CellMLPhysiome: J - N

J


joseph_zavros_merchant_kirschner_2003v0.0.1

Joseph, Zavros, Merchant, Kirschner, 2003

Details

Parameters:

NameDescription
gamma_DCnothing
fnothing
KNSnothing
N_nothing
alpha_ASnothing
alpha_Cscnothing
Nmax1nothing
alpha_Fdnothing
gamma_Pnothing
alpha_NHnothing
alpha_GSnothing
hbnothing
beta_Anothing
kFdnothing
gamma_DAnothing
gamma_Fdmaxnothing
Bas1nothing
alpha_HAnothing
kSAnothing
KASnothing
kappa_NCnothing
k_BCmaxnothing
Bas2nothing
Nmax2nothing
C_Cscnothing
KNG1nothing
gamma_Enothing
kNSnothing
alpha_NG2nothing
gamma_Ascnothing
KGAnothing
k_gmaxnothing
kGnothing
KHAnothing
alpha_GAnothing
alpha_NG1nothing
KNG2nothing
kappa_Hnothing
beta_Gnothing
k_dmaxnothing
alpha_GHnothing
kSGnothing
KNHnothing
KNAnothing
kappa_NEnothing
kSSnothing
gamma_Cscnothing
KFGnothing
kappa_Anothing
kappa_Gnothing
C_Ascnothing
kappa_Snothing
kAN2nothing
KGHnothing
T_Ascnothing
kAN1nothing
alpha_NSnothing
Fdnothing
gmaxnothing
alpha_NAnothing
gamma_Gcnothing
T_Cscnothing
k_Emaxnothing
KGSnothing
k_Fdmaxnothing
alpha_NBnothing
beta_Bnothing
kSHnothing
alpha_Enothing
kappa_Bnothing
kAGnothing
k_BAmaxnothing

States:

NameDescription
P(time)nothing
DC(time)nothing
GtnA(time)nothing
BC(time)nothing
GtnC(time)nothing
Asc(time)nothing
NE(time)nothing
HC(time)nothing
AA(time)nothing
SA(time)nothing
SC(time)nothing
DA(time)nothing
E(time)nothing
BA(time)nothing
NC(time)nothing
Csc(time)nothing
G(time)nothing
AC(time)nothing

K


karagiannis_popel_2004v0.0.1

Karagiannis, Popel, 2004

Details

Parameters:

NameDescription
kcat_M2C10.0045
kiso_M2T233.0
kon_MT1T2M2P140000.0
kon_MT1T23.54e6
kshed_eff2800.0
ki_M2T21.07e-6
kon_M2T25.9e6
kon_M2C12600.0
kcat_MT1C10.00197
km_MT1C12.9e-6
koff_M2C10.0021
kact_eff_m22800.0
k_iso_M2T22.0e-8
ki_MT1T24.9e-9
koff_MT1T2M2P0.0047

States:

NameDescription
M2T2star(time)0.0
MT1cat(time)0.0
M2T2(time)0.0
M2(time)0.0
M2P(time)5.0e-8
C1(time)1.0e-6
T2(time)5.0e-8
MT1(time)1.0e-7
C1dm2(time)0.0
C1dmt1(time)0.0
M2C1(time)0.0
MT1T2M2P(time)0.0
MT1T2(time)0.0

karagiannis_popel_2006v0.0.1

Karagiannis, Popel, 2006

Details

Parameters:

NameDescription
kM2T2_on5.9e6
kMT1T2_on2.98e6
kMT1C1_on1000.0
kM2T2_negativeiso2.0e-8
qMT10.0
kMT1T2M2proMT1_off0.0009
kM2C1_off0.0021
kM2C1_on2600.0
kM2T2_off6.3
kMT1_shedeff2800.0
kMT1T2_off0.202
kMT1C1_off1.0
kMT1C1_cat0.00197
kMT1T2M2pro_off0.0047
kM2T2_iso33.0
kMT1T2M2proMT1_on3000.0
kM2_act0.02
kM2C1_cat0.0045
qT20.0
qpro0.0
kMT1T2M2pro_on140000.0

States:

NameDescription
M2C1(t)8.5e-6
MT1T2M2pro(t)0.0
C1_D(t)0.0
C1(t)0.0
MT1_cat(t)0.0
M2T2(t)7.2e-9
MT1T2M2proMT1(t)5.6e-10
M2_p(t)0.0
M2T2_star(t)0.0
MT1C1(t)2.9e-6
MT1T2(t)1.39e-9
MT1(t)0.0
T2(t)0.0
MT1_t(t)0.0
MT1T2_star(t)0.0
M2(t)0.0

katsnelson_nikitina_chemla_solovyova_coirault_lecarpentier_markhasin_2004v0.0.1

Katsnelson, Nikitina, Chemla, Solovyova, Coirault, Lecarpentier, Markhasin, 2004

Details

Parameters:

NameDescription
a_c5200.0
alpha_P_lengthening16.0
t_d0.033
k_A2.8
q_Ca50.0
alpha_214.6
S_01.14
beta_P_lengthening0.0015
a_on2300.0
Ca_m0.03
B_tot0.4
m_00.9
r_Ca650.0
beta_S_shortening0.006
beta_20.000924
beta_Q5000.0
beta_30.01
F_afterload2.0
alpha_G1.0
b_on2600.0
alpha_S_shortening46.0
A_tot1.0
q_317.3
chi_03.0
a_off290.0
a0.25
mu3.0
alpha_Q10.0
l_00.527
v_star5.3035675
chi0.705
A_half0.6
v_max5.6
q_117.3
lambda96.0
q_star1000.0
alpha_348.0
isotonic0.0
q_415.0
alpha_119.0
q_2259.0
v_0560.0
beta_P_shortening0.0015
alpha_S_lengthening39.0
alpha_P_shortening16.0
b_off182.0
beta_S_lengthening0.008
beta_10.29
d_h0.5
alpha_P4.0

States:

NameDescription
N(time)0.0001
l_3(time)0.089
A(time)0.01
l_2(time)0.439
v(time)0.0
l_1(time)0.437
w(time)0.0
B(time)0.0
Ca_C(time)0.0

keizer_levine_1996v0.0.1

Keizer, Levine, 1996

Details

Parameters:

NameDescription
kb_385.9
ka1500.0
kc_0.1
c10.15
kc1.75
fi0.01
n4.0
v140.0
Co10.0
ka_28.8
m3.0
v20.5
kb1500.0
v31000.0
K30.3

States:

NameDescription
P_O1(time)nothing
P_C1(time)nothing
P_C2(time)nothing
P_O2(time)nothing
Cai(time)nothing
w(time)nothing

kesmir_deboer_1999v0.0.1

Kesmir, Deboer, 1999

Details

Parameters:

NameDescription
pr0.15
SA500.0
mu3.0
rho4.0
sigma5.0
ST50.0
delta_T0.8
KB10000.0
KT100.0
u0.15
z0.02
delta_B0.8
p2.0
d2.0

States:

NameDescription
B10(time)0.0
B9(time)0.0
B1(time)0.0
B5(time)0.0
C_star(time)0.0
B8(time)0.0
M(time)0.0
T(time)0.0
B0(time)3.0
C(time)0.0
B3(time)0.0
B7(time)0.0
A(time)500.0
B2(time)0.0
B4(time)0.0
B6(time)0.0

kholodenko_demin_moehren_hoek_1999v0.0.1

Kholodenko, Demin, Moehren, Hoek, 1999

Details

Parameters:

NameDescription
k146.0
k180.3
k251.0
k90.003
k15_0.0009
k6_0.05
k12_0.0001
k21_0.1
k10_0.06
K16340.0
k1_0.06
k5_0.2
V81.0
k120.0015
K450.0
K8100.0
k31.0
k170.003
k22_0.064
k200.12
k210.003
k100.01
k130.09
k18_0.0009
k7_0.006
k150.3
V161.7
k23_0.021
k20_0.00024
k190.01
k9_0.05
k14_0.06
k220.03
k13_0.6
k61.0
k110.03
k230.1
V4450.0
k11_0.0045
k17_0.1
k3_0.01
k10.003
k2_0.1
k70.3
k24_0.0429
k25_0.03
k19_0.0214
k50.06
k240.009
k20.01

States:

NameDescription
R_Sh_G(time)0.0
EGF(time)680.0
R_PL(time)0.0
R2(time)0.0
R_ShP(time)0.0
Ra(time)0.0
R_Sh_G_S(time)0.0
Sh_G(time)0.0
G_S(time)0.0
R_G_S(time)0.0
ShP(time)0.0
Sh_G_S(time)0.0
R_PLP(time)0.0
RP(time)0.0
PLC_gamma(time)105.0
PLC_gamma_P_I(time)0.0
SOS(time)34.0
Grb(time)85.0
PLC_gamma_P(time)0.0
R_Sh(time)0.0
R(time)100.0
R_G(time)0.0
Shc(time)150.0

kirschner_panetta_1998v0.0.1

Kirschner, Panetta, 1998

Details

Parameters:

NameDescription
mu310.0
s10.0
c0.02
b1.0e-9
mu20.03
s20.0
a1.0
r20.18
p25.0
g2100000.0
p10.1245
g12.0e-7
g31000.0

States:

NameDescription
x(tau)1.0
z(tau)1.0
y(tau)1.0

kneller_ramirez_chartier_courtemanche_nattel_2002v0.0.1

Kneller, Ramirez, Chartier, Courtemanche, Nattel, 2002

Details

Parameters:

NameDescription
T310.0
TRPN_max0.35
K_rel30.0
Ca_up_max15.0
g_Cl_Ca0.3
V_rel96.48
q_Ca0.0
K_sat0.1
delta_CT_n87.8251
i_NaK_max0.6
I_up_max0.005
g_Ca0.24
CMDN_max0.045
g_B_Cl0.0018
g_to0.19824
Cm100.0
g_B_K0.0
Km_K_o1.5
K_mNa87.5
g_Ks0.0561
g_K10.15
tau_tr180.0
g_Kr0.06984
I_NaCa_max1600.0
K_mCa1.38
Na_o140.0
tau_q_Ca2.0
K_up0.00092
g_B_Na0.000674
Ca_o1.8
K_o5.4
V_i13668.0
i_stim-2900.0
g_Na7.8
g_B_Ca0.00113
g_CT0.115
V_up1109.52
i_p_Ca_max0.275
CSQN_max10.0
Cl_o132.0
Km_Na_i10.0
tau_f_Ca2.0
R8.3143
F96.4867
n4.0

States:

NameDescription
Ca_CMDN(time)nothing
oa(time)nothing
oi(time)nothing
Cl_i(time)nothing
xr(time)nothing
v(time)nothing
xs(time)nothing
f(time)nothing
ui(time)nothing
u(time)nothing
j(time)nothing
m(time)nothing
Na_i(time)nothing
w(time)nothing
d(time)nothing
Ca_rel(time)nothing
V(time)nothing
h(time)nothing
ua(time)nothing
Ca_TRPN(time)nothing
K_i(time)nothing
Ca_CSQN(time)nothing
f_Ca(time)nothing
J_Ca_CSQN(time)nothing
Ca_up(time)nothing
Ca_i(time)nothing
J_Ca_TRPN(time)nothing
J_Ca_CMDN(time)nothing

koivumaki_2009v0.0.1

Koivumaki,2009

Details

Parameters:

NameDescription
Kmf_PLB0.15
Na_i14000.0
C_m1.0
T298.0
PKA_reg0.1
kltrpn_pos0.1
SERCA_TOT47.0
kplb_neg6.8
Kmr_PLBKO2500.0
Ca_cyt0.25
Ca_NSR760.0
eta0.35
LTRPN_tot70.0
V_myo2.584e-5
Acap0.0001534
Km_CaM2.38
PLB_tot1.0
A1110.0
PSR1.0
ksat0.1
br_serca_sr0.00625
Ca_pow2.0
kplb_pos1.0
Na_o140000.0
Ca_tau11.5
Ca_tau214.0
CaM_tot24.0
Ca_o1000.0
rest-80.0
KmCa1380.0
J_leak0.0003
KmNa87500.0
CaMKII_reg0.0
A150.0
Kmf_PLBKO0.15
t28.0
kltrpn_neg0.06
t10.5
Kmr_PLB1110.0
kNaCa950.0
Ca_amp2.9
R8.314
F96.5
p2.0

States:

NameDescription
Ca_serca(time)12.0
LTRPN(time)11.0
Ca_cyt(time)0.1
PLB_dephosph(time)0.1

komarova_2005v0.0.1

Komarova 2005

Details

Parameters:

NameDescription
g220.0
beta20.02
g121.0
alpha24.0
alpha13.0
g110.5
k10.24
beta10.2
k20.0017

States:

NameDescription
x2(time)212.132
z(time)100.0
x1(time)10.06066

komarova_smith_dixon_sims_wahl_2003v0.0.1

Komarova, Smith, Dixon, Sims and Wahl, 2003

Details

Parameters:

NameDescription
g220.0
g21-0.5
beta20.02
g121.0
alpha24.0
alpha13.0
g111.1
k10.093
beta10.2
k20.0008

States:

NameDescription
x2(time)212.132
z(time)100.0
x1(time)10.06066

komarova_wodarz_2003v0.0.1

Komarova, Wodarz, 2003

Details

Parameters:

NameDescription
r_51.0
r_10.6
r_30.8
alpha0.1
r_20.7
a0.5
r_40.9
r_81.3
r_61.1
beta0.2
rm1.3
rs1.0
epsilon_m0.1
r_00.5
r_71.2
u0.07
epsilon_s0.99

States:

NameDescription
S_6(time)0.0
M_2(time)0.0
M_0(time)0.5
S_7(time)0.0
M_4(time)0.0
S_3(time)0.0
S_1(time)0.0
S_5(time)0.0
w(time)0.0
M_1(time)0.0
S_4(time)0.0
M(time)0.5
M_7(time)0.0
S_2(time)0.0
M_3(time)0.0
S_0(time)0.5
M_1_2(time)0.0
M_6(time)0.0
M_8(time)0.0
S(time)0.5
M_5(time)0.0
S_8(time)0.0

kongas_vanbeek_2001v0.0.1

Kongas, Vanbeek, 2001

Details

Parameters:

NameDescription
Vb29250.0
R_ADP8.16
Kia900.0
V_hyd4600.0
R_ATP8.16
R_Cr14.6
V_syn_max4600.0
Kid4730.0
Kic222.4
R_PCr14.6
V_cyt0.75
KPi20.0
Kib34900.0
KADP800.0
Kb15500.0
R_Pi18.4
Kd1670.0
V_ims0.0625
Vf6966.0

States:

NameDescription
PCr_i(time)12500.0
Pi(time)8000.0
PCr(time)12500.0
Cr(time)13500.0
ATP_i(time)9644.425
ADP_i(time)2.5
Cr_i(time)13500.0
ATP(time)9644.425
Pi_i(time)8000.0
ADP(time)60.0

korzeniewski_zoladz_2001v0.0.1

Korzeniewski, Zoladz, 2001

Details

Parameters:

NameDescription
k_EFF1.9258
kSN34316.0
T289.0
Ae_SUM1600.2
nA2.5
protonmotive_force190.0
kC1238.95
kPI69.421
kDH28074.0
Nt2970.0
c_buffi0.022
kL12.5
pKa6.8
c_buffe0.025
kL20.038
kUT686.5
pD0.8
KmO120.0
km_A150.0
Ai_SUM16260.0
kDDi282.0
pH_o7.0
dpH0.001
Mg_fi380.0
C_SUM35000.0
kDTi17.0
kEX54572.0
kDDe347.0
R_cm15.0
kC3136.41
kf_CK1.9258
EmU085.0
at135.0
Ema0540.0
BN5.0
km_ADP3.5
kf_AK862.1
Mg_fe4000.0
ct270.0
kb_CK0.00087538
KmN100.0
kDTe24.0
kC4136.41
Emc0250.0
kb_AK22.747
delta_Gp031.9
R0.0083
Ut1350.0
EmN0-320.0
F0.0965

States:

NameDescription
UQH2(time)1.0
ATP_ti(time)1.0
NADH(time)500.0
Hi(time)1.0
PCr(time)1.0
ADP_te(time)1.0
O2(time)1.0
He(time)1.0
Pi_te(time)1.0
Pi_ti(time)1.0
c_2(time)1.0
a_2(time)1.0
ATP_te(time)1.0

kroll_2000v0.0.1

Kroll, 2000

Details

Parameters:

NameDescription
C31.0
K22.0
C50.0
k11.0
C11.0
C21.0
k40.9
k30.05
k60.02
K5.0
k55.0
k21.3
ky0.01

States:

NameDescription
P(time)10.0
Z(time)200.0
X(time)500.0
Y(time)10.0
IL6(time)1.9

kummer_2000v0.0.1

Switching from Simple to Complex Oscillations in Calcium Signaling

Details

We present a new model for calcium oscillations based on experiments in hepatocytes. The model considers feedback inhibition on the initial agonist receptor complex by calcium and activated phospholipase C, as well as receptor type-dependent self-enhanced behavior of the activated G(alpha) subunit. It is able to show simple periodic oscillations and periodic bursting, and it is the first model to display chaotic bursting in response to agonist stimulations. Moreover, our model offers a possible explanation for the differences in dynamic behavior observed in response to different agonists in hepatocytes.

Parameters:

NameDescription
k14153.0
k22.9259
k1013.58
K112.67
k130.12
K150.16
k120.7
k164.85
k10.212
k832.24
K40.19
K170.05
k31.52
K929.09
k71.24
K120.16
k54.88
K61.18
k11153.0

States:

NameDescription
d(time)20.0
b(time)0.01
c(time)0.01
a(time)0.01

kurata_hisatome_imanishi_shibamoto_2002v0.0.1

Kurata, Hisatome, Imanishi, Shibamoto, 2002

Details

Parameters:

NameDescription
K3ni26.44
T310.15
Km_fCa0.00035
K_rel0.0012
TC_tot0.031
Km_Kp1.4
kf_TC88.8
g_h_Na0.1437375
Km_Nap14.0
V_rel4.2223e-15
K1ni395.3
i_NaK_max3.6
Ko5.4
g_to0.18
Kcni26.44
Cm32.0
kb_TC0.446
Qco0.0
g_h_K0.2312625
kf_TMM2.277
Kco3.663
g_Ks0.0259
kf_CM227.7
TMC_tot0.062
tau_tr60.0
g_sus0.02
kf_CQ0.534
P_rel0.5
beta_fCa60.0
CQ_tot10.0
K1no1628.0
K_up0.0006
kb_CM0.542
Cao2.0
Mgi2.5
K2no561.4
tau_dif_Ca0.04
Qn0.4315
g_st0.015
kb_TMM0.751
K3no4.663
g_b_Na0.0054
V_i1.5835e-12
K2ni2.289
kf_TMC227.7
E_CaL45.0
kb_CQ0.445
P_up0.005
Nao140.0
Qci0.1369
Kci0.0207
E_st37.4
V_sub3.5098e-14
kb_TMC0.00751
V_up4.0816e-14
kNaCa125.0
g_CaT0.458
CM_tot0.045
g_CaL0.58
R8.3144e15
F9.6485e16
E_CaT45.0

States:

NameDescription
qa(time)0.426018100136
paF(time)0.3493633709533
piy(time)0.852396631172
f(time)0.626999773853
y(time)0.067156687129
fCQ(time)0.260317260703
fTC(time)0.059206293446
n(time)0.054409723782
fCMs(time)0.074631965653
Ca_sub(time)0.00019074741
fTMC(time)0.602955114871
Nai(time)9.438646305915
q(time)0.531446952485
d(time)0.000602055134
Ca_rel(time)0.296742023718
fTMM(time)0.350600895635
V(time)-58.600291137693
fCa(time)0.589580408056
Ki(time)139.984146485614
fCMi(time)0.116947220413
r(time)0.005550489445
qi(time)0.333330378068
Ca_up(time)1.462338380106
Cai(time)0.000312494921
paS(time)0.629323128348

kyrylov_severyanova_vieira_2005v0.0.1

Kyrylov, Severyanova, Vieira, 2005

Details

Parameters:

NameDescription
a210.031
a22-0.0957
a420.000139
a12-0.0668
S40.01
a33-0.00857
a44-0.000143
a00-0.00843
S10.01
S30.01
S20.01
e20.0
a11-0.004
a100.082
e00.0
a230.0576
S00.01
epsilon0.5
a02-0.44
c00.443
a200.0
a240.000325
e10.0
a320.00869

States:

NameDescription
y2(time)1.17
y3(time)0.95
y1(time)1.4
y4(time)0.65
y0(time)0.4

L


lambeth_kushmerick_2002v0.0.1

Lambeth, Kushmerick, 2002

Details

Parameters:

NameDescription
Keq_GAPDH0.089
K_F6P0.18
V_max_f12000.0
var_e0.01
Keq_PGK57109.0
Keq_CK233.0
K_G6P0.18
Keq_ALD9.5e-5
K_ATP_0.25
Keq_ENOL0.49
K_G1P1.5
K_AMP1.9e-6
K_FBP4.02
d0.01
K_PEP0.08
Ki_GLY_b4.4
Keq_PGLM16.62
Ki_ADP0.135
Ki_Pi4.6
K_PYR7.05
K_F6P_20.0
Keq_PK10304.0
K_three_PG0.2
Keq_PGI0.45
Keq_PGM0.18
K_GLY_f1.7
frac_a0.4
K_FBP_4.02
nH1.75
Keq_TPI0.052
Ki_GLY_f15.0
K_GAP0.32
K_PCr1.11
K_ADP0.3
Lo13.0
K_ADP_2.7
Keq_ADK2.21
K_NADH0.0033
Ka_AMP0.06
K_GLY_b0.15
K_Pi0.2
frac_b0.6
K_NAD0.09
K_two_PG0.014
V_ATPase600.0
Ki_PCr3.9
K_DHAP0.61
K_Cr3.8
Ki_G1P7.4
V_max_r880.0
K_LAC17.0
Keq_LDH16198.0
K_Thirteen_BPG0.0008
K_ATP1.13
Ki_ATP0.87
Keq_GP0.42

States:

NameDescription
PEP(time)0.0194
G6P(time)0.75
Pi(time)4.1
PCr(time)34.67
Cr(time)35.0
AMP(time)0.99
PYR(time)0.0994
two_PG(time)0.005
ATP(time)8.2
GAP(time)0.0355
F6P(time)0.228
Thirteen_BPG(time)0.065
NAD(time)0.5
LAC(time)1.3
DHAP(time)0.0764
FBP(time)0.0723
GLY(time)112.0
G1P(time)0.0589
three_PG(time)0.052
ADP(time)0.013
NADH(time)0.001

Land_et_al_2012v0.0.1

Land et al. 2012

Details

Land et al 2012

Parameters:

NameDescription
T_ref120.0
k_xb0.1
Ca_50ref0.8
perm500.35
n_TRPN2.0
nperm5.0
alpha_10.1
A_1-29.0
a0.35
beta_1-1.5
alpha_20.5
k_off0.1
A_2116.0
beta_01.65

States:

NameDescription
xb(time)0.00046
Q_2(time)0.0
TRPN(time)0.0752
Q_1(time)0.0

landesberg_sideman_1994v0.0.1

Landesberg, Sideman, 1994

Details

Parameters:

NameDescription
fnothing
TRonothing
L_bnothing
F_barnothing
k_minus_hnothing
K_munothing
Ca_rnothing
d_alpha_dtnothing
Bnothing
Q_unothing
g_0nothing
Troponinnothing
I_lnothing
SLnothing
Ca_0nothing
L_anothing
Q_inothing
T_snothing
tau_iRnothing
k_hnothing
Q_onothing
tau_iFnothing
alphanothing
U_snothing
eta_PEnothing
Sp_0nothing
Dnothing
g_1nothing
etanothing
Enothing
Q_snothing
L_znothing
tau_SRnothing
tau_SFnothing
K_maxnothing
L_prime_mnothing
k_1nothing

States:

NameDescription
U_s(time)nothing
Ubar_d(time)nothing
Tbar_s(time)nothing
A_n(time)nothing
Tbar_d(time)nothing
Ubar_s(time)nothing
Abar_d(time)nothing
Rbar_s(time)nothing
Abar_s(time)nothing
Ca(time)nothing
Rbar_d(time)nothing
T_s(time)nothing
R_s(time)nothing
A_s(time)nothing
BCa_h(time)nothing

larsen_olsen_kummer_2003v0.0.1

On the encoding and decoding of calcium signals in hepatocytes

Details

Many different agonists use calcium as a second messenger. Despite intensive research in intracellular calcium signalling it is an unsolved riddle how the different types of information represented by the different agonists, is encoded using the universal carrier calcium. It is also still not clear how the information encoded is decoded again into the intracellular specific information at the site of enzymes and genes. After the discovery of calcium oscillations, one likely mechanism is that information is encoded in the frequency, amplitude and waveform of the oscillations. This hypothesis has received some experimental support. However, the mechanism of decoding of oscillatory signals is still not known. Here, we study a mechanistic model of calcium oscillations, which is able to reproduce both spiking and bursting calcium oscillations. We use the model to study the decoding of calcium signals on the basis of co-operativity of calcium binding to various proteins. We show that this co-operativity offers a simple way to decode different calcium dynamics into different enzyme activities.

Parameters:

NameDescription
K193.5
k200.81
k14153.0
K_M0.62
k1879.0
k100.7
K113.0
k1313.4
K150.16
k_rem3.0
p4.0
k832.24
K214.5
K170.05
K929.09
k122.8
k167.0
k_enz3.0
k10.01
K40.09
k_inact0.04
k_act5.0
k30.64
k72.08
k54.88
k21.75
K61.18

States:

NameDescription
PLC(time)0.01
Ca_ER(time)10.0
Enz(time)0.0
Ca_cyt(time)0.01
Pro(time)0.0
Ca_mit(time)0.001
G_a(time)0.01

lebeau_robson_mckinnon_donald_sneyd_1997v0.0.1

Lebeau, Robson, Mckinnon, Donald, Sneyd, 1997

Details

Parameters:

NameDescription
i_CaTnothing
fnothing
Cainothing
Tnothing
vpnothing
g_K_Canothing
taunothing
Caenothing
Kinothing
i_K_Canothing
Cmnothing
tau_hnothing
tau_nnothing
E_Lnothing
alphanothing
Kenothing
Kpnothing
KCnothing
g_Lnothing
betanothing
g_CaTnothing
g_K_DRnothing
i_K_DRnothing
g_CaLnothing
Ca_eqnothing
tau_m_nothing
Rnothing
i_Leaknothing
Fnothing

States:

NameDescription
V(time)nothing
n(time)nothing
m(time)nothing
h(time)nothing

lebeau_yule_groblewski_sneyd_1999v0.0.1

Lebeau, Yule, Groblewski, Sneyd, 1999

Details

Parameters:

NameDescription
k20.5
alpha_140.0
beta_40.01
K_p0.54
k_flux28.0
alpha_40.06
beta_10.8
k30.5
V_p2.6
k50.02
J_influx0.4
k1_0.88
p3.0

States:

NameDescription
O(time)nothing
I2(time)nothing
c(time)nothing
I1(time)nothing

leloup_goldbeter_1998v0.0.1

Leloup, Goldbeter, 1998

Details

A Model for Circadian Rhythms in Drosophila Incorporating the Formation of a Complex between the PER and TIM proteins

Parameters:

NameDescription
n4.0
V_38.0
k_11.2
V_4P1.0
K_1T2.0
T_1init0.8
K_mT0.2
K_32.0
K_3T2.0
v_sT1.0
K_IT1.0
Y_1init0.8
V_18.0
k_20.2
V_4T1.0
v_dT2.0
K_22.0
V_41.0
k_d0.01
V_21.0
v_d2.0
M_Tinit1.427
V_1P8.0
k_31.2
v_mT0.7
k_sP0.9
P_2init0.01251
K_12.0
K_4P2.0
V_2T1.0
K_1P2.0
k_sT0.9
V_3T8.0
k_dN0.01
Y_0init0.02324
M_Pinit0.09107
T_2init4.733
Y_2init4.733
k_40.6
k_s0.9
K_d0.2
K_dP0.2
T_0init0.542
K_2T2.0
K_42.0
v_dT_dark2.0
K_mP0.2
K_m0.2
V_1T8.0
V_2P1.0
P_1init0.0221
K_I1.0
P_0init0.02324
v_s0.8
K_dT0.2
v_dP2.0
v_dT_light4.0
k_dC0.01
PI3.141592653589793
K_4T2.0
V_3P8.0
K_3P2.0
K_2P2.0
M_init0.09107
v_sP0.8
v_m0.8
K_IP1.0
v_mP0.8

States:

NameDescription
C_N(time)1.203
P_0(time)0.02324
P_2(time)0.01251
T_1(time)0.8
M(time)0.09107
Y_0(time)0.02324
C(time)0.179
T_0(time)0.542
Y_2(time)4.733
Y_1(time)0.8
T_2(time)4.733
P_1(time)0.0221
M_T(time)1.427
M_P(time)0.09107

leloup_goldbeter_2003v0.0.1

Leloup, Goldbeter, 2003

Details

Parameters:

NameDescription
KmB0.4
PCNP_init0.1
Km0.4
MR_init1.5
V11.4
kdmr0.02
V2PC0.2
kdnc0.02
IN_init0.1
CC_init0.1
MC_init1.2
ke0.2
ksC3.2
vdPCN1.4
k30.8
BC_init0.1
vdRC4.4
V3PC2.4
vdCC1.4
ka0.4
vmB1.3
KmP0.3
PCP_init0.1
vsP2.4
MP_init0.1
Kd0.3
k60.4
ks1.2
vdPCC1.4
V2C0.2
V4B0.4
kdmb0.02
V1P9.6
Y_init0.1
vmR1.6
ksB0.32
m2.0
vm2.0
M_init1.2
MB_init9.0
k20.4
n2.0
vdBC3.0
PCN_init0.1
ksR1.7
c2.0
k90.8
vdIN1.6
k80.2
V2P0.6
V3B1.4
V4PC0.2
B0.6
vdRN0.8
vmP2.2
V1C1.2
KmC0.4
KAP0.6
YCP_init0.1
kc1.0
V1B1.4
kdn0.02
KAC0.6
vmC2.0
V1PC2.4
kd0.02
BCP_init0.1
KAR0.6
vsC2.2
KmR0.4
vsB1.8
YC_init0.1
PC_init0.1
k100.4
kdmp0.02
one1.0
ksP1.2
h2.0
V2B0.2
kdm0.02
kdmc0.02
Kdp0.1
k40.4
V20.2
kb0.8
vdPC3.4
vs2.2
A2.2
PCCP_init0.1
BN_init0.1
Kp1.006
PCC_init0.1
vd3.0
k10.8
BNP_init0.1
vsR1.6
CCP_init0.1
KIB2.2
k71.0
RN_init0.1
vdBN3.0
k50.8

States:

NameDescription
IN(time)0.1
PCNP(time)0.1
PCCP(time)0.1
YC(time)0.1
PCN(time)0.1
PCC(time)0.1
MB(time)9.0
MC(time)1.2
BC(time)0.1
BN(time)0.1
PC(time)0.1
MR(time)1.5
M(time)1.2
BCP(time)0.1
CCP(time)0.1
MP(time)0.1
RC(time)0.1
RN(time)0.1
CC(time)0.1
PCP(time)0.1
YCP(time)0.1
Y(time)0.1
BNP(time)0.1

leloup_goldbeter_2004v0.0.1

Leloup, Goldbeter, 2004

Details

Parameters:

NameDescription
vdBC1.0
PCN_init0.1
c4.0
vdIN0.8
KmB0.4
PCNP_init0.1
Km0.4
k80.1
V2PC0.1
V11.0
V2P0.3
V3B1.0
kdnc0.01
IN_init0.1
V4PC0.1
vstot1.0
vmP1.1
B1.0
V1C0.6
CC_init0.1
KmC0.4
KAP0.7
YCP_init0.1
MC_init0.3
kc0.5
V1B1.0
kdn0.01
KAC1.0
ke0.1
vdPCN1.0
vmC1.0
kd0.01
BCP_init0.1
k30.8
BC_init0.1
kstot1.0
YC_init0.1
vdCC0.7
ka0.2
Vphos0.6
vmB0.2
PC_init0.1
KmP0.3
PCP_init0.1
kdmp0.01
V2B0.1
kdm0.01
kdmc0.01
Kdp0.3
k40.2
V20.1
kb0.8
MP_init0.5
Kd0.3
k60.2
vdPC0.7
vdPCC1.0
V2C0.1
V4B0.2
A0.8
PCCP_init0.1
BN_init0.1
Kp0.1
PCC_init0.1
vd1.0
k10.8
kdmb0.01
BNP_init0.1
Y_init0.1
m4.0
CCP_init0.1
KIB0.8
vm1.0
MB_init3.1
M_init0.3
k70.5
vdBN0.5
k50.4
k20.2
n4.0

States:

NameDescription
IN(time)0.1
BC(time)0.1
PCNP(time)0.1
M(time)0.3
PCCP(time)0.1
PC(time)0.1
BN(time)0.1
YC(time)0.1
BCP(time)0.1
YCP(time)0.1
CCP(time)0.1
MP(time)0.5
PCN(time)0.1
CC(time)0.1
PCP(time)0.1
PCC(time)0.1
Y(time)0.1
MB(time)3.1
MC(time)0.3
BNP(time)0.1

leloup_gonze_goldbeter_1999v0.0.1

Leloup, Gonze, Goldbeter, 1999

Details

Parameters:

NameDescription
KIT1.0
ksT0.9
T1_init0.1
V38.0
K4T1.0
P2_init0.1
K32.0
V3P8.0
Km0.5
V18.0
K3T2.0
V2P1.0
KIP1.0
K2T2.0
KmT0.2
T2_init0.1
vmP0.7
V2T1.0
V4P1.0
vdT2.0
vdP2.0
K2P2.0
Y1_init0.1
kd0.01
K41.0
P0_init0.1
T0_init0.1
MT_init1.6
V1T8.0
k31.2
K3P2.0
V4T1.0
K12.0
K22.0
KmP0.2
V3T8.0
vsT1.0
ksP0.9
Y2_init0.1
k40.6
vsP1.0
V21.0
MP_init0.1
kdN0.01
Kd0.13
KI1.0
vmT0.7
KdT0.2
ks0.5
vs1.6
Y0_init0.1
K4P1.0
V41.0
vd1.4
KdP0.2
k10.5
V1P8.0
P1_init0.1
K1P2.0
vm0.505
M_init0.1
kdC0.01
K1T2.0
k20.6
n4.0

States:

NameDescription
T1(time)0.1
P0(time)0.1
FC(time)0.1
M(time)0.1
C(time)0.1
P1(time)0.1
T2(time)0.1
MT(time)1.6
MP(time)0.1
FN(time)0.1
Y1(time)0.1
P2(time)0.1
T0(time)0.1
CN(time)1.25
Y2(time)0.1
Y0(time)0.1

lemaire_tobin_greller_cho_suva_2004v0.0.1

Lemaire, Tobin, Greller, Cho, Suva, 2004

Details

Parameters:

NameDescription
Io0.0
DC0.0021
ko0.35
f00.05
KOP200000.0
SP250.0
kB0.189
dB0.7
k40.017
DA0.7
k63.0
DR0.0007
IP0.0
k10.01
KLP3.0e6
kP86.0
C_s0.005
k30.00058
rL1000.0
K10.0
k50.02
k210.0
IL0.0

States:

NameDescription
R(time)0.0
C(time)0.0
B(time)0.0

lemon_gibson_bennett_2003v0.0.1

Lemon, Gibson, Bennett, 2003

Details

Parameters:

NameDescription
eta_25.2
K_c0.4
epsilon_r0.185
N_a6.02252e17
L1000.0
a_20.2
delta0.001238
C_T67.0
K_e10.0
B_ER120000.0
B_x50.0
r_r10.0
G_T100000.0
eta_345.0
xi0.85
K_2100.0
d_21.05
v5.0e-13
K_x0.2
k_d0.15
B_e150.0
alpha2.781e-5
k_deg1.25
k_a0.017
d_30.943
d_50.0823
k_30.4
eta_1575.0
PIP_2_T5.0e7
d_10.13
R_T20000.0
K_15.0
k_e0.006
K_ER1200.0
k_r0.000175
k_p0.03

States:

NameDescription
PIP_2(time)4.9997e7
G(time)0.0
h(time)0.6155
RS_p(time)0.0
IP_3(time)0.01
RS(time)17000.0
C(time)0.0961

lenbury_pacheenburawana_1991v0.0.1

Lenbury, Pacheenburawana, 1991

Details

Parameters:

NameDescription
omega2.0
alpha0.5
b1.091
gamma0.6
D0.8228
a8.1252
beta0.38

States:

NameDescription
x(time)1.5
y(time)0.95
z(time)1.0

lenbury_pornsawad_2005v0.0.1

Lenbury, Pornsawad, 2005

Details

Parameters:

NameDescription
delta10.5
delta20.38
delta30.6
beta1.091

States:

NameDescription
x(time)1.0
y(time)0.01
z(time)0.01

lenbury_ruktamatakul_amornsamarnkul_2001v0.0.1

Lenbury, Ruktamatakul, Amornsamarnkul, 2001

Details

Parameters:

NameDescription
c10.1
r50.09
r_20.1
delta0.01
r_40.1
r40.03
r_60.1
omega0.05
c_10.1
r_70.05
y_hat1.24
y_1.08
c_20.1
r30.05
c20.1
r_50.1
r_10.2
r_30.1
z_1.01
r70.05
r10.15
r20.12
z_hat2.0
epsilon0.1
c30.005
r60.1

States:

NameDescription
u(time)1.0
v(time)0.0
x(time)5.0
y(time)0.0
z(time)1.0

li_bertram_rinzel_1996v0.0.1

Li, Bertram and Rinzel, 1996

Details

Parameters:

NameDescription
C_m1.0
k_Ca1.0
V_h-30.0
g_K_Ca1.2
K_p15.0
R_pump18.0
V_K-85.0
g_K_DR_D0.14
g_h0.1
K_Ca0.0004
V_NMDA0.0
V_Na55.0
g_K_DR_s6.4
q12.5
g_Na_s3.2
alpha0.5
K_Mg10.0
g_Na3.2
K_Na15.0
g_L0.18
V_L-50.0
beta0.104
I_APP-6.7
Na_eq8.0
g_NMDA1.25
V_Ca120.0
Mg_o1.4
g_Ca_T1.5
g_Ca_L0.19
g_K_DR3.2
g_Na_NMDA1.0
g_c0.0
g_A2.0
p0.5

States:

NameDescription
h(time)1.0
a(time)0.1
V_s(time)-64.0
Na(time)5.09
m_L(time)0.1
h_T(time)0.1
Ca(time)0.0
b(time)0.1
m_h(time)0.1
n(time)0.002
V_D(time)-25.0
m_T(time)0.1

li_kuang_mason_2006v0.0.1

Li, Kuang, Mason, 2006

Details

Parameters:

NameDescription
C31000.0
Rm210.0
Gin0.54
a1300.0
Ub72.0
alpha0.29
C480.0
di0.06
E0.2
Um940.0
beta1.77
C12000.0
C2144.0
ti100.0
U040.0
Vp3.0
C526.0
Vg10.0
Rg180.0
Vi11.0

States:

NameDescription
G(time)1000.0
I(time)9000.0

li_rinzel_1994v0.0.1

Li, Rinzel, 1994

Details

Parameters:

NameDescription
c10.185
v41.8
v140.0
d_inh0.4
k_er0.18
a1.0
d_act0.4
IP30.6
k_pl0.1
d_ip30.2
epsilon0.01

States:

NameDescription
j_in(time)1.2
h(time)0.8
v3(time)0.6
C(time)0.2
v2(time)0.02
c0(time)2.0

li_smith_2009v0.0.1

Li, Smith, 2009

Details

Parameters:

NameDescription
const56.6755
T308.0
Km_CSQN800.0
delta_V_L7.0671
stim_offset100.0
P_ryr_const1-0.09
Km_Nai21000.0
k_plus_a0.006075
kf0.023761
Bmax109.0
Km_Cl10.0
Ko5400.0
i_NaK_max1.66
on_rate0.05
Cm1.0
K_L0.0964
vmup_init0.3158
E_Cl-40.0
g_Kto_f0.4067
k_sat0.1
K_mNa86500.0
eta0.35
V_L-2.0
g_Ks0.00575
g_K10.2938
i_CaL_max4.0
tau_tr20.0
g_Kr0.078
Acap0.00013866
K_mCa1380.0
Km_pCa0.4
P_ryr_const2-0.225
k_minus_a0.07125
P_CaL19.1078
stim_duration3.0
k_minus_b0.965
v14.5
i_pCa_max0.9
Cao1400.0
b14.0
Vmyo2.2e-5
g_Nab0.0026
tau_xfer8.0
Km_up0.412
g_Kto_s0.0
a0.07
Km_Ko1500.0
stim_period333.3333333
kb0.036778
Kd0.6
k_plus_b0.00405
CSQN_tot15000.0
off_rate0.00068
Nao134000.0
g_Na13.0
VJSR1.022e-7
k_plus_c0.009
g_Cab0.00088
stim_amplitude-15.0
tau_L972.9715
g_ClCa10.0
VNSR1.786e-6
m3.0
phi_L1.6411
g_Kss0.05
v21.0e-5
k_minus_c0.0008
Vss1.264e-9
g_Kur0.16
k_NaCa772.8991
R8.314
t_L1.1683
F96.5
n4.0

States:

NameDescription
C_Na2(time)0.01702105
O_K(time)0.0004858865
I(time)0.009171979
O_Na(time)2.639399e-7
ato_f(time)0.001937245
P_C2(time)0.3797679
I2_Na(time)5.460299e-6
C_K2(time)0.0005301217
O(time)4.373318e-6
IC_Na2(time)0.005985434
C_Na1(time)0.0001581035
P_RyR(time)2.290355e-9
ito_f(time)0.9999985
nKs(time)0.002206261
I1_Na(time)1.799179e-5
Nai(time)16522.45
Cass(time)0.1043777
y_gate(time)0.8876797
IC_Na3(time)0.2543133
ato_s(time)0.02000568
V(time)-85.64004
IF_Na(time)5.56206e-5
CaJSR(time)730.0589
C_K1(time)0.0007799137
CaMKt(time)0.08989079
aur(time)0.02000568
iur(time)0.9822006
iKss(time)1.0
P_O1(time)0.003825599
Ki(time)141474.0
I_K(time)7.519518e-5
CaNSR(time)841.106
ito_s(time)0.9308568
Cai(time)0.1040595
P_O2(time)1.835831e-8
aKss(time)0.8883113

lindblad_murphey_clark_giles_1996v0.0.1

Lindblad, Murphey, Clark, Giles, 1996

Details

Parameters:

NameDescription
KmK10.59
T308.0
stim_start0.1
P_Na1.4e-6
Mg_i2.5
d_NaCa0.0003
alpha_rel200.0
k_NaK_K1.0
i_NaK_max0.06441
I_up_max2.8
g_to0.050002
g_B_Cl0.00012
k_CaP0.0002
Cm5.0e-5
shiftK1-3.6
Ca_c2.5
Vol_rel4.41e-8
Vol_i1.26e-5
k_rel0.0003
Cl_c132.0
Vol_up3.969e-7
g_Ks0.0025
g_K10.005088
k_xcs0.4
tau_tr0.01
g_Kr0.0035
g_Ca_L0.004
steepK11.393
stim_duration0.0008
K_c5.0
Na_c140.0
g_B_Na6.4e-5
E_Ca_T38.0
stim_period1.0
stim_end100000.0
k_NaK_Na11.0
k_srca0.5
Cl_i30.0
i_CaP_max0.009509
g_B_Ca3.1e-5
stim_amplitude-2.0
k_cyca0.0003
Vol_Ca5.884e-6
E_Ca_app60.0
g_Ca_T0.006
gamma0.45
k_NaCa2.0e-5
k_F30.815
R8314.472
F96485.3415

States:

NameDescription
O_TC(time)0.01442
F3(time)0.68492
s2(time)0.39871
O_Calse(time)0.41837
f_T(time)0.30752
s3(time)0.57363
d_L(time)3.0e-5
s1(time)0.5753
m(time)0.01309
Na_i(time)8.4
O_C(time)0.02981
d_T(time)0.00046
Ca_rel(time)0.59984
h2(time)0.61493
O_TMgMg(time)0.67476
V(time)-69.83663
p_i(time)0.76898
p_a(time)0.00016
z(time)0.02032
K_i(time)100.0
r(time)6.0e-5
F1(time)0.21603
f_L(time)0.99981
h1(time)0.706
Ca_up(time)0.64913
Ca_i(time)7.305e-5
F2(time)0.00205
O_TMgC(time)0.23532

liu_hu_peng_liu_1999v0.0.1

Liu, Hu, Peng, Liu, 1999

Details

Parameters:

NameDescription
a21200.0
a13460.0
a20.0023
a11.7e-5
lambda_10.059
a150.1
a229400.0
a183800.0
a70.28
a1218.0
lambda_30.0986
a536.0
a1957.0
a270.57
a30.6
lambda_53.0e-5
lambda_40.024
a140.46
a445.0
a6216.0
lambda_20.028
a100.18
a80.36
a11150.0
a17150.0
a2310.0
a250.04
a260.00097
a160.04
a90.0003
a202600.0
a280.0017
a24320.0

States:

NameDescription
x4(time)60.61
x3(time)6.51
x5(time)12.61
x2(time)0.04665
x1(time)0.01067

livshitz_rudy_2007v0.0.1

Livshitz, Rudy, 2007

Details

Parameters:

NameDescription
prnak0.01833
GNa16.0
qn9.0
gcab0.003016
ganai0.75
GKsmax0.433
iupbar0.00875
tau4.75
Temp310.0
pk1.93e-7
stim_offset0.0
kmup0.00092
ibarpca1.15
tautr120.0
kmko1.5
GKpmax0.00552
kmpca0.0005
c20.0001
K_Relss1.0
l0.01
trpnbar0.07
gako0.75
kmtrpn0.0005
c10.00025
Na_o140.0
nsrbar15.0
stim_duration3.0
ibarnak2.25
csqnbar10.0
Ca_o1.8
stim_period400.0
kmcmdn0.00238
pna6.75e-7
kappa0.125
gacai1.0
K_o4.5
ganao0.75
gacao0.341
ra0.0011
GNab0.004
kmnai10.0
GK1max0.75
gcat0.05
kmca0.0006
kmcsqn0.8
pca0.00054
stim_amplitude-15.0
gammas0.15
gaki0.75
R8314.0
cmdnbar0.05
F96485.0
gkrmax0.02614

States:

NameDescription
d(time)3.2514786721066e-27
g(time)0.952834331760863
xr(time)0.000162194715543637
Ca_JSR_T(time)7.87371650296567
Ca_NSR(time)2.71518235696672
V(time)-89.4356034692784
f(time)0.997404948824816
K_i(time)139.730914103161
J(time)0.996100688673679
Rel(time)1.06874246141923e-23
Over(time)1.0e-12
xs1(time)0.0285147332973946
b(time)0.000927461915392873
H(time)0.994401369032678
Ca_T(time)0.0257059808595638
m(time)0.000734780346592185
xs2(time)0.0764114040188678
Na_i(time)16.612739313555

lockwood_ewy_hermann_holford_2006v0.0.1

Lockwood, Ewy, Hermann, Holford, 2006

Details

Application of Clinical Trial Simulation to Compare Proof-of-Concept Study Designs for Drugs with a Slow Onset of Effect; An Example in Alzheimer’s Disease

Parameters:

NameDescription
t_half_eq_p6.0
t_half_el_p7.0
alpha0.0164
beta_a-0.047
k_ab115.44
CL_ic763.2
age40.0
S030.0
epsilon0.0
beta_P-3.0
Vp222.0
CeA25.0
smk1.0
Vc172.0

States:

NameDescription
CC(time)0.0
PC(time)0.0
A_in(time)25.0

lokta_volterrav0.0.1

Lokta, Volterra

Details

Predator-prey equations

Parameters:

NameDescription
B1.0
A1.0
C1.0
D1.0

States:

NameDescription
x(t)3.0
y(t)6.0

Lorenz_1963v0.0.1

Deterministic Nonperiodic Flow

Details

The Lorenz attractor, named for Edward N. Lorenz, is an example of a non-linear dynamic system corresponding to the long-term behavior of the Lorenz oscillator. The Lorenz oscillator is a 3-dimensional dynamical system that exhibits chaotic flow, noted for its lemniscate shape. The map shows how the state of a dynamical system (the three variables of a three-dimensional system) evolves over time in a complex, non-repeating pattern.

From http://en.wikipedia.org/wiki/Lorenz_attractor

States:

NameDescription
z(t)1.05
x(t)0.0
y(t)1.0

lovell_cloherty_celler_dokos_2004v0.0.1

Lovell, Cloherty, Celler, Dokos, 2004

Details

Parameters:

NameDescription
K3ninothing
PKNa_snothing
beta1_Eslopenothing
Tnothing
beta4_0nothing
g_bClnothing
alpha2_Eslopenothing
beta2_0nothing
Iup_maxnothing
beta1_0nothing
alpha4_0nothing
beta4_infinitynothing
Vupnothing
K1ninothing
PKNa_rnothing
alpha3_infinitynothing
Venothing
Cabnothing
alpha3_Eslopenothing
g_f_Knothing
beta3_Eslopenothing
Kbnothing
beta3nothing
P_f_Knothing
g_tonothing
Kcninothing
Cmnothing
beta2_E50nothing
beta4nothing
Qconothing
alpha3_E50nothing
beta1_E50nothing
beta4_Eslopenothing
alpha2_0nothing
alpha1_infinitynothing
Kconothing
g_Ksnothing
alpha2_infinitynothing
alpha4_Eslopenothing
alpha1_Eslopenothing
tau_bnothing
g_Krnothing
Km_Caupnothing
tau_trnothing
alpha4_E50nothing
alpha1_E50nothing
alpha3_0nothing
Km_Nanothing
tau_relnothing
beta3_E50nothing
K1nonothing
Clbnothing
alpha1_0nothing
beta3_infinitynothing
Km_fnothing
K2nonothing
Qnnothing
Nabnothing
Km_Carelnothing
beta2_infinitynothing
beta3_0nothing
beta4_E50nothing
K3nonothing
alpha3nothing
K2ninothing
Vinothing
Qcinothing
Kcinothing
g_Nanothing
alpha4nothing
alpha2_E50nothing
g_f_Nanothing
beta2_Eslopenothing
kNaCanothing
g_CaTnothing
Km_Knothing
Ip_maxnothing
g_CaLnothing
alpha4_infinitynothing
beta1_infinitynothing
Rnothing
Vrelnothing
Fnothing
Kb_Knothing

States:

NameDescription
Caup(time)nothing
A_Kr(time)nothing
Em(time)nothing
A_to(time)nothing
Cli(time)nothing
A_CaL(time)nothing
Cao(time)nothing
A_f(time)nothing
Clo(time)nothing
Ko(time)nothing
A_Ks(time)nothing
I2(time)nothing
Ki(time)nothing
A_CaT(time)nothing
I3(time)nothing
Cai(time)nothing
Nai(time)nothing
Carel(time)nothing
A_Na(time)nothing
I1(time)nothing
Nao(time)nothing

luo_rudy_1991v0.0.1

Luo, Rudy, 1991

Details

Parameters:

NameDescription
g_b0.03921
stim_duration2.0
T310.0
C1.0
stim_start100.0
Nao140.0
g_Na23.0
PR_NaK0.01833
E_b-59.87
g_Kp0.0183
Ki145.0
stim_end9000.0
stim_period1000.0
Nai18.0
stim_amplitude-25.5
Ko5.4
R8314.0
F96484.6

States:

NameDescription
d(time)0.00302126301779861
j(time)0.989108212766685
V(time)-84.3801107371
h(time)0.982660523699656
X(time)0.0417603108167287
m(time)0.00171338077730188
Cai(time)0.00017948816388306
f(time)0.999967936476325

luo_rudy_1994v0.0.1

Luo, Rudy, 1994

Details

Parameters:

NameDescription
gamma_Cai1.0
gamma_Cao0.34
T310.0
P_Na6.75e-9
Km_Ca0.0006
delta_Ca_i20.0
K_mup0.00092
G_rel_max60.0
delta_Ca_ith0.00018
K_sat0.1
Ko5.4
gamma_Nao0.75
tau_on2.0
Cm0.01
stimCurrent0.5
stimDuration0.5
P_ns_Ca1.75e-9
V_NSR0.0552
Am200.0
PR_NaK0.01833
K_mNa87.5
eta0.35
V_myo0.68
tau_tr180.0
Ca_NSR_max15.0
g_K_max0.00282
K_mCa1.38
g_K1_max0.0075
Cao1.8
g_Nab1.41e-5
t_CICR0.0
gamma_Nai0.75
K_mpCa0.0005
V_JSR0.0048
gamma_Ki0.75
K_m_ns_Ca0.0012
tau_off2.0
I_pCa0.0115
I_NaK0.015
Nao140.0
K_mNai10.0
P_Ca5.4e-6
g_Na0.16
stimPeriod1000.0
I_up0.005
g_Cab3.016e-5
g_Kp0.000183
K_mrel0.0008
gamma_Ko0.75
K_NaCa20.0
K_mKo1.5
R8314.5
P_K1.93e-9
F96845.0

States:

NameDescription
d(time)0.0
V(time)-84.624
X(time)0.0
Ca_NSR(time)1.8
h(time)1.0
f(time)1.0
Ca_JSR(time)1.8
Ki(time)145.0
j(time)1.0
m(time)0.0
Cai(time)0.00012
Nai(time)10.0

M


macgregor_leng_2005v0.0.1

Macgregor, Leng, 2005

Details

Parameters:

NameDescription
delta_r0.2
c0.01
Ise10.0
theta_330.0
Is250.0
theta_11.0
n14.0
k80.07
theta_230.0
delta60.0
sr-0.56
k40.5
sb0.029
g20.008
k65.0
n35.0
g11.0
j110.0
gmax5.0
k10.1
Ih50.0
n22.0
delta115.0
k30.018
delta_b0.3
k75.0
k571.0
k20.002

States:

NameDescription
hh(time)0.0
g(time)2.0
r(time)0.0
h(time)0.0
s(time)0.0
f(time)0.3
se(time)0.0

magnus_keizer_1997v0.0.1

Magnus, Keizer, 1997

Details

Parameters:

NameDescription
pH_mnothing
nanothing
fnothing
rbnothing
Jmax_antnothing
Tnothing
Na_inothing
Ca_inothing
Lnothing
pbnothing
K_Canothing
Jmax_uninothing
pH_inothing
ATP_mnothing
panothing
gnothing
Cmitonothing
g_Hnothing
pc2nothing
ATP_inothing
r2nothing
ADP_inothing
pc1nothing
rho_F1nothing
p2nothing
p1nothing
rc2nothing
p3nothing
V_offsetnothing
bnothing
fmnothing
K_transnothing
ranothing
rho_resnothing
r3nothing
V_Bnothing
NAD_mnothing
K_resnothing
Jmax_Na_Canothing
Pi_mnothing
K_Nanothing
NADH_mnothing
K_actnothing
r1nothing
K_F1nothing
rc1nothing
Rnothing
Fnothing
nnothing

States:

NameDescription
V(time)nothing
Ca_m(time)nothing
ADP_m(time)nothing

magnus_keizer_1998v0.0.1

Magnus, Keizer, 1998

Details

Parameters:

NameDescription
K_ttnothing
nanothing
k_Canothing
Cnothing
V_Knothing
K_Canothing
Jmax_ANTnothing
beta3nothing
ATP_mnothing
beta6nothing
K_ddnothing
g_Hnothing
pc2nothing
Jmax_NaCanothing
k_minus_2nothing
g_K_ATPnothing
K_tdnothing
r2nothing
glunothing
Tminnothing
rho_F1nothing
p1nothing
pc1nothing
n_hydnothing
ATP_m_freenothing
tau_hydnothing
p3nothing
bnothing
K_transnothing
beta7nothing
beta1nothing
r3nothing
k_hydnothing
k_plus_2nothing
alphanothing
K_resnothing
gamma2nothing
beta5nothing
Jp_TCAnothing
f_inothing
K_actnothing
r1nothing
rc1nothing
Fnothing
nnothing
pH_mnothing
fnothing
Tnothing
tau_Ca_fnothing
k_plus_3nothing
delta_psi_offsetnothing
Lnothing
pbnothing
delta_J_gly_totalnothing
beta2nothing
tau_Inothing
Jmax_uninothing
g_Canothing
J_red_basalnothing
K_Ca2nothing
pH_inothing
panothing
gnothing
beta4nothing
Cmitonothing
beta_maxnothing
u2nothing
k_minus_3nothing
rc2nothing
p2nothing
g_NSnothing
fmnothing
K_NSnothing
Ca_onothing
TJnothing
ranothing
delta_J_hyd_maxnothing
rho_resnothing
u1nothing
K_Nanothing
Pi_mnothing
K_glunothing
g_K_drnothing
gamma1nothing
K_F1nothing
Rnothing
rbnothing
Na_inothing

States:

NameDescription
NADH_m(time)nothing
V(time)nothing
I(time)nothing
Ca_m(time)nothing
C(time)nothing
B(time)nothing
J(time)nothing
delta_J_hyd(time)nothing
delta_psi(time)nothing
n(time)nothing
ADP_i(time)nothing
ADP_m(time)nothing
Ca_i(time)nothing

mahajan_shiferaw_sato_baher_olcese_xie_yang_chen_restrepo_karma_garfinkel_qu_weiss_2008v0.0.1

Mahajan, Shiferaw, Sato, Baher, Olcese, Xie, Yang, Chen, Restrepo, Karma, Garfinkel, Qu, Weiss, 2008

Details

Parameters:

NameDescription
gca182.0
T308.0
cup0.5
ay0.05
kmem0.3
stim_offset0.0
xmcai0.0036
s68.0
sx3.0
av11.3
wca8.0
tca78.0329
xmcao1.3
taur30.0
k2t0.00224
vx-40.0
xmnao87.5
vy-40.0
gtos0.04
prNaK0.01833
gNaK1.5
bcal24.0
xkon0.0327
xkdna0.3
r23.0
xkmko1.5
xkmnai12.0
vyr-40.0
ksar13.0
gkr0.0125
syr11.32
gtof0.11
Na_o136.0
gleak2.069e-5
vth0.0
gks0.1386
K_i140.0
stim_duration3.0
taups0.5
Ca_o1.8
gdyad9000.0
taupo1.0
gryr2.58079
stim_period400.0
k1t0.00413
xkcal7.0
ax0.3576
s1t0.00195
K_o5.4
taud4.0
srmax47.0
xmnai12.3
cstar90.0
gna12.0
gbarsr26841.8
gkix0.3
taua100.0
cpt6.09365
srkd0.6
gNaCa0.84
sy4.0
kj50.0
tau33.0
pca0.00054
stim_amplitude-15.0
r10.3
cat3.0
bsar42.0
btrop70.0
vup0.4
bmem15.0
R8.314472
xkoff0.0196
F96.4853415
k20.000103615

States:

NameDescription
trops(time)19.864701949854
xi2ca(time)0.004173008466
xi1ba(time)3.3616596e-5
xr(time)0.007074239331
Ca_NSR(time)104.450004990523
xtof(time)0.003643592594
xir(time)0.006679257264
c2(time)0.979322592773
xh(time)0.990691306716
xs1(time)0.048267587131
Ca_dyad(time)1.716573130685
xs2(time)0.105468807033
Na_i(time)11.441712311614
V(time)-87.169816169406
Ca_submem(time)0.226941113355
xj(time)0.993888937283
c1(time)1.8211252e-5
ytos(time)0.174403618112
xtos(time)0.00364776906
Ca_JSR(time)97.505463697266
xm(time)0.001075453357
ytof(time)0.993331326442
xi1ca(time)0.001208153482
xi2ba(time)0.015242594688
tropi(time)22.171689894953
Ca_i(time)0.256752008084

maldonado_borchers_findeisen_allgower_2006v0.0.1

Maldonado, Borchers, Findeisen and Allgower, 2006

Details

Parameters:

NameDescription
Io0.0
SP250.0
X_c0.0009127
k_yd1.0
K_l_p3.0e6
D_A0.7
k_nokl100.0
k_nod1000.0
k_res0.01
k_y1.0
Il0.0
IP0.0
X_bss0.0007282
k_B0.189
k_for0.001
C_s0.005
k30.00058
k_pger0.0001
K10.0
k_Fs1.0
K_o_p200000.0
f00.05
ko0.35
X_y0.0073
X_yss0.0073
k_rB1.0
X_b0.0007282
k_nopg10.0
dB0.7
k40.017
k_byp0.1
k63.0
k_opgd0.35
k_yno20000.0
D_C0.189
D_R0.0007
k10.01
k_nopge1.0
k_pged100.0
kP86.0
X_noe0.0
k_ypge100.0
X_pgex0.0
k50.02
rl1000.0
k210.0

States:

NameDescription
x_no(time)0.02
xy(time)0.0073
xc(time)0.0009127
xr(time)0.0007734
r_B(time)0.9912
x_kl(time)0.01
x_pge(time)0.01
x_opg(time)0.01
xb(time)0.0007282

maleckar_greenstein_trayanova_giles_2009v0.0.1

Maleckar, Greenstein, Trayanova, Giles, 2009

Details

Parameters:

NameDescription
gamma_Na0.45
k_Ca0.025
T306.15
P_Na0.0018
tau_K10.0
Mg_i2.5
stim_offset0.0
d_NaCa0.0003
tau_di0.01
alpha_rel200000.0
i_NaK_max68.55
I_up_max2800.0
phi_Na_en0.0
k_CaP0.0002
Cm50.0
Ca_b1.8
Vol_rel4.41e-5
Vol_i0.005884
g_kur2.25
Na_b130.0
Vol_up0.0003969
g_Ks1.0
g_K13.1
k_xcs0.4
tau_tr0.01
g_Kr0.5
k_rel_i0.0003
g_Ca_L6.75
ACh1.0e-24
pow_K_NaK_Na_1536.4829
stim_duration0.006
g_B_Na0.060599
k_rel_d0.003
stim_period1.0
K_NaK_K1.0
k_srca0.5
g_t8.25
tau_Ca24.7
Vol_d0.00011768
r_recov0.815
i_CaP_max4.0
Vol_c0.000800224
g_B_Ca0.078681
stim_amplitude-15.0
tau_Na14.3
k_cyca0.0003
E_Ca_app60.0
K_NaCa0.0374842
R8314.0
F96487.0
K_b5.4

States:

NameDescription
O_TC(time)0.012922
O_Calse(time)0.431547
O(time)1.38222
n(time)0.004374
d_L(time)1.4e-5
m(time)0.003289
f_L1(time)0.998597
s(time)0.948597
Na_i(time)8.516766
O_C(time)0.026766
pa(time)5.3e-5
Ca_rel(time)0.632613
h2(time)0.873881
O_TMgMg(time)0.714463
V(time)-74.031982
K_c(time)5.560224
f_L2(time)0.998586
Ca_c(time)1.815768
K_i(time)129.485991
Ca_d(time)7.1e-5
r(time)0.001089
F1(time)0.470055
h1(time)0.877202
Na_c(time)130.022096
Ca_up(time)0.649195
a_ur(time)0.000367
Ca_i(time)6.5e-5
F2(time)0.002814
O_TMgC(time)0.190369
i_ur(time)0.96729

maltsev_2009v0.0.1

Maltsev 2009

Details

Parameters:

NameDescription
K3ni26.44
T310.15
Km_fCa0.00035
TC_tot0.031
Km_Kp1.4
kf_TC88.8
Km_Nap14.0
K1ni395.3
EC50_SR0.45
i_NaK_max2.88
Ko5.4
MaxSR15.0
Kcni26.44
Cm32.0
L_sub0.02
g_to0.252
alpha_fCa0.021
kb_TC0.446
Qco0.0
V_nsr_part0.0116
kf_TMM2.277
Kco3.663
g_Ks0.0259
kf_CM227.7
TMC_tot0.062
kim0.005
V_i_part0.46
g_Kr0.08113973
kf_CQ0.534
tau_tr40.0
g_sus0.02
g_b_Ca0.0006
CQ_tot10.0
K1no1628.0
K_up0.0006
kb_CM0.542
Cao2.0
g_if0.15
Mgi2.5
VIf_half-64.0
K2no561.4
Ki140.0
Qn0.4315
g_st0.003
tau_dif_Ca0.04
kb_TMM0.751
koCa10.0
K3no4.663
kom0.06
g_b_Na0.00486
K2ni2.289
kf_TMC227.7
MinSR1.0
ks250000.0
E_CaL45.0
kb_CQ0.445
P_up0.012
Qci0.1369
Nao140.0
HSR2.5
kiCa0.5
E_st37.4
Kci0.0207
kb_TMC0.00751
Nai10.0
V_jsr_part0.0012
kNaCa187.5
L_cell70.0
g_CaT0.1832
R_cell4.0
g_CaL0.464
CM_tot0.045
R8314.4
F96485.0
E_CaT45.0

States:

NameDescription
qa(time)0.42380243163
paS(time)0.453100576739
paF(time)0.144755091176
dT(time)0.00504393374639
I(time)7.86181717518e-8
pi_(time)0.849409822329
y(time)0.113643187247
fT(time)0.420757825415
fCQ(time)0.273207128393
O(time)1.7340201253e-7
Ca_nsr(time)1.49348117734
fTC(time)0.0291316176172
n(time)0.0264600410928
fCMs(time)0.054381370046
Ca_sub(time)0.000138112560112
fTMC(time)0.432694959597
q(time)0.694241313965
Ca_jsr(time)0.316762674605
RI(time)0.311951987007
fTMM(time)0.501049376634
fCa(time)0.711395919653
fCMi(time)0.0594880901438
r(time)0.00558131733359
qi(time)0.447294008304
Vm(time)-57.9639346865
R(time)0.688047760973
dL(time)0.000584545564405
Cai(time)0.000150018670943
fL(time)0.862381249774

margaridamartins_mendes_coreiro_pocesfreire_2001v0.0.1

Margaridamartins, Mendes, Coreiro, Pocesfreire, 2001

Details

Parameters:

NameDescription
HTA1.0
Kmq0.49
V0.0812
Kmp0.61
Kms0.61
Keq0.61
D_lactate0.0

States:

NameDescription
SDLGSH(time)1.0
GSH(time)1.0

marhl_haberichter_brumen_heinrich_2000v0.0.1

Marhl, Haberichter, Brumen, Heinrich, 2000

Details

Parameters:

NameDescription
k_m0.00625
beta_ER0.0025
k_plus0.1
K15.0
K20.8
k_ch4100.0
k_leak0.05
Ca_tot90.0
rho_m0.01
k_in300.0
k_minus0.01
k_out125.0
Pr_tot120.0
beta_m0.0025
rho_ER0.01
K35.0
k_pump20.0

States:

NameDescription
Ca_cyt(time)0.05
Ca_m(time)0.4
Ca_ER(time)1.0

marhl_schuster_brumen_heinrich_1997v0.0.1

Marhl, Schuster, Brumen, Heinrich, 1997

Details

Parameters:

NameDescription
k_pump76.0
T310.0
k_leak10.0
A_tot3890.0
Ca_tot45.0
C_tot5000.0
Vcyt5.84e-11
k_minus0.5
rho0.01
S0.00616
Pr_tot600.0
g_Ca_max100.0
K_Ca5.0
R8.3143
F96.4867
k_plus0.1

States:

NameDescription
Pr(time)nothing
Ca_cyt(time)nothing

martinov_vitvitsky_mosharov_banerjee_ataullakhanov_2000v0.0.1

Martinov, Vitvitsky, Mosharov, Banerjee, Ataullakhanov, 2000

Details

Parameters:

NameDescription
V_MATIIImax22870.0
Km2_MATIII21.1
Ki_GNMT20.0
V_MATImax561.0
V_METmax4544.0
Km_GNMT4500.0
V_GNMTmax10600.0
Km_MATI41.0
alpha_d1333.0
K_AHC0.1
Ki_MATI50.0
Km2_MET_A10.0
Ado1.0

States:

NameDescription
AdoHcy(time)3.0
AdoMet(time)60.0

marwan_2003v0.0.1

Marwan, 2003

Details

Parameters:

NameDescription
glucose1.0
alpha250.0
alpha130.0
kia0.1
kai0.8
kd0.1
Ifr_sigma_fr_phi_fr0.1
kx0.2
kG0.1
ky1.0
Ir_sigma_r_phi_r0.0

States:

NameDescription
Pr(time)0.0
prepreS(time)200.0
Pfr(time)10.0
Ya(time)0.9
V(time)50.0
Xa(time)0.0
S(time)0.0
Xi(time)6.0
preS(time)0.0

matsuoka_sarai_kuratomi_ono_noma_2003v0.0.1

Matsuoka, Sarai, Kuratomi, Ono, Noma, 2003

Details

Parameters:

NameDescription
Y_d0.027
k_C_U0.143
P_lCa0.11
stim_start50.0
T310.0
P_Na2860.0
P_Ks_Na0.2016
P_NaCa6.81
KForceEC140000.0
L0.9623799975411884
V_rel160.0
Km_CaSR0.08
Km_Ki32.88
Km_Nai8.75
B1.2
k_C_CCa6.954
P_Ks_K5.04
k_CCa_UCa0.0003
Ko5.4
P_Cab0.04
CMDN_max0.05
P_KATP0.0236
Cm132.0
Z_20.0039
P_SR_T386.0
k_AI_AP8.75e-5
P_bNSC0.385
P_NaK21.0
h_c0.005
beta_y20.004444
Y_40.12
Y_139.0
k31.0
k_UCa_CCa0.35
Z_10.03
ZeroForceEL0.97
Adenosine_Total5.0
ProducingRate_Max0.003
P_Kr0.00864
Z_31560.0
ForceFactor1.8e6
P_RyR62000.0
k_CCa_C0.0042
Km_ATP0.1
KForceLinearEc200.0
P_CaL8712.0
stim_duration2.0
P_SR_L459.0
Y_30.03
Cao1.8
P_to_K0.033
k_U_UCa6.954
Km_Cai0.00138
Km_Ko0.258
stim_period400.0
stim_end1.0e6
Km_Nao87.5
Km_CaCyto0.0008
k40.000849
N2333.0
K_mCMDN0.00238
K_mCSQN0.8
L_a1.17
Y_20.0039
Vi8000.0
k_AP_AI0.004
P_to_Na0.00297
k_U_C0.35
Nao140.0
Km_Cao1.38
Diadid_Factor-150.0
Partition0.32
V_up400.0
P_K1_01.146
k10.01
i_max162500.0
stim_amplitude-4000.0
CSQN_max10.0
P_CaT612.0
T_t0.07
R8.3143
k20.04
F96.4867

States:

NameDescription
y2(time)0.20443083454225305
Caup(time)2.611712901567567
p_U(time)0.17246483915629204
X(time)0.9573749975411884
p_AP_CaL(time)1.5445004166497696e-6
p_open_RyR(time)0.00034314360001543243
p_close_RyR(time)0.19135178123107768
y1(time)1.6882718240109127e-5
y(time)0.6080573900752752
Ca_Total(time)9.455741736977666
pCaCB(time)0.001990153835322864
p_AI_Na(time)0.40285968661346977
ATPi(time)4.657102729020499
y3(time)0.967887666264921
p_RP_CaL(time)0.9968480629364956
Nai(time)4.925761439682025
p_AP_Na(time)1.779648367445368e-5
p_UCa(time)6.098246017787626e-5
pCB(time)0.00042941813853474524
p_RP_Na(time)0.3556412697995689
Ki(time)143.1837333000449
p_C(time)0.4250747299372254
Vm(time)-85.95752434460744
p_AI_CaL(time)0.000877325391245903
pCa(time)0.02490898775497523

maurya_bornheimer_venkatasubramanian_subramaniam_2005v0.0.1

Maurya et al. 2005

Details

Parameters:

NameDescription
G_tot1.0e-8
P_minus225.0
P_minus425.0
k1529000.0
P_minus30.013
k21.28
P_minus10.013

States:

NameDescription
Pi_(time)0.0044
RG(time)0.0
T(time)0.000468
RGD(time)0.0
GD(time)1.0e-8
GAD(time)0.0
GT(time)0.0
RGT(time)0.0
A(time)0.0
G(time)0.0
R(time)0.0
GA(time)0.0
RGAT(time)0.0
RGA(time)0.0
D(time)0.000149
GAT(time)0.0
RGAD(time)0.0

mazhari_greenstein_winslow_marban_nuss_2001v0.0.1

Mazhari, Greenstein, Winslow, Marban, Nuss, 2001

Details

Parameters:

NameDescription
Kb0.1348
Kf0.0266
Vm-80.0

States:

NameDescription
O(time)nothing
I(time)nothing
C2(time)nothing
C1(time)nothing
C3(time)nothing

mcallister_noble_tsien_1975v0.0.1

Mcallister, Noble, Tsien, 1975

Details

Parameters:

NameDescription
g_Clb0.01
g_si0.8
C10.0
E_Cl-70.0
g_Na150.0
g_Nab0.105
E_K-110.0
g_qr2.5
E_si70.0
E_Na40.0
E_K1-30.0
g_si_0.04
E_s-52.0

States:

NameDescription
d(time)0.00293135
r(time)0.13500116
V(time)-78.041367
h(time)0.78656359
m(time)0.02566853
x2(time)0.0176854
s(time)0.75473994
f(time)0.80873917
x1(time)0.02030289
q(time)3.11285794

mclean_su_vandenbogert_2003v0.0.1

Mclean, Su, Vandenbogert, 2003

Details

Parameters:

NameDescription
g_max1.5
L_CE_opt0.01
W0.63
A0.25
L_slack0.0025
k_SEE1.0e6
a0.8
S2.0
F_max7000.0
F_min10.0
V_max0.93
gamma5.67

States:

NameDescription
g_V_CE(time)nothing
L_CE(time)nothing

mears_sheppard_atwater_rojas_bertram_sherman_1997v0.0.1

Mears 1997

Details

Parameters:

NameDescription
V_CRAC0.0
sloper3.0
f0.01
kerp0.09
dip30.2
sigma_er1.0
g_K_Ca1200.0
Vm_f-20.0
Vj-53.0
V_K-70.0
Sj2.0
IP30.0
g_Ca_f810.0
Vn-15.0
verp0.24
Sm_s10.0
lambda_n1.85
lambda_er250.0
Cm6158.0
dinh0.4
kmp0.35
Vm_s-16.0
Sm_f7.5
Ca_er_bar40.0
Sn6.0
g_K3900.0
g_K_ATP150.0
dact0.35
perl0.003
V_Ca100.0
g_leak0.0
gamma3.607e-6
g_Ca_s510.0
vmp0.08
g_CRAC75.0
kdkca0.55

States:

NameDescription
jm(time)0.12
V(time)-61.0
n(time)0.0005
Ca_i(time)0.11
Ca_er(time)60.0

Medrano-Gracia-PCA-2013: Medrano_Gracia_PCA_2013v0.0.1

Large Scale Left Ventricular Shape Atlas Using Automated Model Fitting to Contours

Details

The model gives a statistical model of left ventricular cardiac shape (built using Principal Components Analysis). In this repository, the data has been converted into JSON format, and can be loaded into a WebGL based model visualiser.

michailova_mcculloch_2001v0.0.1

Michailova, Mcculloch, 2001

Details

Parameters:

NameDescription
k_a_minus576.0
K_mEGTA0.00015
stim_start0.1
k_minus_CaADP193500.0
Vmaxr0.318
tau_xfer_MgADP0.0534
k_minus_MgATP10875.0
omega10.0
k_b_minus1930.0
k_plus_CaATP225000.0
V_NSR2.1e-6
ADP_tot0.005
K_mNa87.5
eta0.35
k_minus_MgADP84500.0
LTRPN_tot0.07
g_Ks0.0027134
tau_tr0.0005747
g_Kr0.0034
K_mCa1.38
k_a_plus1.215e13
V_ss1.2e-9
Na_o138.0
fprime7.0
v11800.0
b2.0
g_Nab0.0031
tau_xfer0.0267
tau_xfer_MgATP0.0534
MgATP_i02.888
tau_xfer_CaATP0.0534
gprime7000.0
k_ltrpn_minus40.0
I_pCa0.05
I_NaK0.693
k_plus_MgATP125000.0
CSQN_tot15.0
N_rb1.0
g_Kp0.002216
stim_amplitude-100.0
m3.0
F96.4853415
n4.0
f300.0
K_mNa_i10.0
T310.0
C_sc0.001
K_SR1.0
i_Ca_half-0.265
k_htrpn_plus20000.0
K_sat0.2
K_mK113.0
tau_xfer_CaADP0.0534
tau_xfer_Mg0.0267
ATP_tot7.0
k_htrpn_minus0.066
g2000.0
k_b_plus4.05e9
k_c_plus100.0
g_K12.8
V_myo2.584e-5
k_c_minus0.8
k_plus_MgADP125000.0
EGTA_tot0.0
stim_duration0.0005
K_mK_o1.5
Ca_o2.0
K_mpCa5.0e-5
a2.0
tau_factor1.0
stim_period1.0
stim_end1.0e8
V_JSR1.6e-7
K_mCSQN0.8
K_mCMDN0.00238
K_o4.0
K_fb0.000168
k_minus_CaATP45000.0
A_cap0.0001534
k_ltrpn_plus40000.0
CMDN_tot0.05
N_fb1.2
HTRPN_tot0.14
g_to10.23815
P_Ca0.0003125
g_Na12.8
Vmaxf0.0813
g_Cab0.0003842
k_plus_CaADP125000.0
K_rb3.29
K_NaCa0.3
R8.314472
P_K5.79e-7

States:

NameDescription
Ca_NSR(time)0.262
MgADP_i(time)0.00298
C0(time)0.997208
y(time)0.798
C3(time)1.63909e-14
HTRPNCa(time)0.98
O(time)9.84546e-21
C_Ca0(time)0.00272826
CaADP_i(time)1.1e-7
Mg_ss(time)1.0
C_Ca3(time)2.87031e-15
X_to1(time)2.63
LTRPNCa(time)0.078
X_ks(time)0.264
V(time)-96.1638
C_Ca1(time)6.99215e-7
C1(time)6.38897e-5
O_Ca(time)0.0
P_O2(time)0.0
C_Ca2(time)6.71989e-11
X_kr(time)0.51
P_C1(time)0.47
Ca_ss(time)0.0001315
P_C2(time)0.53
C2(time)1.535e-9
CaATP_i(time)0.000237
MgATP_ss(time)6.4395
j(time)0.99254
CaATP_ss(time)0.00025
m(time)0.0328302
C4(time)6.56337e-20
Y_to1(time)0.99
Na_i(time)10.0
CaADP_ss(time)1.3e-7
Mg_i(time)1.0
MgATP_i(time)6.4395
C_Ca4(time)4.59752e-20
h(time)0.988354
K_i(time)159.48
P_O1(time)0.0
Ca_JSR(time)0.2616
MgADP_ss(time)0.00298
Ca_i(time)8.464e-5

michailova_saucerman_belik_mcculloch_2005v0.0.1

Michailova 2005

Details

Parameters:

NameDescription
k_a_minus576.0
K_mEGTA0.00015
stim_start0.1
k_minus_CaADP193500.0
Vmaxr0.318
tau_xfer_MgADP0.0534
k_minus_MgATP10875.0
omega10.0
k_b_minus1930.0
k_plus_CaATP225000.0
V_NSR2.1e-6
ADP_tot0.005
gd0.89
K_mNa87.5
eta0.35
k_minus_MgADP84500.0
LTRPN_tot0.07
g_Ks0.0027134
tau_tr0.0005747
g_Kr0.0034
K_mCa1.38
k_a_plus1.215e13
V_ss1.2e-9
Na_o138.0
v11800.0
b2.0
g_Nab0.0031
tau_xfer0.0267
tau_xfer_MgATP0.0534
MgATP_i02.888
tau_xfer_CaATP0.0534
k_ltrpn_minus40.0
I_pCa0.05
I_NaK0.693
k_plus_MgATP125000.0
k_MgATP_ss1.4
CSQN_tot15.0
N_rb1.0
g_Kp0.002216
stim_amplitude-100.0
m3.0
K_o_normal4.5
F96.4853415
n4.0
f300.0
K_mNa_i10.0
T310.0
k_MgADP0.4
C_sc0.001
K_SR1.0
k_htrpn_plus20000.0
G_K_ATP0.05
K_sat0.2
K_mK113.0
p_prime_k6.658e-7
tau_xfer_CaADP0.0534
tau_xfer_Mg0.0267
ATP_tot7.0
k_htrpn_minus0.066
g2000.0
k_b_plus4.05e9
k_c_plus100.0
g_K12.8
V_myo2.584e-5
k_c_minus0.8
k_plus_MgADP125000.0
EGTA_tot0.0
stim_duration0.0005
K_mK_o1.5
Ca_o2.0
K_mpCa5.0e-5
a2.0
tau_factor1.0
stim_period1.0
stim_end1.0e8
V_JSR1.6e-7
K_mCSQN0.8
K_mCMDN0.00238
K_o4.0
K_fb0.000168
k_minus_CaATP45000.0
go0.08
k_ltrpn_plus40000.0
A_cap0.0001534
CMDN_tot0.05
N_fb1.2
HTRPN_tot0.14
g_to10.23815
P_Ca0.0003594
g_Na12.8
k_ATP0.6
Vmaxf0.0813
g_Cab0.0003842
k_plus_CaADP125000.0
K_rb3.29
K_NaCa0.3
R8.314472

States:

NameDescription
X_kr(time)0.51
P_C1(time)0.47
Ca_ss(time)0.0001315
MgADP_i(time)0.00298
P_C2(time)0.53
v(time)0.1
y(time)0.798
Ca_NSR(time)0.262
HTRPNCa(time)0.98
CaATP_i(time)0.000237
MgATP_ss(time)6.4395
CaADP_i(time)1.1e-7
Mg_ss(time)1.0
CaATP_ss(time)0.00025
j(time)0.99254
X_to1(time)2.63
m(time)0.0328302
Y_to1(time)0.99
w(time)0.1
CaADP_ss(time)1.3e-7
Mg_i(time)1.0
MgATP_i(time)6.4395
Na_i(time)10.0
LTRPNCa(time)0.078
X_ks(time)0.264
V(time)-96.1638
h(time)0.988354
z(time)0.1
K_i(time)159.48
P_O1(time)0.0
Ca_JSR(time)0.2616
MgADP_ss(time)0.00298
P_O2(time)0.0
Ca_i(time)8.464e-5

miftakhov_abdusheva_christensen_1999v0.0.1

Miftakhov, Abdusheva, Christensen, 1999

Details

Parameters:

NameDescription
E_Ca80.0
K_c0.00425
E_Cl-40.0
alpha0.12
tau_x_Ca500.0
g_Cl0.003
rho125.0
g_K0.3
E_K-75.0
g_Ca_K0.03
g_Ca_L0.004
g_Ca_T0.51
lamda12.5
Cm2.5

States:

NameDescription
V(time)-55.0
n(time)0.01
h(time)0.01
x_Ca(time)0.01
Ca(time)0.0001

mijailovich_butler_fredburg_2000v0.0.1

Mijailovich, Butler, Fredburg, 2000

Details

Parameters:

NameDescription
fp0.44
gp0.11
gp10.22
fp10.88
gx0.11
k50.1
k20.1
g10.01

States:

NameDescription
AMp(time)0.0
Mp(time)0.0
M(time)1.0
AM(time)0.0

mikane_araki_kohno_nakayama_suzuki_shimuzi_matsubara_hirakawa_takaki_suga_1997v0.0.1

Mikane, Araki, Kohno, Nakayama, Suzuki, Shimuzi, Matsubara, Hirakawa, Takaki, Suga, 1997

Details

Parameters:

NameDescription
Ca_tot_released35.0
f400000.0
total_CB150.0
g10.0
total_Tn70.0
k_210.0
k_31000.0
k_15.0e6

States:

NameDescription
TnCa_t(time)0.0
cumCB_off_t(time)0.0
Ca_released(time)0.0
Ca_t(time)0.0
CB_on_t(time)0.0
Ca_sequestered(time)0.0
cumCB_on_t(time)0.0

mitchell_schaeffer_2003v0.0.1

Mitchell, Schaeffer, 2003

Details

Parameters:

NameDescription
tau_out6.0
IstimPeriod500.0
IstimAmplitude0.2
tau_in0.3
IstimPulseDuration1.0
tau_open120.0
tau_close150.0
V_gate0.13
IstimStart0.0
IstimEnd50000.0

States:

NameDescription
Vm(time)8.20413566106744e-6
h(time)0.8789655121804799

mittler_sulzer_neumann_perelson_1998v0.0.1

Mittler, Sulzer, Neumann, Perelson, 1998

Details

Parameters:

NameDescription
p774.0
tau_p0.0
c3.0
VI_0200000.0
m0.01
k2.4e-5
b0.25
delta0.5
n4.0

States:

NameDescription
VNI(time)0.0
VI(time)200000.0
E2(time)0.0
I(time)0.1
E3(time)0.0
E4(time)0.0
E1(time)0.0

modularmassactionprimerv0.0.1

A Primer on Modular Mass Action Modelling with CellML

Details

Example code for the book chapter 'A Primer on Modular Mass Action Modelling with CellML'. Please select one of the Exposures below to access the code.

morris_lecar_1981v0.0.1

Morris and Lecar 1981

Details

Parameters:

NameDescription
i_app300.0
V3-1.0
E_L-50.0
E_Ca100.0
C20.0
g_L2.0
V414.5
lambda_n_bar0.066666667
lambda_m_bar1.0
V110.0
g_K8.0
E_K-70.0
V215.0
g_Ca4.0

States:

NameDescription
V(time)-50.0
n(time)0.001
m(time)0.1

muller_obeyesekere_mills_ram_2008v0.0.1

Muller, Obeyesekere, Mills, Ram, 2008

Details

Parameters:

NameDescription
b110.0
f240.8
f130.6
f350.3
a110.0
a210.0
b210.0
d10.2
E10.0
f140.1
f531.5
f450.1
d51.0
h360.1
d31.0
d60.001
d41.1
d20.1

States:

NameDescription
y2(time)0.0
y3(time)0.0
y1(time)0.0
y4(time)0.0
y5(time)0.0
y6(time)0.0

N


nagano_gerritsen_2001v0.0.1

Nagano and Gerritsen, 2001

Details

Parameters:

NameDescription
slope2.0
alpha1449.027
L_slack0.42
B_REL5.2
width0.888
A_REL0.41
F_max3277.4
Factor1.0
F_asympt1.5
L_ce_opt0.055
q1.0

States:

NameDescription
L_ce(time)0.05

nagerl_novo_mody_vergara_2000v0.0.1

Nagerl, Novo, Mody, Vergara, 2000

Details

Parameters:

NameDescription
koff_Dnothing
Ca_Tnothing
kon_Dnothing
alphanothing
D_Tnothing
kon_Binothing
kon_DMnothing
Binothing
koff_DMnothing
DM_Tnothing
koff_Binothing
koff_DM_nothing
tau_photolysisnothing
t_pulsenothing

States:

NameDescription
CaD(time)nothing
CaDM2(time)nothing
CaDM1(time)nothing
CaBi(time)nothing

nelson_murray_perelson_2000v0.0.1

Nelson, Murray, Perelson, 2000

Details

Parameters:

NameDescription
delta_10.03
c3.0
m0.01
np1.0
N480.0
k3.43e-5
lambda5.0
tau1.0
delta0.5

States:

NameDescription
VNI(time)0.0
VI(time)134000.0
T(time)180.0
T_star(time)3.6

nelson_perelson_1995v0.0.1

Nelson, Perelson 1995

Details

Parameters:

NameDescription
N_0300.0
k_12.4e-5
s_010.0
T_max1500.0
k_1_2.4e-7
r0.03
k_s0.48
mu_TD0.02
t_c7305.0
mu_V2.4
mu_b0.24
D_00.1
theta1.0
mu_T0.02
mu_D0.76
mu_bD0.12
k_20.017
gamma25.0
t_DIV2557.0
k_1D2.4e-5

States:

NameDescription
T_D2(time)0.0
T_2(time)0.0
V_(time)0.0
V(time)0.001
T(time)1000.0
T_1(time)0.0
D(time)0.0
T_D1(time)0.0
D_ode(time)0.0

neumann_lam_dahari_gretch_wiley_layden_perelson_1998v0.0.1

Neumann, Lam, Dahari, Gretch, Wiley, Layden, Perelson, 1998

Details

Parameters:

NameDescription
delta0.5
beta3.0e-7
c5.0
epsilon0.99
eta0.8
s10.0
p100.0
d0.02

States:

NameDescription
V(time)9.4e6
I(time)0.0
T(time)1000.0

niederer_hunter_smith_2006v0.0.1

Niederer, Hunter, Smith, 2006

Details

Parameters:

NameDescription
T_ref56.2
Ca_50ref0.00105
n_Hill3.0
z_p0.85
A_1-29.0
a0.35
K_z0.15
alpha_20.13
alpha_r10.002
A_2138.0
beta_04.9
k_on100.0
k_Ref_off0.2
alpha_30.625
n_Rel3.0
Ca_TRPN_Max0.07
alpha_r20.00175
gamma_trpn2.0
alpha_10.03
beta_1-4.0
A_3129.0
alpha_00.008

States:

NameDescription
Q_2(time)0.0
Q_3(time)0.0
TRPN(time)0.067593139865
z(time)0.014417937837
Q_1(time)0.0

niederer_smith_2007v0.0.1

Niederer, Smith, 2007

Details

Parameters:

NameDescription
KA21.4935205515214
kp14677.0
Cle126.0
PP_co2e0.05
g_Cl2.0e-5
Ae140.0
B_CMDN0.05
K_CMDN0.00238
scale_K0.0
alpha_20.13
k_on100.0
d100.0
Na_e140.0
J_CO20.0
theta_R0.012
g_H4.0e-6
K_HCO30.008017
k_sat0.1
K_mNa87.5
eta0.35
delta_VL7.0
J_R2.0e-11
Nae140.0
K_mCa1.38
ib131.2044223705215
A_3129.0
alpha_00.008
g_SAC4.1333e-7
kr_co2hyd0.481
a_endo0.583
Na_o140.0
Ca_50ref0.00105
pKa_ib27.48048792987277
n_Hill3.0
km1777.92
b14.0
g_ss7.0e-6
K_z0.15
V_SR2.098e-6
g_pCa3.5e-6
g_D6.5e-11
b_endo0.417
alpha_r10.002
P_atm760.0
f_Na0.2
g_NCX0.0385
K_m_Na10.0
n_Rel3.0
g_t3.5e-5
n_Hi2.91
pH_scale1.0
gamma_trpn2.0
g_f1.45e-6
K_Cl983.5
stim_amplitude-0.0006
tau_L650.0
Pco25.8e-5
phi_L2.35
K_RyR0.041
NO_on0.0
g_SRl5.2e-6
kf_co2hyd0.000365
kp26.656
F96487.0
ib26.84513535697271
T295.0
c0.01
K_m_K1.5
A_1-29.0
phi_R_base0.05
pKa_ib16.40013149605198
K_He6.53e-5
i_NaK_max9.5e-5
K_L0.00022
g_B_K1.38e-7
g_Ko1.2e-6
Q_10Scaler0.35
alpha_r20.00175
J_L9.13e-13
V_myo2.584e-5
g_K12.4e-5
KB1.77948608115949e-7
K_Hi0.000183
CO_2sol0.03253
tau_R2.43
CmF0.0001
SAC_on0.0
E_R-10.0
T_ref56.2
stim_duration10.0
V_L0-2.0
z_p0.85
B_TRPN0.07
Ca_o2.0
g_B_Na8.015e-8
K_mpCa0.0005
a0.35
Ca_e2.0
delta0.075
stim_period1000.0
pH_e7.4
ExtensionRatio1.0
N75000.0
K_o5.4
TRPN_tot0.07
A_cap0.01534
beta_04.9
A_2138.0
pH_on0.0
K_SERCA0.0005
alpha_30.625
g_SERCA0.00045
g_Na0.0008
alpha_10.03
K_Na4866.11
g_Cab2.4216e-8
beta_1-4.0
k_off0.2
scale_Na0.0
n_He2.18
t_L1.0
R8314.5
K_OH0.0008907

States:

NameDescription
z_1(time)0.988955429362334
y(time)0.00331726547133295
z_2(time)0.00860686643357905
s_slow(time)0.530207467628341
j(time)0.675294627571238
Q_3(time)0.0
z_3(time)0.00241692704700704
m(time)0.00419283833975832
s(time)0.922573773425153
Na_i(time)10.9735342589175
HCO3i(time)15.1428688811927
TRPN(time)0.0670845085340179
V(time)-80.5561112771341
Cli(time)16.2285651746901
h(time)0.675647510010602
r_ss(time)0.00289374682707489
z(time)0.0175189833295748
K_i(time)142.021261491871
s_ss(time)0.308572839431787
Q_2(time)0.0
r(time)0.00218107055088884
CO2i(time)1.23610845162584
Ca_SR(time)0.843733859307907
Ca_i(time)8.60587059887361e-5
pH_i(time)7.20905044774657
Q_1(time)0.0

noble_1962v0.0.1

Noble, 1962

Details

Parameters:

NameDescription
E_L-60.0
g_L75.0
E_Na40.0
g_Na_max400000.0
Cm12.0

States:

NameDescription
V(time)-87.0
h(time)0.8
m(time)0.01
n(time)0.01

noble_2000v0.0.1

Noble, 2000

Details

Parameters:

NameDescription
T310.0
stim_start200.0
g_Kr20.0017
P_kna0.03
alpha_Calmod100000.0
g_bca0.00025
alpha_Trop100000.0
length74.0
d_NaCa0.0
K_leak_rate0.05
alpha_up0.4
i_NaK_max0.7
g_to0.005
delta_f0.0001
Trop0.05
Cm9.5e-5
beta_up0.03
FRiNaCa0.001
g_Kr10.0028
FrICa0.7
K_cyca0.0003
beta_Trop200.0
K_mNa40.0
g_bna0.0006
g_Ks0.0016
g_K10.5
delta_m1.0e-5
P_Ca_L1.0
KCaChoff0.01
K_srca0.5
V_e_ratio0.4
Na_o140.0
V_ds_ratio0.1
stim_duration0.002
speed_d3.0
Kdecay10.0
K_m_rel250.0
g_tos0.0
n_NaCa3.0
Kmdsinact0.001
Ca_o2.0
shift_h0.0
V_up_ratio0.01
stim_period1.0
stim_end600.0
K_mk110.0
K_m_Ca_ds0.01
Calmod0.02
radius12.0
beta_Calmod50.0
K_o4.0
K_m_Ca_cyt0.0005
K_xcs0.4
V_rel_ratio0.1
P_CaK0.002
K_mK1.0
g_Na0.5
speed_f0.3
g_pna0.0027
stim_amplitude-6.0
P_CaNa0.01
gamma0.2
k_NaCa0.0005
R8314.472
F96485.3415

States:

NameDescription
d(time)0.0
Ca_Trop(time)0.0003732
xr2(time)2.0e-7
Ca_rel(time)0.6460487
V(time)-92.8915042
h(time)0.9944559
xs(time)0.0006469
f(time)0.0
K_i(time)136.1745362
ProdFrac(time)0.6950649
ActFrac(time)0.0049039
Ca_ds(time)2.7e-6
r(time)0.0
m(time)0.0016111
xr1(time)1.02e-5
Ca_i(time)1.49e-5
s(time)0.9948645
Ca_up(time)0.36963
Na_i(time)7.6713487
Ca_Calmod(time)0.0005841