**nw+Tw**nw);
    vD[16-1]= as_*ATMP;
    vD[17-1]= bs2*((damageSSB**kDnSS)/((kDkmSS**kDnSS)+(damageSSB**kDnSS)));
    vD[18-1]= as_*ATRac;
    vD[19-1]= Mdm2product1/tau1;
    vD[20-1]= p53ac/tau1;
    vD[21-1]= Mdm2product2/tau2;
    vD[22-1]= Mdm2product1/tau2;
    vD[23-1]= Mdm2product3/tau3;
    vD[24-1]= Mdm2product2/tau3;
    vD[25-1]= Mdm2product4/tau4;
    vD[26-1]= Mdm2product3/tau4;
    vD[27-1]= Mdm2product5/tau5;
    vD[28-1]= Mdm2product4/tau5;
    vD[29-1]= Mdm2product6/tau6;
    vD[30-1]= Mdm2product5/tau6;
    vD[31-1]= Mdm2product7/tau7;
    vD[32-1]= Mdm2product6/tau7;
    vD[33-1]= Mdm2product8/tau8;
    vD[34-1]= Mdm2product7/tau8;
    vD[35-1]= Mdm2product9/tau9;
    vD[36-1]= Mdm2product8/tau9;
    vD[37-1]= Mdm2pro/tau10;
    vD[38-1]= Mdm2product9/tau10;
    vD[39-1]= Wip1product1/tau11;
    vD[40-1]= p53ac/tau11;
    vD[41-1]= Wip1product2/tau12;
    vD[42-1]= Wip1product1/tau12;
    vD[43-1]= Wip1product3/tau13;
    vD[44-1]= Wip1product2/tau13;
    vD[45-1]= Wip1product4/tau14;
    vD[46-1]= Wip1product3/tau14;
    vD[47-1]= Wip1product5/tau15;
    vD[48-1]= Wip1product4/tau15;
    vD[49-1]= Wip1product6/tau16;
    vD[50-1]= Wip1product5/tau16;
    vD[51-1]= Wip1product7/tau17;
    vD[52-1]= Wip1product6/tau17;
    vD[53-1]= Wip1product8/tau18;
    vD[54-1]= Wip1product7/tau18;
    vD[55-1]= Wip1product9/tau19;
    vD[56-1]= Wip1product8/tau19;
    vD[57-1]= Wip1pro/tau20;
    vD[58-1]= Wip1product9/tau20;
    vD[59-1]=kD[42-1]*ARF*Mdm2;
    vD[60-1]=kD[43-1]*ARF*pMdm2;
    vD[61-1]=kD[44-1]*MDM4*p53ac;
    vD[62-1]=kD[45-1]*p53ac_MDM4;
    vD[63-1]=fixdsb1*BRCA2*damageDSB;
    vD[64-1]=fixmsh*MSH6*damageSSB;
    vD[65-1]=fixmgmt*MGMT*damageSSB;
    vD[66-1]=(kDDbasal+kDDE*(Etop/(Etop+kDEtop)))*(((Ma+Me)**kDnSP)/(((Ma+Me)**kDnSP)+(kDkmSP**kDnSP)));




    # ## vC **
    vC = np.zeros(shape=(104))
    #vC[1-1]=vsprb; #pRb(Rb) synthesis
    vC[2-1]=kpc1*pRB*E2F; #pRb binding to E2F
    vC[3-1]=kpc2*pRBc1; #dissociation of that pRbE2F complex
    vC[4-1]=V1*(pRB/(K1+pRB))*(Md+Mdp27); #pRb phosphorylation
    vC[5-1]=V2*(pRBp/(K2+pRBp)); #pRb dephosphorylation
    vC[6-1]=kdprb*pRB; #pRb degradation
    vC[7-1]=V3*(pRBp/(K3+pRBp))*Me; #pRbp phosphorylating to pRbpp
    vC[8-1]=V4*(pRBpp/(K4+pRBpp)); #pRbpp dephosphorylation to pRbp
    vC[9-1]=kpc3*pRBp*E2F; #pRbp binding to E2F
    vC[10-1]=kpc4*pRBc2; #pRbp dissociation from E2F
    vC[11-1]=kdprbp*pRBp; #pRbp degradation
    vC[12-1]=kdprbpp*pRBpp; #pRbpp degradation
    #vC[13-1]=vse2f; #E2F synthesis
    vC[14-1]=V1e2f*Ma*(E2F/(E2F+K1e2f)); #E2F phosphorylation by active CYCACDK2
    vC[15-1]=V2e2f*(E2Fp/(E2Fp+K2e2f)); #pE2F dephosphorylation to E2F
    vC[16-1]=kde2f*E2F; #E2F degradation
    vC[17-1]=kde2fp*E2Fp; #pE2F degradation
    #vC[18-1]=kcd1+kcd2*E2F*(Ki7/(Ki7+pRB))*(Ki8/(Ki8+pRBp)); #cycd synthesis due to E2f inhibited by pRb and pRbp
    vC[19-1]=kcom1*Cd*(cdk4tot-(Mdi+Md+Mdp27+Mdp21)); #cycd binding to cdk4/6
    vC[20-1]=kdecom1*Mdi; #dissociation of CYCD from CYCDCDK4/6(i) complex
    vC[21-1]=Vdd*(Cd/(Kdd+Cd)); #maximum cycd degradation
    vC[22-1]=kddd*Cd; #non specific cycd degradation
    vC[23-1]=Vm2d*(Md/(K2d+Md)); #inactivation of CYCDCK4/6(a) or Md
    vC[24-1]=Vm1d*(Mdi/(K1d+Mdi)); #activation of CYCDCDK4/6(i) or Mdi
    vC[25-1]=kc1*Md*p27; #CYCDCDK4/6(a) or Md binding to p27
    vC[26-1]=kc2*Mdp27; #dissociation of CYCDCDK4/6p27 coplex or Mdp27 to Md
    #vC[27-1]=kce*E2F*(Ki9/(Ki9+pRB))*(Ki10/(Ki10+pRBp)); #CYCE synthesis ##Keep like this for now.
    vC[28-1]=kcom2*Ce*(cdk2tot-(Mei+Me+Mep27+Mep21+Mai+Ma+Map27+Map21)); #CYCE going into complex with cdk2
    vC[29-1]=kdecom2*Mei; #dissociation of complex CYCECDK2(i)
    vC[30-1]=Vde*(Skp2/(Kdceskp2+Skp2))*(Ce/(Kde+Ce)); #CYCE degradation
    vC[31-1]=Vm2e*(Wee1+ib2)*(Me/(K2e+Me)); #inactivation of CYCECDK2
    vC[32-1]=Vm1e*Pe*(Mei/(K1e+Mei)); #activation of CYCECDK2
    vC[33-1]=kc3*Me*p27; #CYCECDK2 binding to p27
    vC[34-1]=kc4*Mep27; #dissociation of CYCECDK2p27
    #vC[35-1]=vsskp2; #synthesis of SKP2
    vC[36-1]=Vdskp2*(Skp2/(Kdskp2+Skp2))*(Cdh1a/(Kcdh1+Cdh1a)); #max SKP2 degradation
    vC[37-1]=kddskp2*Skp2; #non-specific SKP2 degradation
    #vC[38-1]=vspei; #synthesis of inactivated CDC25(i) or pei
    vC[39-1]=V6e*(xe1+xe2*Chk1)*(Pe/(K6e+Pe)); #Pei inactivation
    vC[40-1]=Vm5e*(Me+ae)*(Pei/(K5e+Pei)); #Pei activation
    vC[41-1]=kdpei*Pei; #Pei degradation
    vC[42-1]=kdpe*Pe; #Pe degradation
    #vC[43-1]=kca*E2F*(Ki11/(Ki11+pRB))*(Ki12/(Ki12+pRBp)); #CYCA synthesis induced by E2F inhibited by pRb and pRbp ##Keep like this for now.
    vC[44-1]=kcom3*Ca*(cdk2tot-(Mei+Me+Mep27+Mep21+Mai+Ma+Map27+Map21)); #CYCA binding to CDK2 making CYCACDK2(i) Mai
    vC[45-1]=kdecom3*Mai; #dissociation of Mai complex
    vC[46-1]=Vda*(Ca/(Kda+Ca))*(Cdc20a/(Kacdc20+Cdc20a)); #CYCA degradation induced by Cdc20(a)
    vC[47-1]=kdda*Ca; #non specific CYCA degradation
    vC[48-1]=Vm2a*(Wee1+ib3)*(Ma/(K2a+Ma)); #inactivation of CYCACDK2(a) or Ma complex
    vC[49-1]=Vm1a*Pa*(Mai/(K1a+Mai)); #activation of CYCACDK2(i) or Mai complex
    vC[50-1]=kc5*Ma*p27; #Ma binding to P27 making CYCACDK2p27
    vC[51-1]=kc6*Map27; #dissociation of Map27 to Map and p27
    vC[52-1]=V1p27*Me*(p27/(p27+K1p27)); #inactivation of p27 by CYCECDK2(a)
    vC[53-1]=V2p27*(p27p/(p27p+K2p27)); #activation of p27
    vC[54-1]=Vdp27p*(Skp2/(Skp2+Kdp27skp2))*(p27p/(p27p+Kdp27p)); #max p27p degradation
    vC[55-1]=kddp27p*p27p; #non specific p27p degradation
    vC[56-1]=V2cdh1*(Cdh1a/(K2cdh1+Cdh1a))*(Ma+Mb); #inactivation of Cdh1(a)
    vC[57-1]=V1cdh1*(Cdh1i/(K1cdh1+Cdh1i)); #activation of Cdh1(1)
    vC[58-1]=kdcdh1i*Cdh1i; #inactive Cdh1(i) degradation
    #vC[59-1]=vscdh1a; #synthesis of Cdh1(a)
    vC[60-1]=kdcdh1a*Cdh1a; #Cdh1(a) degradation
    #vC[61-1]=vspai; #CDC25(i) Pai synthesis
    vC[62-1]=V6a*(xa1+xa2*Chk1)*(Pa/(K6a+Pa)); #Pa Cdc25(a) inactivation to Pai
    vC[63-1]=Vm5a*(Ma+aa)*(Pai/(K5a+Pai)); #Pai activation to Pa
    vC[64-1]=kdpai*Pai; #Pai degradation
    vC[65-1]=kdpa*Pa; #Pa degradation
    #vC[66-1]=vcb; #CYCB synthesis
    vC[67-1]=kcom4*Cb*(cdk1tot-(Mbi+Mb+Mbp27+Mbp21)); #CYCB forming CYCBCDK1(i) complex
    vC[68-1]=kdecom4*Mbi; #dissociation of CYCBCDK1(i) complex
    vC[69-1]=Vdb*(Cb/(Kdb+Cb))*((Cdc20a/(Kdbcdc20+Cdc20a))+(Cdh1a/(Kdbcdh1+Cdh1a))); #max CYCB degradation induced by Cdc20(a)
    vC[70-1]=kddb*Cb; #non specific CYCB degradation
    vC[71-1]=Vm2b*(Wee1+ib1)*(Mb/(K2b+Mb)); #Mb inactivation to Mbi
    vC[72-1]=Vm1b*Pb*(Mbi/(K1b+Mbi)); #Mbi becoming active
    vC[73-1]=kc7*Mb*p27; #Mb (active CYCBCDK1) binding to p27
    vC[74-1]=kc8*Mbp27; #dissociation of Mb and p27
    #vC[75-1]=vscdc20i; #cdc20(i) synthesis
    vC[76-1]=Vm3b*Mb*(Cdc20i/(K3b+Cdc20i)); #activation of cdc20(i) through phosphorylation by CYCBCDK1
    vC[77-1]=Vm4b*(Cdc20a/(K4b+Cdc20a)); #cdc20(a) inactivation to cdc20(i)
    vC[78-1]=kdcdc20i*Cdc20i; #cdc20i degradation
    vC[79-1]=kdcdc20a*Cdc20a; #degradation of cdc20a
    #vC[80-1]=vspbi; #synthesis of inactive CDC25 Pbi
    vC[81-1]=V6b*(xb1+xb2*Chk1)*(Pb/(K6b+Pb)); #inactivation of CDC25 (Pb)
    vC[82-1]=Vm5b*(Mb+ab)*(Pbi/(K5b+Pbi)); #activation of CDC25(i) (Pbi)
    vC[83-1]=kdpbi*Pbi; #degradation of inactive CDC25 (Pbi)
    vC[84-1]=kdpb*Pb; #degradation of active CDC25 (Pb)
    #vC[85-1]=vswee1; #Wee1 synthesis
    vC[86-1]=Vm7b*(Mb+ib)*(Wee1/(K7b+Wee1)); #wee1 inactivation through phosphorylation due to CYCBCDK1
    vC[87-1]=Vm8b*(Wee1p/(K8b+Wee1p)); #wee1p(wee1(i)) activation through dephosphorylation
    vC[88-1]=kdWee1*Wee1; #wee1 degradation
    vC[89-1]=kdWee1p*Wee1p; #wee1p degradation
    vC[90-1]=V1chk*ATRac*((Chk1tot-Chk1)/(K1chk+(Chk1tot-Chk1))); #activation of Chk1 through phosphorylation by kinase ATR
    vC[91-1]=V2chk*(Chk1/(K2chk+Chk1)); #Chk1 inactivation through dephosphorylation
    vC[92-1]=kdde*Ce;#non-specific cycE degradation
    #vC[93-1]=vs1p27; #+ basal p27 synthesis
    #vC[94-1]=vs2p27*E2F*(Ki13/(Ki13+pRB))*(Ki14/(Ki14+pRBp)); #+ synthesis of p27 induced by E2F, inhibited by pRB and pRBp ##Keep like this for now.
    vC[95-1]=kddp27*p27; #- non-specific p27 degradation.
    vC[96-1]=kc9*Md*p21; #CYCDCDK4/6(a) or Md binding to p21
    vC[97-1]=kc10*Mdp21; #dissociation of CYCDCDK4/6p21 coplex or Mdp21 to Md
    vC[98-1]=kc11*Me*p21; #CYCECDK2 binding to p21
    vC[99-1]=kc12*Mep21; #dissociation of CYCECDK2p21
    vC[100-1]=kc13*Ma*p21; #Ma binding to P21 making CYCACDK2p21
    vC[101-1]=kc14*Map21; #dissociation of Map21 to Map and p21
    vC[102-1]=kc15*Mb*p21; #Mb (active CYCBCDK1) binding to p21
    vC[103-1]=kc16*Mbp21; #dissociation of Mb and p21


    vC[103]=kddp21*p21; #-non-specific p21 degradation
    vC[0:104]=vC[0:104]*eps;






    # ## vA **
    vA = np.zeros(shape=(87))

    # NOTE
    vA[0]=kA[0]*L*R *Vc[0]/Ve[0];




    vA[2-1]=kA[2-1]*L_R;
    vA[3-1]=kA[3-1]*L_R;
    vA[4-1]=kA[4-1]*Ractive*flip;
    vA[5-1]=kA[5-1]*Ractive_flip;
    vA[6-1]=kA[6-1]*Ractive*pC8;
    vA[7-1]=kA[7-1]*Ractive_pC8;
    vA[8-1]=kA[8-1]*Ractive_pC8;
    vA[9-1]=kA[9-1]*C8*Bar;
    vA[10-1]=kA[10-1]*C8_Bar;
    vA[11-1]=kA[11-1]*C8*pC3;
    vA[12-1]=kA[12-1]*C8_pC3;
    vA[13-1]=kA[13-1]*C8_pC3;
    vA[14-1]=kA[14-1]*C3*pC6;
    vA[15-1]=kA[15-1]*C3_pC6;
    vA[16-1]=kA[16-1]*C3_pC6;
    vA[17-1]=kA[17-1]*pC8*C6;
    vA[18-1]=kA[18-1]*C6_C8;
    vA[19-1]=kA[19-1]*C6_C8;
    vA[20-1]=kA[20-1]*C3*XIAP;
    vA[21-1]=kA[21-1]*C3_XIAP;
    vA[22-1]=kA[22-1]*C3_XIAP;
    vA[23-1]=kA[23-1]*C3*PARP;
    vA[24-1]=kA[24-1]*C3_PARP;
    vA[25-1]=kA[25-1]*C3_PARP;
    vA[26-1]=kA[26-1]*C8*Bid;
    vA[27-1]=kA[27-1]*C8_Bid;
    vA[28-1]=kA[28-1]*C8_Bid;
    vA[29-1]=kA[29-1]*tBid*Bcl2c;
    vA[30-1]=kA[30-1]*tBid_Bcl2c;
    vA[31-1]=kA[31-1]*tBid*Bax;
    vA[32-1]=kA[32-1]*tBid_Bax;
    vA[33-1]=kA[33-1]*tBid_Bax;
    vA[34-1]=kA[34-1]*Baxactive;
    vA[35-1]=kA[35-1]*Baxm;
    vA[36-1]=kA[36-1]*Baxm*Bcl2;
    vA[37-1]=kA[37-1]*Baxm_Bcl2;
    vA[38-1]=kA[38-1]*Baxm**2;
    vA[39-1]=kA[39-1]*Bax2;
    vA[40-1]=kA[40-1]*Bcl2*Bax2;
    vA[41-1]=kA[41-1]*Bax2_Bcl2;
    vA[42-1]=kA[42-1]*Bax2**2;
    vA[43-1]=kA[43-1]*Bax4;
    vA[44-1]=kA[44-1]*Bcl2*Bax4;
    vA[45-1]=kA[45-1]*Bax4_Bcl2;
    vA[46-1]=kA[46-1]*M*Bax4;
    vA[47-1]=kA[47-1]*Bax4_M;
    vA[48-1]=kA[48-1]*Bax4_M;
    vA[49-1]=kA[49-1]*Mactive*CytoCm;
    vA[50-1]=kA[50-1]*Mactive_CytoCm;
    vA[51-1]=kA[51-1]*Mactive_CytoCm;
    vA[52-1]=kA[52-1]*Mactive*Smacm;
    vA[53-1]=kA[53-1]*Mactive_Smacm;
    vA[54-1]=kA[54-1]*Mactive_Smacm;
    vA[55-1]=kA[55-1]*CytoCr;
    vA[56-1]=kA[56-1]*CytoC;
    vA[57-1]=kA[57-1]*CytoC*Apaf;
    vA[58-1]=kA[58-1]*CytoC_Apaf;
    vA[59-1]=kA[59-1]*CytoC_Apaf;
    vA[60-1]=kA[60-1]*Apafactive*pC9;
    vA[61-1]=kA[61-1]*Apop;
    vA[62-1]=kA[62-1]*pC3*Apop;
    vA[63-1]=kA[63-1]*Apop_C3;
    vA[64-1]=kA[64-1]*Apop_C3;
    vA[65-1]=kA[65-1]*Smacr;
    vA[66-1]=kA[66-1]*Smac;
    vA[67-1]=kA[67-1]*XIAP*Apop;
    vA[68-1]=kA[68-1]*Apop_XIAP;
    vA[69-1]=kA[69-1]*XIAP*Smac;
    vA[70-1]=kA[70-1]*Smac_XIAP;
    vA[71-1]=kA[71-1]*Bcl2c*BAD;
    vA[72-1]=kA[72-1]*Bcl2c_BAD;
    vA[73-1]=kA[73-1]*Bcl2c*PUMA;
    vA[74-1]=kA[74-1]*Bcl2c_PUMA;
    vA[75-1]=kA[75-1]*Bcl2c*NOXA;
    vA[76-1]=kA[76-1]*Bcl2c_NOXA;


    vA[77-1]=kA[77-1]*BIM*Bax;

    vA[78-1]=kA[78-1]*BIM_Bax;
    vA[79-1]=kA[79-1]*BIM_Bax;
    vA[80-1]=kA[80-1]*Bcl2c*BIM;
    vA[81-1]=kA[81-1]*Bcl2c_BIM;
    vA[82-1]=kA[82-1]*Mactive;
    vA[83-1]=kA[83-1]*Smacr;
    vA[84-1]=kA[84-1]*CytoCr;
    vA[85-1]=kA[85-1]*Bcl2c;
    vA[86-1]=kA[86-1]*Bcl2;
    vA[87-1]=kA[87-1]*pC8;



    # ## vR **
    vR = np.zeros(shape=(158))
    # NOTE
    vR[1-1]=kR[1-1]*E1*E *Vc[0]/Ve[0];

    vR[2-1]=kR[2-1]*EE1 ;
    vR[3-1]=kR[3-1]*EE1*E2 ;
    vR[4-1]=kR[4-1]*EE1E2 ;
    vR[5-1]=kR[5-1]*EE1*E1 ;
    vR[6-1]=kR[6-1]*EE1E1 ;
    vR[7-1]=kR[7-1]*EE1E1*E *Vc[0]/Ve[0];
    vR[8-1]=2*kR[8-1]*EE1EE1 ;
    vR[9-1]=kR[9-1]*EE1EE1 ;
    vR[10-1]=kR[10-1]*EE1*EE1 ;
    vR[11-1]=kR[11-1]*EE1*E3 ;
    vR[12-1]=kR[12-1]*EE1E3 ;
    vR[13-1]=kR[13-1]*EE1E3*H *Vc[0]/Ve[0];
    vR[14-1]=kR[14-1]*EE1HE3 ;
    vR[15-1]=kR[15-1]*EE1HE3 ;
    vR[16-1]=kR[16-1]*EE1*HE3 ;
    vR[17-1]=kR[17-1]*EE1*Ev3 ;
    vR[18-1]=kR[18-1]*EE1Ev3 ;
    vR[19-1]=kR[19-1]*EE1*E4 ;
    vR[20-1]=kR[20-1]*EE1E4 ;
    vR[21-1]=kR[21-1]*EE1E4*H *Vc[0]/Ve[0];
    vR[22-1]=kR[22-1]*EE1HE4 ;
    vR[23-1]=kR[23-1]*EE1HE4 ;
    vR[24-1]=kR[24-1]*EE1*HE4 ;
    vR[25-1]=kR[25-1]*H*E3 *Vc[0]/Ve[0];
    vR[26-1]=kR[26-1]*HE3 ;
    vR[27-1]=kR[27-1]*HE3*E2 ;
    vR[28-1]=kR[28-1]*E2HE3 ;
    vR[29-1]=kR[29-1]*HE3*E1 ;
    vR[30-1]=kR[30-1]*E1HE3 ;
    vR[31-1]=kR[31-1]*E1HE3*E *Vc[0]/Ve[0];
    vR[32-1]=kR[32-1]*EE1HE3 ;
    vR[33-1]=kR[33-1]*HE3*E3 ;
    vR[34-1]=kR[34-1]*HE3E3 ;
    vR[35-1]=kR[35-1]*HE3E3*H *Vc[0]/Ve[0];
    vR[36-1]=2*kR[36-1]*HE3HE3 ;
    vR[37-1]=kR[37-1]*HE3HE3 ;
    vR[38-1]=kR[38-1]*HE3*HE3 ;
    vR[39-1]=kR[39-1]*HE3*Ev3 ;
    vR[40-1]=kR[40-1]*HE3Ev3 ;
    vR[41-1]=kR[41-1]*HE3*E4 ;
    vR[42-1]=kR[42-1]*HE3E4 ;
    vR[43-1]=kR[43-1]*HE3E4*H *Vc[0]/Ve[0];
    vR[44-1]=kR[44-1]*HE3HE4 ;
    vR[45-1]=kR[45-1]*HE3HE4 ;
    vR[46-1]=kR[46-1]*HE3*HE4 ;
    vR[47-1]=kR[47-1]*H*E4 *Vc[0]/Ve[0];
    vR[48-1]=kR[48-1]*HE4 ;
    vR[49-1]=kR[49-1]*HE4*E2 ;
    vR[50-1]=kR[50-1]*E2HE4 ;
    vR[51-1]=kR[51-1]*HE4*E1 ;
    vR[52-1]=kR[52-1]*E1HE4 ;
    vR[53-1]=kR[53-1]*E1HE4*E *Vc[0]/Ve[0];
    vR[54-1]=kR[54-1]*EE1HE4 ;
    vR[55-1]=kR[55-1]*HE4*E3 ;
    vR[56-1]=kR[56-1]*E3HE4 ;
    vR[57-1]=kR[57-1]*E3HE4*H *Vc[0]/Ve[0];
    vR[58-1]=kR[58-1]*HE3HE4 ;
    vR[59-1]=kR[59-1]*HE4*Ev3 ;
    vR[60-1]=kR[60-1]*HE4Ev3 ;
    vR[61-1]=kR[61-1]*HE4*E4 ;
    vR[62-1]=kR[62-1]*HE4E4 ;
    vR[63-1]=kR[63-1]*HE4E4*H *Vc[0]/Ve[0];
    vR[64-1]=2*kR[64-1]*HE4HE4 ;
    vR[65-1]=kR[65-1]*HE4HE4 ;
    vR[66-1]=kR[66-1]*HE4*HE4 ;
    vR[67-1]=kR[67-1]*E1*ppERK ;
    vR[68-1]=kR[68-1]*pE1 ;
    vR[69-1]=kR[69-1]*E2*ppERK ;
    vR[70-1]=kR[70-1]*pE2 ;
    vR[71-1]=kR[71-1]*E4*ppERK ;
    vR[72-1]=kR[72-1]*pE4 ;
    vR[73-1]=kR[73-1]*Met*HGF *Vc[0]/Ve[0];
    vR[74-1]=kR[74-1]*HGF_Met ;
    vR[75-1]=kR[75-1]*HGF_Met*Met ;
    vR[76-1]=kR[76-1]*HGF_Met_Met ;
    vR[77-1]=kR[77-1]*HGF_Met_Met*HGF *Vc[0]/Ve[0];
    vR[78-1]=2*kR[78-1]*HGF_Met_HGF_Met ;
    vR[79-1]=kR[79-1]*HGF_Met_HGF_Met ;
    vR[80-1]=kR[80-1]*HGF_Met*HGF_Met ;
    vR[81-1]=kR[81-1]*Pr*P *Vc[0]/Ve[0];
    vR[82-1]=kR[82-1]*PPr ;
    vR[83-1]=kR[83-1]*PPr*PPr ;
    vR[84-1]=kR[84-1]*PPrPPr ;
    vR[85-1]=2*kR[85-1]*PPrPPr ;
    vR[86-1]=kR[86-1]*PPrPr ;
    vR[87-1]=kR[87-1]*Fr*F *Vc[0]/Ve[0];
    vR[88-1]=kR[88-1]*FFr;
    vR[89-1]=kR[89-1]*FFr*FFr;
    vR[90-1]=kR[90-1]*FFrFFr;
    vR[91-1]=2*kR[91-1]*FFrFFr;
    vR[92-1]=kR[92-1]*F*FFrFr *Vc[0]/Ve[0];
    vR[93-1]=kR[93-1]*FFrFr;
    vR[94-1]=kR[94-1]*Fr*FFr;
    vR[95-1]=kR[95-1]*Ir*Ir;
    vR[96-1]=kR[96-1]*IrIr;
    vR[97-1]=kR[97-1]*Isr*Isr;
    vR[98-1]=kR[98-1]*Isr_Isr;
    vR[99-1]=kR[99-1]*E1_ppERK;
    vR[100-1]=kR[100-1]*E1_ppERK;
    vR[101-1]=kR[101-1]*E2_ppERK;
    vR[102-1]=kR[102-1]*E2_ppERK;
    vR[103-1]=kR[103-1]*E4_ppERK;
    vR[104-1]=kR[104-1]*E4_ppERK;
    vR[105-1]=kR[105-1]*E1*E1;
    vR[106-1]=kR[106-1]*E1E1;
    vR[107-1]=kR[107-1]*E1*E2;
    vR[108-1]=kR[108-1]*E1E2;
    vR[109-1]=kR[109-1]*E1*E3;
    vR[110-1]=kR[110-1]*E1E3;
    vR[111-1]=kR[111-1]*E1*E4;
    vR[112-1]=kR[112-1]*E1E4;
    vR[113-1]=kR[113-1]*E2*E2;
    vR[114-1]=kR[114-1]*E2E2;
    vR[115-1]=kR[115-1]*E2*E3;
    vR[116-1]=kR[116-1]*E2E3;
    vR[117-1]=kR[117-1]*E2*E4;
    vR[118-1]=kR[118-1]*E2E4;
    vR[119-1]=kR[119-1]*E3*E4;
    vR[120-1]=kR[120-1]*E3E4;
    vR[121-1]=kR[121-1]*E4*E4;
    vR[122-1]=kR[122-1]*E4E4;
    vR[123-1]=2*kR[123-1]*E*E1E1 *Vc[0]/Ve[0];
    vR[124-1]=kR[124-1]*EE1E1;
    vR[125-1]=kR[125-1]*E*E1E2 *Vc[0]/Ve[0];
    vR[126-1]=kR[126-1]*EE1E2;
    vR[127-1]=kR[127-1]*E*E1E3 *Vc[0]/Ve[0];
    vR[128-1]=kR[128-1]*EE1E3;
    vR[129-1]=kR[129-1]*H*E1E3 *Vc[0]/Ve[0];
    vR[130-1]=kR[130-1]*E1HE3;
    vR[131-1]=kR[131-1]*E*E1E4 *Vc[0]/Ve[0];
    vR[132-1]=kR[132-1]*EE1E4;
    vR[133-1]=kR[133-1]*H*E1E4 *Vc[0]/Ve[0];
    vR[134-1]=kR[134-1]*E1HE4;
    vR[135-1]=kR[135-1]*H*E2E3 *Vc[0]/Ve[0];
    vR[136-1]=kR[136-1]*E2HE3;
    vR[137-1]=kR[137-1]*H*E2E4 *Vc[0]/Ve[0];
    vR[138-1]=kR[138-1]*E2HE4;
    vR[139-1]=2*kR[139-1]*H*E3E4 *Vc[0]/Ve[0];
    vR[140-1]=kR[140-1]*E3HE4;
    vR[141-1]=2*kR[141-1]*H*E4E4 *Vc[0]/Ve[0];
    vR[142-1]=kR[142-1]*HE4E4;
    vR[143-1]=kR[143-1]*Met*Met;
    vR[144-1]=kR[144-1]*Met_Met;
    vR[145-1]=2*kR[145-1]*HGF*Met_Met;
    vR[146-1]=kR[146-1]*HGF_Met_Met;
    vR[147-1]=kR[147-1]*Fr*Fr;
    vR[148-1]=kR[148-1]*FrFr;
    vR[149-1]=2*kR[149-1]*F*FrFr;
    vR[150-1]=kR[150-1]*FFrFr;
    vR[151-1]=kR[151-1]*IrIr*I *Vc[0]/Ve[0];
    vR[152-1]=kR[152-1]*IIrIr;
    vR[153-1]=kR[153-1]*IIrIr*I *Vc[0]/Ve[0];
    vR[154-1]=kR[154-1]*IIrIrI;
    vR[155-1]=kR[155-1]*Isr_Isr*IN *Vc[0]/Ve[0];
    vR[156-1]=kR[156-1]*IN_Isr_Isr;
    vR[157-1]=kR[157-1]*IN_Isr_Isr*IN *Vc[0]/Ve[0];
    vR[158-1]=kR[158-1]*IN_Isr_Isr_IN;


    # ## vRP **
    fac=1;

    ps_G2_SOS= np.array([9,10,10,10,8,8,11,11,7,8,8,9,9,10,11,11,9,12,12,2,2,1,1,8,8,5,7,5,7])*fac;
    ps_PI3K1= np.array([4,2,2,2,10,10,4,4,12,10,10,12,12,6,4,4,12,6,6,6,6,6,6,14,16,10.5,14.5,10.5,14.5])*fac;
    ps_PI3K2=ps_PI3K1;
    ps_PLCg= np.array([4,4,4,4,3,3,3,3,3,3,3,2,2,3,3,3,2,2,2,4,4,5,5,2,6,1.5,3.5,1.5,3.5])*fac;



    # # Equations
    vRP1 = np.multiply(kRP1,SCD); # Phosphorylation
    vRP2 = np.multiply(kRP2,pSCD); # Dephosphorylation


    vRP3 = np.multiply(kRP3,SCD)*Sp; # Binding Spouty

    vRP4 = np.multiply(kRP4,Sp_SCD); # Dissociation Sprouty
    kmCblint=2;
    vRP5 = np.multiply(kRP5,(pSCD/(kmCblint+pSCD)))*Cbl + np.multiply(kRP5[8],pSCD); # Internalization
    vRP6 = np.multiply(kRP6,pSCDint); # Dephosphorylation
    vRP7 = np.multiply(kRP7,SCDint); # Phosphorylation
    vRP8 = np.multiply(kRP8,SCDint); # Recycling
    vRP9 = np.multiply(np.multiply(ps_G2_SOS,kRP9),pSCDint_bind)*G2_SOS; # Int binding G2-SOS
    vRP10 = np.multiply(kRP10,pSCDint_G2_SOS); # Int dissociating from G2-SOS
    vRP11 = np.multiply(np.multiply(np.multiply(ps_G2_SOS,kRP11),pSCD_bind),G2_SOS); #pSCD binding G2-SOS
    vRP12 = np.multiply(kRP12,pSCD_G2_SOS); #pSCD dissociating G2-SOS
    vRP13 = np.multiply(np.multiply(np.multiply(ps_PLCg,kRP13),pSCD_bind),PLCg);
    vRP14 = np.multiply(kRP14,pSCD_PLCg);
    vRP15 = np.multiply(np.multiply(np.multiply(ps_PI3K1,kRP15),pSCD_bind),PI3K1);
    vRP16 = np.multiply(kRP16,pSCD_PI3K1);
    vRP17 = np.multiply(np.multiply(np.multiply(ps_PI3K2,kRP17),pSCD_bind),PI3K2);
    vRP18 = np.multiply(kRP18,pSCD_PI3K2);
    vRP19 = np.multiply(np.multiply(kRP19,pSCDint_G2_SOS),RasD); #Binding to RasDint
    vRP20 = np.multiply(kRP20,pSCDint_G2_SOS_RasD); #Dissociation
    vRP21 = np.multiply(kRP21,pSCDint_G2_SOS_RasD); #Making product
    vRP22 = np.multiply(np.multiply(kRP22,pSCD_G2_SOS),RasD); #Binding to RasD
    vRP23 = np.multiply(kRP23,pSCD_G2_SOS_RasD); #Dissociation
    vRP24 = np.multiply(kRP24,pSCD_G2_SOS_RasD); #Making product
    vRP25 = np.multiply(np.multiply(kRP25,pSCD_PLCg),PIP2); #Binding to PIP2
    vRP26 = np.multiply(kRP26,pSCD_PLCg_PIP2); #Dissociation
    vRP27 = np.multiply(kRP27,pSCD_PLCg_PIP2); #Making product
    vRP28 = np.multiply(np.multiply(kRP28,pSCD_PI3K1),PIP2); #Binding to PIP2
    vRP29 = np.multiply(kRP29,pSCD_PI3K1_PIP2); #Dissociation
    vRP30 = np.multiply(kRP30,pSCD_PI3K1_PIP2); #Making product
    vRP31 = np.multiply(np.multiply(kRP31,pSCD_PI3K2),PIP); #Binding to PIP2
    vRP32 = np.multiply(kRP32,pSCD_PI3K2_PIP); #Dissociation
    vRP33 = np.multiply(kRP33,pSCD_PI3K2_PIP); #Making product



    # # IGFR and INSR binding IRS
    ps_IRS=2*4;
    vRP34 = np.zeros(shape=(16))
    vRP34[0]=ps_IRS * np.multiply(np.multiply(np.multiply(fac,kRP34[0]),pIIrIr),IRS);
    vRP34[1]=np.multiply(kRP34[1],pIIrIr_IRS);
    vRP34[2]=ps_IRS * np.multiply(np.multiply(np.multiply(fac,kRP34[2]),pIN_Isr_Isr),IRS);
    vRP34[3]=np.multiply(kRP34[3],pIN_Isr_Isr_IRS);


    vRP34[4]=ps_IRS * np.multiply(np.multiply(np.multiply(fac,kRP34[4]),pIIrIrI),IRS);
    vRP34[5]=np.multiply(kRP34[5],pIIrIrI_IRS);
    vRP34[6]= ps_IRS * np.multiply(np.multiply(np.multiply(fac,kRP34[6]),pIN_Isr_Isr_IN),IRS);
    vRP34[7]=np.multiply(kRP34[7],pIN_Isr_Isr_IN_IRS);

    vRP34[8]= ps_IRS * np.multiply(np.multiply(np.multiply(fac,kRP34[8]),pIIrIr_int),IRS);
    vRP34[9]=np.multiply(kRP34[9],pIIrIr_int_IRS);
    vRP34[10]=ps_IRS * np.multiply(np.multiply(np.multiply(fac,kRP34[10]),pIN_Isr_Isr_int),IRS);
    vRP34[11]= np.multiply(kRP34[11],pIN_Isr_Isr_int_IRS);
    vRP34[12]=ps_IRS * np.multiply(np.multiply(np.multiply(fac,kRP34[12]),pIIrIrI_int),IRS);
    vRP34[13]=np.multiply(kRP34[13],pIIrIrI_int_IRS);
    vRP34[14]=ps_IRS * np.multiply(np.multiply(np.multiply(fac,kRP34[14]),pIN_Isr_Isr_IN_int),IRS);
    vRP34[15]=np.multiply(kRP34[15],pIN_Isr_Isr_IN_int_IRS);






    # ## vP **
    vP = np.zeros(shape=(190))
    vP[1-1]=kP[1-1]*RasT*CRaf;
    vP[2-1]=kP[2-1]*RasT_CRaf;
    vP[3-1]=kP[3-1]*RasT*BRaf;
    vP[4-1]=kP[4-1]*RasT_BRaf;
    vP[5-1]=kP[5-1]*RasT_CRaf*RasT_CRaf;
    vP[6-1]=kP[6-1]*RasT_CRaf_CRaf;
    vP[7-1]=kP[7-1]*RasT_BRaf*RasT_BRaf;
    vP[8-1]=kP[8-1]*RasT_BRaf_BRaf;
    vP[9-1]=kP[9-1]*RasT_CRaf*RasT_BRaf;
    vP[10-1]=kP[10-1]*RasT_CRaf_BRaf;
    vP[11-1]=0;#kP[11-1]*RasT_BRaf*CRaf;
    vP[12-1]=0;#kP[12-1]*RasT_CRaf_BRaf;
    vP[13-1]=kP[13-1]*MEK*RasT_CRaf_CRaf;
    vP[14-1]=kP[14-1]*MEK_RasT_CRaf_CRaf;
    vP[15-1]=kP[15-1]*MEK_RasT_CRaf_CRaf;
    vP[16-1]=kP[16-1]*pMEK*RasT_CRaf_CRaf;
    vP[17-1]=kP[17-1]*pMEK_RasT_CRaf_CRaf;
    vP[18-1]=kP[18-1]*pMEK_RasT_CRaf_CRaf;
    vP[19-1]=kP[19-1]*MEK*RasT_BRaf_BRaf;
    vP[20-1]=kP[20-1]*MEK_RasT_BRaf_BRaf;
    vP[21-1]=kP[21-1]*MEK_RasT_BRaf_BRaf;
    vP[22-1]=kP[22-1]*pMEK*RasT_BRaf_BRaf;
    vP[23-1]=kP[23-1]*pMEK_RasT_BRaf_BRaf;
    vP[24-1]=kP[24-1]*pMEK_RasT_BRaf_BRaf;
    vP[25-1]=kP[25-1]*MEK*RasT_CRaf_BRaf;
    vP[26-1]=kP[26-1]*MEK_RasT_CRaf_BRaf;
    vP[27-1]=kP[27-1]*MEK_RasT_CRaf_BRaf;
    vP[28-1]=kP[28-1]*pMEK*RasT_CRaf_BRaf;
    vP[29-1]=kP[29-1]*pMEK_RasT_CRaf_BRaf;
    vP[30-1]=kP[30-1]*pMEK_RasT_CRaf_BRaf;
    vP[31-1]=kP[31-1]*pMEK;
    vP[32-1]=kP[32-1]*ppMEK;
    vP[33-1]=kP[33-1]*ERK*ppMEK;
    vP[34-1]=kP[34-1]*ERK_ppMEK;
    vP[35-1]=kP[35-1]*ERK_ppMEK;
    vP[36-1]=kP[36-1]*pERK*ppMEK;
    vP[37-1]=kP[37-1]*pERK_ppMEK;
    vP[38-1]=kP[38-1]*pERK_ppMEK;
    vP[39-1]=kP[39-1]*ppERKnuc*MKP1;
    vP[40-1]=kP[40-1]*ppERKnuc_MKP1;
    vP[41-1]=kP[41-1]*ppERKnuc_MKP1;
    vP[42-1]=kP[42-1]*pMKP1;
    vP[43-1]=kP[43-1]*pcFos;
    vP[44-1]=kP[44-1]*pTSC2;
    vP[45-1]=kP[45-1]*pRSKnuc;
    vP[46-1]=kP[46-1]*G2_SOS*ppERK;
    vP[47-1]=kP[47-1]*G2_SOS_ppERK;
    vP[48-1]=kP[48-1]*G2_SOS_ppERK;
    vP[49-1]=kP[49-1]*G2_pSOS;
    vP[50-1]=kP[50-1]*CRaf*ppERK;
    vP[51-1]=kP[51-1]*CRaf_ppERK;
    vP[52-1]=kP[52-1]*CRaf_ppERK;
    vP[53-1]=kP[53-1]*pCRaf;
    vP[54-1]=kP[54-1]*RasD*DAG_GRP;
    vP[55-1]=kP[55-1]*RasD_DAG_GRP;
    vP[56-1]=kP[56-1]*RasD_DAG_GRP;
    vP[57-1]=kP[57-1]*RasT*NF1;
    vP[58-1]=kP[58-1]*RasT_NF1;
    vP[59-1]=kP[59-1]*RasT_NF1;
    vP[60-1]=kP[60-1]*NF1*ppERK;
    vP[61-1]=kP[61-1]*NF1_ppERK;
    vP[62-1]=kP[62-1]*NF1_ppERK;
    vP[63-1]=kP[63-1]*pNF1;
    vP[64-1]=kP[64-1]*pERK*MKP3;
    vP[65-1]=kP[65-1]*pERK_MKP3;
    vP[66-1]=kP[66-1]*pERK_MKP3;
    vP[67-1]=kP[67-1]*ppERK*MKP3;
    vP[68-1]=kP[68-1]*ppERK_MKP3;
    vP[69-1]=kP[69-1]*ppERK_MKP3;
    vP[70-1]=kP[70-1]*RSK*ppERK;
    vP[71-1]=kP[71-1]*RSK_ppERK;
    vP[72-1]=kP[72-1]*RSK_ppERK;
    vP[73-1]=kP[73-1]*pRSK;
    vP[74-1]=kP[74-1]*ppERK;
    vP[75-1]=kP[75-1]*ERKnuc;
    vP[76-1]=kP[76-1]*ppERKnuc*pMKP1;
    vP[77-1]=kP[77-1]*ppERKnuc_pMKP1 ;
    vP[78-1]=kP[78-1]*ppERKnuc_pMKP1 ;
    vP[79-1]=kP[79-1]*ERKnuc;
    vP[80-1]=kP[80-1]*pRSK;
    vP[81-1]=kP[81-1]*MKP1*pRSKnuc;
    vP[82-1]=kP[82-1]*pRSKnuc_MKP1;
    vP[83-1]=kP[83-1]*pRSKnuc_MKP1;
    vP[84-1]=kP[84-1]*MKP1*ppERKnuc;
    vP[85-1]=kP[85-1]*ppERKnuc_MKP1;
    vP[86-1]=kP[86-1]*ppERKnuc_MKP1;
    vP[87-1]=kP[87-1]*cFos*pRSKnuc;
    vP[88-1]=kP[88-1]*cFos_pRSKnuc;
    vP[89-1]=kP[89-1]*cFos_pRSKnuc;
    vP[90-1]=kP[90-1]*cFos*ppERKnuc;
    vP[91-1]=kP[91-1]*cFos_ppERKnuc;
    vP[92-1]=kP[92-1]*cFos_ppERKnuc;
    vP[93-1]=kP[93-1]*pcFos*cJun;
    vP[94-1]=kP[94-1]*pcFos_cJun;
    vP[95-1]=kP[95-1]*GRP*DAG;
    vP[96-1]=kP[96-1]*DAG_GRP;
    vP[97-1]=kP[97-1]*DAG*PKC;
    vP[98-1]=kP[98-1]*DAG_PKC;
    vP[99-1]=kP[99-1]*RKIP*DAG_PKC;
    vP[100-1]=kP[100-1]*RKIP_DAG_PKC;
    vP[101-1]=kP[101-1]*RKIP_DAG_PKC;
    vP[102-1]=kP[102-1]*pRKIP;
    vP[103-1]=kP[103-1]*RKIP*CRaf;
    vP[104-1]=kP[104-1]*RKIP_CRaf;
    vP[105-1]=kP[105-1]*PIP3*PTEN;
    vP[106-1]=kP[106-1]*PIP3_PTEN;
    vP[107-1]=kP[107-1]*PIP3_PTEN;
    vP[108-1]=kP[108-1]*PIP3*AKT;
    vP[109-1]=kP[109-1]*PIP3_AKT;
    vP[110-1]=kP[110-1]*PIP3*PDK1;
    vP[111-1]=kP[111-1]*PIP3_PDK1;
    vP[112-1]=kP[112-1]*Rictor*mTOR;
    vP[113-1]=kP[113-1]*mTORC2;
    vP[114-1]=kP[114-1]*PIP3_AKT*PIP3_PDK1;
    vP[115-1]=kP[115-1]*PIP3_AKT_PIP3_PDK1;
    vP[116-1]=kP[116-1]*PIP3_AKT_PIP3_PDK1;
    vP[117-1]=kP[117-1]*PIP3_pAKT;
    vP[118-1]=kP[118-1]*PIP3_pAKT*mTORC2;
    vP[119-1]=kP[119-1]*PIP3_pAKT_mTORC2;
    vP[120-1]=kP[120-1]*PIP3_pAKT_mTORC2;
    vP[121-1]=kP[121-1]*PIP3_ppAKT;
    vP[122-1]=kP[122-1]*PIP3_ppAKT;
    vP[123-1]=kP[123-1]*PIP3*ppAKT;
    vP[124-1]=kP[124-1]*GSK3b*ppAKT;
    vP[125-1]=kP[125-1]*GSK3b_ppAKT;
    vP[126-1]=kP[126-1]*GSK3b_ppAKT;
    vP[127-1]=kP[127-1]*pGSK3b;


    vP[127]=(kP[127]*bCATENIN*GSK3b**4)/(200**4+GSK3b**4);

    vP[131-1]=kP[131-1]*pbCATENIN;
    vP[132-1]=kP[132-1]*bCATENIN;
    vP[133-1]=kP[133-1]*bCATENINnuc;
    vP[134-1]=kP[134-1]*TSC2*ppAKT;
    vP[135-1]=kP[135-1]*TSC2_ppAKT;
    vP[136-1]=kP[136-1]*TSC2_ppAKT;
    vP[137-1]=kP[137-1]*TSC2*ppERK;
    vP[138-1]=kP[138-1]*TSC2_ppERK;
    vP[139-1]=kP[139-1]*TSC2_ppERK;
    vP[140-1]=kP[140-1]*TSC1*TSC2;
    vP[141-1]=kP[141-1]*TSC;
    vP[142-1]=0;
    vP[143-1]=0;
    vP[144-1]=0;
    vP[145-1]=0;
    vP[146-1]=kP[146-1]*mTORC1;

    vP[146]=(kP[146]*mTORC1active*TSC**4)/(.1+TSC**4);

    vP[148-1]=kP[148-1]*Raptor*mTOR;
    vP[149-1]=kP[149-1]*mTORC1;
    vP[150-1]=kP[150-1]*EIF4EBP1*mTORC1active;
    vP[151-1]=kP[151-1]*EIF4EBP1_mTORC1active;
    vP[152-1]=kP[152-1]*EIF4EBP1_mTORC1active;
    vP[153-1]=kP[153-1]*pEIF4EBP1;
    vP[154-1]=kP[154-1]*S6K*mTORC1active;
    vP[155-1]=kP[155-1]*S6K_mTORC1active;
    vP[156-1]=kP[156-1]*S6K_mTORC1active;
    vP[157-1]=kP[157-1]*pS6K;
    vP[158-1]=kP[158-1]*FOXO*ppAKT;
    vP[159-1]=kP[159-1]*FOXO_ppAKT;
    vP[160-1]=kP[160-1]*FOXO_ppAKT;
    vP[161-1]=kP[161-1]*pFOXO;
    vP[162-1]=kP[162-1]*PI3K1*mTORC1active;
    vP[163-1]=kP[163-1]*PI3K1_mTORC1active;
    vP[164-1]=kP[164-1]*PI3K1_mTORC1active;
    vP[165-1]=kP[165-1]*pPI3K1;
    vP[166-1]=kP[166-1]*PI3KC1*PI3KR1;
    vP[167-1]=kP[167-1]*PI3K1;
    vP[168-1]=kP[168-1]*PI3P;
    vP[169-1]=kP[169-1]*SOS*G2;
    vP[170-1]=kP[170-1]*G2_SOS;
    vP[171-1]=kP[171-1]*EIF4E*EIF4EBP1;
    vP[172-1]=kP[172-1]*EIF4EBP1_EIF4E;
    vP[173-1]=kP[173-1];
    vP[174-1]=kP[174-1]*pbCATENIN*TSC;
    vP[175-1]=kP[175-1]*pERK;
    vP[176-1]=kP[176-1]*ppERK;
    vP[177-1]=kP[177-1]*ppERKnuc;
    vP[178-1]=kP[178-1]*ppAKT;
    vP[179-1]=kP[179-1]*pAKT;
    vP[180-1]=kP[180-1]*RhebT;
    vP[181-1]=kP[181-1]*FOXO;
    vP[182-1]=kP[182-1]*FOXOnuc;
    vP[183-1]=kP[183-1]*PIP2;
    vP[184-1]=kP[184-1]*PIP3;
    vP[185-1]=kP[185-1]*RasD;
    vP[186-1]=kP[186-1]*RasT;
    vP[187-1]=kP[187-1]*MEKi*ppMEK;
    vP[188-1]=kP[188-1]*MEKi_ppMEK;
    vP[189-1]=kP[189-1]*AKTi*AKT;
    vP[190-1]=kP[190-1]*AKTi_AKT;


    # ## vDA **
    # # NONE as these are all transcriptional control mechanisms.


    # ## vDP **
    vDP = np.zeros(shape=(4))
    vDP[0]=kDP[0]*ppAKT*Mdm2;
    vDP[1]=kDP[1]*ppAKT_Mdm2;
    vDP[2]=kDP[2]*ppAKT_Mdm2;
    vDP[3]=kDP[3]*pMdm2;


    # ## vPA **
    vPA = np.zeros(shape=(11))
    vPA[1-1]=kPA[1-1]*ppERK*BIM;
    vPA[2-1]=kPA[2-1]*ppERK_BIM;
    vPA[3-1]=kPA[3-1]*ppERK_BIM;
    vPA[4-1]=kPA[4-1]*pBIM;
    vPA[5-1]=kPA[5-1]*ppAKT*BAD;
    vPA[6-1]=kPA[6-1]*ppAKT_BAD;
    vPA[7-1]=kPA[7-1]*ppAKT_BAD;
    vPA[8-1]=kPA[8-1]*ppERK*BAD;
    vPA[9-1]=kPA[9-1]*ppERK_BAD;
    vPA[10-1]=kPA[10-1]*ppERK_BAD;
    vPA[11-1]=kPA[11-1]*pBAD;



    # ## vPC **
    # # NONE as these are all transcriptional control mechanisms.
    #
    # ## vDC **
    # # NONE as these are all transcriptional control mechanisms.
    #
    #
    # ## vDd (none)
    # # Removed all Dd and Cd degradation reactions. These are controlled from
    # # within these submodels, respectively.
    #
    # ## vCd (none)
    # # # removed all degradation reactions because cell cycle model handles that
    # # # internally.
    #


    # ## vAd
    # NOTE
    Ads= np.array([L_R,
    Ractive,
    Ractive_flip,
    Ractive_pC8,
    C8,
    C8_Bar,
    C8_pC3,
    C3,
    C3_pC6,
    C6,
    C6_C8,
    C3_XIAP,
    C3_PARP,
    cPARP,
    C8_Bid,
    tBid,
    tBid_Bcl2c,
    tBid_Bax,
    Baxactive,
    Baxm,
    Bcl2,
    Baxm_Bcl2,
    Bax2,
    Bax2_Bcl2,
    Bax4,
    Bax4_Bcl2,
    CytoCr,
    Smacr,
    CytoC,
    CytoC_Apaf,
    Apafactive,
    Apop,
    Apop_C3,
    Smac,
    Apop_XIAP,
    Smac_XIAP,
    C3_Ub,
    Bcl2c_BAD,
    Bcl2c_PUMA,
    Bcl2c_NOXA,
    BIM_Bax,
    Bcl2c_BIM,
    ppERK_BIM,
    pBIM,
    ppAKT_BAD,
    pBAD,
    ppERK_BAD]);



    new = np.zeros(shape=(Ads.shape[0],1))

    counter = 0
    for itemb in Ads:
        new[counter,0] = itemb
        counter = counter + 1

    Ads = new







    Rds= np.array([pE1,
    pE2,
    pE4,
    E1E1,
    E1E2,
    E1E3,
    E1E4,
    E2E2,
    E2E3,
    E2E4,
    E3E4,
    E4E4,
    Met_Met,
    FrFr,
    IrIr,
    Isr_Isr,
    EE1,
    HE3,
    HE4,
    HGF_Met,
    PPr,
    FFr,
    EE1E2,
    EE1Ev3,
    EE1E1,
    EE1E3,
    EE1E4,
    E2HE3,
    E1HE3,
    HE3E3,
    HE3Ev3,
    HE3E4,
    E2HE4,
    HE4Ev3,
    E1HE4,
    E3HE4,
    HE4E4,
    HGF_Met_Met,
    PPrPr,
    FFrFr,
    IIrIr,
    IN_Isr_Isr,
    EE1EE1,
    EE1HE3,
    EE1HE4,
    HE3HE3,
    HE3HE4,
    HE4HE4,
    HGF_Met_HGF_Met,
    PPrPPr,
    FFrFFr,
    IIrIrI,
    IN_Isr_Isr_IN,
    E1_ppERK,
    E2_ppERK,
    E4_ppERK]);

    new = np.zeros(shape=(Rds.shape[0],1))

    counter = 0
    for itemc in Rds:
        new[counter,0] = itemc
        counter = counter + 1

    Rds = new







    RPds=xRP;

    Pds= np.array([G2_SOS,
    G2_pSOS,
    PI3K1,
    pPI3K1,
    mTORC1,
    mTORC1active,
    PIP,
    PI3P,
    DAG,
    DAG_GRP,
    RasT,
    pNF1,
    pCRaf,
    RasT_CRaf,
    RasT_CRaf_BRaf,
    pMEK,
    ppMEK,
    ERKnuc,
    ppERKnuc,
    pRSK,
    pRSKnuc,
    pMKP1,
    pcFos,
    pcFos_cJun,
    bCATENINnuc,
    pbCATENIN,
    IP3,
    PIP2,
    PIP3,
    PIP3_AKT,
    pAKT,
    ppAKT,
    PIP3_PDK1,
    PIP3_pAKT,
    mTORC2,
    PIP3_ppAKT,
    pGSK3b,
    pTSC2,
    TSC,
    DAG_PKC,
    pRKIP,
    RKIP_CRaf,
    pERK,
    ppERK,
    pFOXO,
    RhebT,
    pS6K,
    pEIF4EBP1,
    G2_SOS_ppERK,
    CRaf_ppERK,
    RasD_DAG_GRP,
    RasT_NF1,
    NF1_ppERK,
    MEK_RasT_CRaf_BRaf,
    pMEK_RasT_CRaf_BRaf,
    ERK_ppMEK,
    pERK_ppMEK,
    RSK_ppERK,
    pRSKnuc_MKP1,
    ppERKnuc_MKP1,
    cFos_pRSKnuc,
    cFos_ppERKnuc,
    RKIP_DAG_PKC,
    PIP3_PTEN,
    PIP3_AKT_PIP3_PDK1,
    PIP3_pAKT_mTORC2,
    GSK3b_ppAKT,
    bCATENIN_GSK3b,
    TSC2_ppAKT,
    TSC2_ppERK,
    RhebT_TSC,
    EIF4EBP1_mTORC1active,
    S6K_mTORC1active,
    FOXO_ppAKT,
    PI3K1_mTORC1active,
    pERK_MKP3,
    ppERK_MKP3,
    ppERKnuc_pMKP1,
    RasT_BRaf,
    RasT_BRaf_BRaf,
    MEK_RasT_BRaf_BRaf,
    pMEK_RasT_BRaf_BRaf,
    EIF4EBP1_EIF4E,
    RasT_CRaf_CRaf,
    MEK_RasT_CRaf_CRaf,
    pMEK_RasT_CRaf_CRaf,
    FOXOnuc,
    MEKi_ppMEK,
    AKTi_AKT]);



    new = np.zeros(shape=(Pds.shape[0],1))

    counter = 0
    for itemd in Pds:
        new[counter,0] = itemd
        counter = counter + 1

    Pds = new






    Xds = np.zeros(shape=(606))



    count = 0

    for itemea in Ads[:,0]:
        Xds[count] = itemea
        count = count + 1

    for itemeb in Rds[:,0]:
        Xds[count] = itemeb
        count = count + 1

    for itemec in RPds:
        Xds[count] = itemec
        count = count + 1



    for itemed in Pds[:,0]:
        Xds[count] = itemed
        count = count + 1








    vXd= np.multiply(kXd,Xds);



    # ## PUTTING IT TOGETHER  ##






    vRP = np.zeros(shape=(973))



    count = 0


    for itemf in vRP1:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP2:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP3:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP4:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP5:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP6:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP7:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP8:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP9:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP10:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP11:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP12:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP13:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP14:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP15:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP16:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP17:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP18:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP19:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP20:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP21:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP22:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP23:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP24:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP25:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP26:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP27:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP28:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP29:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP30:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP31:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP32:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP33:
        vRP[count] = itemf
        count = count+1

    for itemf in vRP34:
        vRP[count] = itemf
        count = count+1


    #############



    # v=[vbR;vdR;vTL;vTLCd';vE';vD';vC';vA';vR';vRP;vP';vDP';vPA';vXd];
    # v_temp = [vbR,vdR,vTL,np.matrix.transpose(vTLCd),np.matrix.transpose(vE),np.matrix.transpose(vD),np.matrix.transpose(vC),np.matrix.transpose(vA),np.matrix.transpose(vR),vRP,np.matrix.transpose(vP),np.matrix.transpose(vDP),np.matrix.transpose(vPA),vXd]
    # v_temp = [vbR,vdR,vTL,vTLCd,vE,vD,vC,vA,vR,vRP,vP,vDP,vPA,vXd]







    ########



    v = np.zeros(shape=(2449,1))



    count = 0

    #[vbR,vdR,vTL,vTLCd,vE,vD,vC,vA,vR,vRP,vP,vDP,vPA,vXd]

    for itemg in vbR:
        v[count,0] = itemg
        count = count+1

    for itemg in vdR:
        v[count,0] = itemg
        count = count+1

    for itemg in vTL:
        v[count,0] = itemg
        count = count+1

    for itemg in vTLCd:
        v[count,0] = itemg
        count = count+1

    for itemg in vE:
        v[count,0] = itemg
        count = count+1

    for itemg in vD:
        v[count,0] = itemg
        count = count+1

    for itemg in vC:
        v[count,0] = itemg
        count = count+1

    for itemg in vA:
        v[count,0] = itemg
        count = count+1

    for itemg in vR:
        v[count,0] = itemg
        count = count+1

    for itemg in vRP:
        v[count,0] = itemg
        count = count+1

    for itemg in vP:
        v[count,0] = itemg
        count = count+1

    for itemg in vDP:
        v[count,0] = itemg
        count = count+1

    for itemg in vPA:
        v[count,0] = itemg
        count = count+1

    for itemg in vXd:
        v[count,0] = itemg
        count = count+1


    #########


    # v = np.matrix(v);
    # v = np.matrix.transpose(v)


    v = v[0:2448,:]
    # getting rid of two 0s on the end to get the sizes to match


    S_PARCDL_float = S_PARCDL * 1.0

    # NOTE
    ndot= np.dot(S_PARCDL_float, (np.multiply(v,(VvPARCDL*1E12))));




    # fixing divide by zero issue

    count = 0
    i = 0
    for element in VxPARCDL[:,0]:
        if element == 0:
            # VxPARCDL[i,0] = 1
            count = count + 1
        i = i + 1



    nans_index = np.zeros(shape=(count))

    count = 0
    i = 0
    for element in VxPARCDL[:,0]:
        if element == 0:

            VxPARCDL[i,0] = 1
            nans_index[count] = i
            count = count+1
        i = i + 1








    ydot=ndot/(VxPARCDL*1E12);




    for item in nans_index:
        ydot[np.int32(item)] = 0




    # flag=0;

    # NOTE commented out because was breaking compiler, don't think this is important since it never gets filled
    # new_data = [];

    # ydot[np.isnan(ydot)] = 0

    # to_return = []
    # for i in range(0,774):
    #     to_return.append(ydot[i,0])

    to_return = np.zeros(shape=(774))

    counter = 0

    for itemq in ydot[:,0]:
        to_return[counter] = itemq
        counter = counter + 1



    return to_return
    # return to_return


    #
    #     # # NOTE - everything after this point is just for debugging
    #     #
    #     # v_list = []
    #     # for i in range(0,2448):
    #     #     v_list.append(v[i,0])
    #     #
    #     #
    # correct_ydot = []
    #
    # with open('correct_ydot.csv', newline='') as csvfile:
    #     spamreader = csv.reader(csvfile, delimiter=' ', quotechar='|')
    #     for row in spamreader:
    #         x = ', '.join(row)
    #         x = x.split(',')
    #         correct_ydot.append(float(x[0]))
    # #
    # #
    # # correct_v = []
    # #
    # # with open('correct_v.csv', newline='') as csvfile:
    # #     spamreader = csv.reader(csvfile, delimiter=' ', quotechar='|')
    # #     for row in spamreader:
    # #         x = ', '.join(row)
    # #         x = x.split(',')
    # #         correct_v.append(float(x[0]))
    # #
    # problem_indices = []
    #
    # accurate = 0
    # #
    # # # NOTE - ydot debug
    #
    # for i in range(len(to_return)):
    #     if abs(to_return[i] - correct_ydot[i]) < 0.0000000001:
    #         accurate = accurate+1
    #     else:
    #         print(to_return[i],correct_ydot[i])
    #         print("bad")
    #         print(i)
    #         print()
    #         problem_indices.append(i)
    #
    # #
    # #
    # # # NOTE - v comparison
    # # # for i in range(len(v_list)):
    # # #     if abs(v_list[i] - correct_v[i]) < 0.0000001:
    # # #         # print(to_return[i],correct_ydot[i])
    # # #         # print("good")
    # # #         # print(i)
    # # #         accurate = accurate+1
    # # #     else:
    # # #         # print(i)
    # # #         print(v_list[i],correct_v[i])
    # # #         print("bad")
    # # #         print(i)
    # # #         print()
    # # #         problem_indices.append(i)
    # # #
    # # #
    # print()
    #
    # print(accurate/len(to_return))
    #
    # # #
    # print(accurate/774)
    # # #
    # print("number wrong: " + str(774-accurate))
    # # #
    # # # print()
    # print(problem_indices)