7.1.1. intro_to_wc_modeling.cell_modeling package

7.1.1.2. Submodules

7.1.1.3. intro_to_wc_modeling.cell_modeling.model_composition module

Model composition tutorial

  • Glycolysis model (Teusink et al., 2000)

  • Glycerol synthesis model (Cronwright et al., 2002)

Author

Jonathan Karr <jonrkarr@gmail.com>

Author

Yin Hoon Chew <yinhoon.chew@mssm.edu>

Date

2017-08-30

Copyright

2017, Karr Lab

License

MIT

class intro_to_wc_modeling.cell_modeling.model_composition.GlycerolModel[source]

Bases: object

Glycerol synthesis model (Cronwright et al., 2002)

Based on the version from JWS Online

ADP[source]

ADP concentration (mM)

Type

float

ATP[source]

ATP concentration (mM)

Type

float

DHAP[source]

DHAP concentration (mM)

Type

float

GLY[source]

GLY concentration (mM)

Type

float

F16BP[source]

F16BP concentration (mM)

Type

float

NAD[source]

NAD concentration (mM)

Type

float

NADH[source]

NADH concentration (mM)

Type

float

Phi[source]

Pi concentration (mM)

Type

float

V2[source]

forward rate constant (mM min-1)

Type

float

Vf1[source]

reverse rate constant (mM min-1)

Type

float

K1adp[source]

ADP forward affinity constant (mM)

Type

float

K1atp[source]

ATP forward affinity constant (mM)

Type

float

K1dhap[source]

DHAP forward affinity constant (mM)

Type

float

K1f16bp[source]

F16BP forward affinity constant (mM)

Type

float

K1g3p[source]

G3P forward affinity constant (mM)

Type

float

K1nad[source]

NAD forward affinity constant (mM)

Type

float

K1nadh[source]

NADH forward affinity constant (mM)

Type

float

K2g3p[source]

G3P reverse affinity constant (mM)

Type

float

K2phi[source]

Pi reverse affinity constant (mM)

Type

float

Keq1[source]

Equilibrium constant (dimensionless)

Type

float

g3p_0[source]

initial G3P concentration (mM)

Type

numpy.array

x_0[source]

initial species concentrations (mM)

Type

numpy.array

ADP = 2.17[source]
ATP = 2.37[source]
DHAP = 0.59[source]
F16BP = 6.01[source]
GLY = 0.0[source]
K1adp = 2.0[source]
K1atp = 0.73[source]
K1dhap = 0.54[source]
K1f16bp = 4.8[source]
K1g3p = 1.2[source]
K1nad = 0.93[source]
K1nadh = 0.023[source]
K2g3p = 3.5[source]
K2phi = 1.0[source]
Keq1 = 10000.0[source]
NAD = 1.45[source]
NADH = 1.87[source]
Phi = 1.0[source]
V2 = 53.0[source]
Vf1 = 47.0[source]
dg3p_dt(x)[source]

Calculate time derivative of the G3P concentration

Parameters

x (numpy.array) – species concentrations (mM)

Returns

time derivative of the G3P concentration (mM min-1)

Return type

float

dx_dt(x)[source]

Calculate the time derivative of the species concentrations

Parameters

x (numpy.array) – species concentrations (mM)

Returns

time derivative of the species concentrations (mM min-1)

Return type

numpy.array

g3p_0 = 0[source]
plot_simulation_results(t, dhap, g3p)[source]

Plot simulation results

Parameters

  • t (numpy.array) – time (min)

  • dhap (numpy.array) – DHAP concentration (mM)

  • g3p (numpy.array) – G3P concentration (mM)

Returns

figure

Return type

matplotlib.figure.Figure

simulate(t_0=0, t_end=20.0, t_step=0.2)[source]

Simulate the model

Parameters

  • t_0 (float, optional) – start time (min)

  • t_end (float, optional) – end time (min)

  • t_step (float, optional) – time step to record predicted concentrations (min)

Returns

  • numpy.array: time (min)

  • numpy.array: DHAP concentration (mM)

  • numpy.array: G3P concentration (mM)

Return type

tuple

v_1(x)[source]

Calculate the rate of Glycerol 3-phosphate dehydrogenase (DHAP <=> G3P)

Parameters

x (numpy.array) – species concentrations (mM)

Returns

rate of Glycerol 3-phosphate dehydrogenase (mM min-1)

Return type

float

v_2(x)[source]

Calculate the rate of Glycerol 3-phosphatase (G3P <=> Gly)

Parameters

x (numpy.array) – species concentrations (mM)

Returns

rate of Glycerol 3-phosphatase (mM min-1)

Return type

float

property x_0[source]
class intro_to_wc_modeling.cell_modeling.model_composition.GlycolysisModel[source]

Bases: object

Glycolysis model (Teusink et al., 2000)

Based on the version from JWS Online

CPFKAMP[source]
Type

float

CPFKATP[source]
Type

float

CPFKF16BP[source]
Type

float

CPFKF26BP[source]
Type

float

CPFKF6P[source]
Type

float

CiPFKATP[source]
Type

float

F26BP[source]
Type

float

KATPASE[source]
Type

float

KGLYCOGEN[source]
Type

float

KPFKAMP[source]
Type

float

KPFKF16BP[source]
Type

float

KPFKF26BP[source]
Type

float

KSUCC[source]
Type

float

KTREHALOSE[source]
Type

float

KeqADH[source]
Type

float

KeqAK[source]
Type

float

KeqALD[source]
Type

float

KeqENO[source]
Type

float

KeqG3PDH[source]
Type

float

KeqGLK[source]
Type

float

KeqGLT[source]
Type

float

KeqPGI[source]
Type

float

KeqPGK[source]
Type

float

KeqPGM[source]
Type

float

KeqPYK[source]
Type

float

KeqTPI[source]

ratio of GAP to DHAP at equilibrium

Type

float

KiADHACE[source]
Type

float

KiADHETOH[source]
Type

float

KiADHNAD[source]
Type

float

KiADHNADH[source]
Type

float

KiPFKATP[source]
Type

float

KmADHACE[source]
Type

float

KmADHETOH[source]
Type

float

KmADHNAD[source]
Type

float

KmADHNADH[source]
Type

float

KmALDDHAP[source]
Type

float

KmALDF16P[source]
Type

float

KmALDGAP[source]
Type

float

KmALDGAPi[source]
Type

float

KmENOP2G[source]
Type

float

KmENOPEP[source]
Type

float

KmG3PDHDHAP[source]
Type

float

KmG3PDHGLY[source]
Type

float

KmG3PDHNAD[source]
Type

float

KmG3PDHNADH[source]
Type

float

KmGAPDHBPG[source]
Type

float

KmGAPDHGAP[source]
Type

float

KmGAPDHNAD[source]
Type

float

KmGAPDHNADH[source]
Type

float

KmGLKADP[source]
Type

float

KmGLKATP[source]
Type

float

KmGLKG6P[source]
Type

float

KmGLKGLCi[source]
Type

float

KmGLTGLCi[source]
Type

float

KmGLTGLCo[source]
Type

float

KmPDCPYR[source]
Type

float

KmPFKATP[source]
Type

float

KmPFKF6P[source]
Type

float

KmPGIF6P[source]
Type

float

KmPGIG6P[source]
Type

float

KmPGKADP[source]
Type

float

KmPGKATP[source]
Type

float

KmPGKBPG[source]
Type

float

KmPGKP3G[source]
Type

float

KmPGMP2G[source]
Type

float

KmPGMP3G[source]
Type

float

KmPYKADP[source]
Type

float

KmPYKATP[source]
Type

float

KmPYKPEP[source]
Type

float

KmPYKPYR[source]
Type

float

L0[source]
Type

float

SUMAXP[source]
Type

float

VmADH[source]
Type

float

VmALD[source]
Type

float

VmENO[source]
Type

float

VmG3PDH[source]
Type

float

VmGAPDHf[source]
Type

float

VmGAPDHr[source]
Type

float

VmGLK[source]
Type

float

VmGLT[source]
Type

float

VmPDC[source]
Type

float

VmPFK[source]
Type

float

VmPGI[source]
Type

float

VmPGK[source]
Type

float

VmPGM[source]
Type

float

VmPYK[source]
Type

float

gR[source]
Type

float

nPDC[source]
Type

float

CO2[source]
Type

float

ETOH[source]
Type

float

GLCo[source]
Type

float

GLY[source]
Type

float

SUCC[source]
Type

float

Trh[source]
Type

float

ACE_0[source]

initial ACE concentration (mM)

Type

float

BPG_0[source]

initial BPG concentration (mM)

Type

float

F16BP_0[source]

initial F16BP concentration (mM)

Type

float

F6P_0[source]

initial F6P concentration (mM)

Type

float

G6P_0[source]

initial G6P concentration (mM)

Type

float

GLCi_0[source]

initial GLCi concentration (mM)

Type

float

NAD_0[source]

initial NAD concentration (mM)

Type

float

NADH_0[source]

initial NADH concentration (mM)

Type

float

P2G_0[source]

initial P2G concentration (mM)

Type

float

P3G_0[source]

initial P3G concentration (mM)

Type

float

PEP_0[source]

initial PEP concentration (mM)

Type

float

PYR_0[source]

initial PYR concentration (mM)

Type

float

Prb_0[source]

initial high energy phosphates (2*ATP + ADP) concentration (mM)

Type

float

TRIO_0[source]

initial triose-phosphate (DHAP + GAP) concentration (mM)

Type

float

x_0[source]

initial species concentrations (mM)

Type

numpy.array

ACE_0 = 0.04[source]
BPG_0 = 0.0[source]
CO2 = 1.0[source]
CPFKAMP = 0.0845[source]
CPFKATP = 3.0[source]
CPFKF16BP = 0.397[source]
CPFKF26BP = 0.0174[source]
CPFKF6P = 0.0[source]
CiPFKATP = 100.0[source]
ETOH = 50.0[source]
F16BP_0 = 0.1[source]
F26BP = 0.02[source]
F6P_0 = 0.28[source]
G6P_0 = 1.39[source]
GLCi_0 = 0.087[source]
GLCo = 50.0[source]
GLY = 0.15[source]
KATPASE = 39.5[source]
KGLYCOGEN = 6.0[source]
KPFKAMP = 0.0995[source]
KPFKF16BP = 0.111[source]
KPFKF26BP = 0.000682[source]
KSUCC = 21.4[source]
KTREHALOSE = 2.4[source]
KeqADH = 6.9e-05[source]
KeqAK = 0.45[source]
KeqALD = 0.069[source]
KeqENO = 6.7[source]
KeqG3PDH = 4300.0[source]
KeqGLK = 3800.0[source]
KeqGLT = 1.0[source]
KeqPGI = 0.314[source]
KeqPGK = 3200.0[source]
KeqPGM = 0.19[source]
KeqPYK = 6500.0[source]
KeqTPI = 0.045[source]
KiADHACE = 1.1[source]
KiADHETOH = 90.0[source]
KiADHNAD = 0.92[source]
KiADHNADH = 0.031[source]
KiPFKATP = 0.65[source]
KmADHACE = 1.11[source]
KmADHETOH = 17.0[source]
KmADHNAD = 0.17[source]
KmADHNADH = 0.11[source]
KmALDDHAP = 2.4[source]
KmALDF16P = 0.3[source]
KmALDGAP = 2.0[source]
KmALDGAPi = 10.0[source]
KmENOP2G = 0.04[source]
KmENOPEP = 0.5[source]
KmG3PDHDHAP = 0.4[source]
KmG3PDHGLY = 1.0[source]
KmG3PDHNAD = 0.93[source]
KmG3PDHNADH = 0.023[source]
KmGAPDHBPG = 0.0098[source]
KmGAPDHGAP = 0.21[source]
KmGAPDHNAD = 0.09[source]
KmGAPDHNADH = 0.06[source]
KmGLKADP = 0.23[source]
KmGLKATP = 0.15[source]
KmGLKG6P = 30.0[source]
KmGLKGLCi = 0.08[source]
KmGLTGLCi = 1.1918[source]
KmGLTGLCo = 1.1918[source]
KmPDCPYR = 4.33[source]
KmPFKATP = 0.71[source]
KmPFKF6P = 0.1[source]
KmPGIF6P = 0.3[source]
KmPGIG6P = 1.4[source]
KmPGKADP = 0.2[source]
KmPGKATP = 0.3[source]
KmPGKBPG = 0.003[source]
KmPGKP3G = 0.53[source]
KmPGMP2G = 0.08[source]
KmPGMP3G = 1.2[source]
KmPYKADP = 0.53[source]
KmPYKATP = 1.5[source]
KmPYKPEP = 0.14[source]
KmPYKPYR = 21.0[source]
L0 = 0.66[source]
NADH_0 = 0.39[source]
NAD_0 = 1.2[source]
P2G_0 = 0.1[source]
P3G_0 = 0.1[source]
PEP_0 = 0.1[source]
PYR_0 = 3.36[source]
Prb_0 = 5.0[source]
SUCC = 0.0[source]
SUMAXP = 4.1[source]
TRIO_0 = 5.17[source]
Trh = 0.0[source]
VmADH = 810.0[source]
VmALD = 322.258[source]
VmENO = 365.806[source]
VmG3PDH = 70.15[source]
VmGAPDHf = 1184.52[source]
VmGAPDHr = 6549.68[source]
VmGLK = 226.452[source]
VmGLT = 97.264[source]
VmPDC = 174.194[source]
VmPFK = 182.903[source]
VmPGI = 339.677[source]
VmPGK = 1306.45[source]
VmPGM = 2525.81[source]
VmPYK = 1088.71[source]
dACE_dt(x)[source]
dBPG_dt(x)[source]
dF16BP_dt(x)[source]
dF6P_dt(x)[source]
dG6P_dt(x)[source]
dGLCi_dt(x)[source]
dNADH_dt(x)[source]
dNAD_dt(x)[source]
dP2G_dt(x)[source]
dP3G_dt(x)[source]
dPEP_dt(x)[source]
dPYR_dt(x)[source]
dPrb_dt(x)[source]
dTRIO_dt(x)[source]
dx_dt(x)[source]

Calculate the time derivative of the species concentrations

Parameters

x (numpy.array) – species concentrations (mM)

Returns

time derivative of the species concentrations (mM min-1)

Return type

numpy.array

gR = 1.12[source]
nPDC = 1.9[source]
plot_simulation_results(t, dhap)[source]

Plot simulation results

Parameters

  • t (numpy.array) – time (min)

  • dhap (numpy.array) – DHAP concentration (mM)

Returns

figure

Return type

matplotlib.figure.Figure

simulate(t_0=0, t_end=20.0, t_step=0.2)[source]

Simulate the model

Parameters

  • t_0 (float, optional) – start time (min)

  • t_end (float, optional) – end time (min)

  • t_step (float, optional) – time step to record predicted concentrations (min)

Returns

  • numpy.array: time (min)

  • numpy.array: DHAP concentration (mM)

Return type

tuple

v_1(x)[source]
v_10(x)[source]
v_11(x)[source]
v_12(x)[source]
v_13(x)[source]
v_14(x)[source]
v_15(x)[source]
v_16(x)[source]
v_17(x)[source]
v_2(x)[source]
v_3(x)[source]
v_4(x)[source]
v_5(x)[source]
v_6(x)[source]
v_7(x)[source]
v_8(x)[source]
v_9(x)[source]
property x_0[source]
class intro_to_wc_modeling.cell_modeling.model_composition.MergedModel[source]

Bases: object

Merged model

glycolysis_model[source]

glycolysis model

Type

GlycolysisModel

glycerol_model[source]

glycerol model

Type

GlycerolModel

x_0[source]

initial species concentrations (mM)

Type

numpy.array

dx_dt(x)[source]

Calculate the time derivative of the species concentrations

Parameters

x (numpy.array) – species concentrations (mM)

Returns

time derivative of the species concentrations (mM min-1)

Return type

numpy.array

simulate(t_0=0, t_end=20.0, t_step=0.2)[source]

Simulate the model

Parameters

  • t_0 (float, optional) – start time (min)

  • t_end (float, optional) – end time (min)

  • t_step (float, optional) – time step to record predicted concentrations (min)

Returns

  • numpy.array: time (min)

  • numpy.array: DHAP concentration (mM)

  • numpy.array: G3P concentration (mM)

Return type

tuple

v_18(x)[source]
v_19(x)[source]
property x_0[source]
intro_to_wc_modeling.cell_modeling.model_composition.main(out_dir=None)[source]

Simulate individual models and combined model, plot results, and save plots

Parameters

out_dir (str, optional) – path to directory to save results

7.1.1.4. Module contents