CellMLPhysiome: S - Z

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S


smith_1980 @ v0.0.1

Smith, 1980

nothing

Parameters:

Name Description
c 100.0
b3 1.39
g2 0.7
b2 0.97
h 12.0
g1 10.0
b1 1.29

States:

Name Description
T(time) 15.0
R(time) 0.5
L(time) 22.0

Observables: none

smith_abdala_koizumi_rybak_paton_2007 @ v0.0.1

Smith, Abdala, Koizumi, Rybak and Paton 2007

nothing

Parameters: none

States: none

Observables: none

smith_chase_nokes_shaw_wake_2004 @ v0.0.1

Smith Chase 2004

nothing

Parameters: none

States: none

Observables: none

smith_crampin_2004 @ v0.0.1

Smith, Crampin, 2004

nothing

Parameters:

Name Description
minus_k1 172.1
eq_NaPi 224.0
body_temp 310.0
eq_HPi 0.000169
eq_K_e 0.213
partition_factor -0.031288692380984445
cPi_sum 4.2
minus_k2 40.1
cH 8.1283e-5
k4 320.0
eq_Na_base_i 2.49
eq_KPi 292.0
eq_MgATP 2.51
cK_e 5.4
eq_K_i 0.5
cMgATP 9.8
k1 1050.0
gas_const 8.314
cK_i 140.0
k3 2000.0
minus_k4 40.1
minus_k3 79287.1
cNa_e 150.0
faraday_const 96485.0
eq_Na_base_e 15.5
k2 481.0

States:

Name Description
Vm(time) -150.0
cMgADP(time) 0.01
cNa_i(time) 50.0

Observables: none

sneyd_dufour_2002 @ v0.0.1

Sneyd, Dufour, 2002

nothing

Parameters:

Name Description
k_2a 37.4
k_4a 4.0
k_3a 0.11
k_3b 29.8
c 1.0
L_3 0.025
l_4a 1.7
l_4b 2.5
L_1 0.12
l_2b 0.8
k_1a 0.64
k_4b 0.54
k_1b 0.04
k_2b 1.4
l_6a 4707.0
l_6b 11.4
l_2a 1.7
p 10.0
L_5 54.7

States:

Name Description
O(time) 0.0
I_2(time) 0.0
A(time) 0.0
R(time) 1.0
I_1(time) 0.0

Observables: none

sneyd_tsaneva_atanasova_yule_thompson_shuttleworth_2004 @ v0.0.1

Sneyd, Tsaneva-Atanasova, Yule, Thompson, Shuttleworth, 2004

nothing

Parameters: none

States: none

Observables: none

sneyd_tsanevaatanasova_bruce_straub_giovannucci_yule_2003 @ v0.0.1

Sneyd, Tsanevaatanasova, Bruce, Straub, Giovannucci, Yule, 2003

nothing

Parameters: none

States: none

Observables: none

sneyd_wetton_charles_sanderson_1995 @ v0.0.1

Snyed, Wetton, Charles, Sanderson, 1995

Intercellular calcium waves mediated by diffusion of inostol trisphosphate: a two dimensional model.

Parameters:

Name Description
tau_h 0.2
b 0.11
k_flux 3.0
beta 0.15
IPR_3_flux 0.72
k_mu 0.01
k_2 0.7
V_p 0.08
gamma 1.0
k_gamma 0.27
k_p 1.0
k_1 0.7

States:

Name Description
P(time) 0.0
h(time) 1.0
c(time) 0.3

Observables: none

snyder_palmer_moore_2000 @ v0.0.1

Snyder, Palmer, Moore, 2000

nothing

Parameters:

Name Description
k_on2 1.3e7
Bmax_c 0.00012
Vmax_s 0.000525
k_s 9.0
Kb_c 9.6e-7
Ca_e 0.002
k_on1 2.0e9
V_s 0.07
K_ons 8772.0
Bmax_f1 0.0002
Kb_dye 2.0e-7
kf 2500.0
Kb_f2 1.3e-5
K_offs 5.596536
V_c 0.9287
Rt 1.5e-7
Bmax_f2 0.0011
Km_s 2.5e-7
k_off2 3.9
Vmax_NaCaX 0.0012
Km_NaCaX 3.6e-5
k_off1 1400.0
k1 0.2
dye_c 0.0
V_f 0.0013
Bmax_s 0.008
Kb_f1 1.7e-5

States:

Name Description
Ca_f(time) 1.2e-7
Ca_CSQ(time) 0.0
Ca_S2(time) 0.0
Ca_2_S1(time) 0.0
S1(time) 0.0
Ca_c(time) 1.0e-7
cas2(time) 0.0
cas1(time) 0.0
Ca_s(time) 0.000201
S2(time) 0.0

Observables: none

sobie_dilly_dossantoscruz_lederer_jafri_2002 @ v0.0.1

Sobie, Dilly, Dossantoscruz, Lederer, Jafri, 2002

nothing

Parameters: none

States: none

Observables: none

soboleva_vetharaniam_nixon_montenegro_pearson_sneyd_2005 @ v0.0.1

Soboleva, Vetharaniam, Nixon, Montenegro, Pearson, Sneyd, 2005

nothing

Parameters:

Name Description
T 9.0
delta_U 7.5
b 100.0
d01 13.0
a 358000.0
P0 0.25
delta_R 1.905
ti 1.0
kappa 240000.0
alpha0 4.15
s 371000.0
delta_x 0.207
kappa0 6550.0
delta_b1 7.5
alpha1 3.02
G 35.6
P1 20.0
PE 20.55
d12 4720.0
b0 263.0
a0 23300.0
delta_b2 50.0

States:

Name Description
B1(time) 1.0
R(time) 1.0
B2(time) 1.0
x(time) 0.0
U(time) 1.0

Observables: none

spiro_parkinson_othmer_1997 @ v0.0.1

Spiro, Parkinson, Othmer, 1997

nothing

Parameters:

Name Description
k1c 0.17
Z 40.0
k2c 0.017
k4a 10.0
k4b 17.0
k13 34.56
k9 45.0
k10 48.0
k_5 70.0
k1a 10.0
k_4 30000.0
L 3.0
k8 15.0
k3a 10.0
k2b 17.0
k2a 10.0
k_y 500000.0
kb 800000.0
k_2 30000.0
Y0 20.0
k6 7.0e7
k11 0.0
k12 16.5
k1b 17.0
k_3 400000.0
B0 1.7
k_7 70.0
k4c 0.51
k3c 5.1
k_b 0.35
k7 7.0e7
k_6 70.0
k3b 17.0
ky 3.0e7
R 0.3
k5 7.0e7
k_1 400000.0

States:

Name Description
T2pR(time) 0.01
LT3pR(time) 0.01
LT2pR(time) 0.01
T3(time) 0.01
T2p(time) 0.01
LT4(time) 0.01
LT2p(time) 0.01
LT3p(time) 0.01
T3pR(time) 0.01
T4(time) 0.01
LT2R(time) 0.01
LT4p(time) 0.01
LT3(time) 0.01
LT3R(time) 0.01
T3p(time) 0.01
Yp(time) 0.01
T2R(time) 0.01
T2(time) 0.01
LT2(time) 0.01
T3R(time) 0.01
T4p(time) 0.01
Bp(time) 0.01

Observables: none

Spronck_Martens_2012 @ v0.0.1

Spronck, 2012

A lumped parameter model of cerebral blood flow control combining 1 cerebral autoregulation and neurovascular coupling

Parameters: none

States: none

Observables: none

sriram_bernot_kepes_2007 @ v0.0.1

Sriram, Bernot, Kepes, 2007

nothing

Parameters:

Name Description
k_c3 0.6
j_3 0.6
v_d3 3.0
k_m1 5.0
k_m2 5.0
j_1 0.9
v_d2 1.052
k_d3 0.8
v_12 15.0
k_d2 0.9
k_c1 0.2
k_c2 0.22
v_10 15.0
k_100 10.0
v_11 15.0
k_d5 0.16
k_d6 0.16
k_d4 0.16
k_d1 0.8
k_120 10.0
j_2 0.5
k_m3 5.0
v_d1 6.0
k_110 10.0
n 2.0

States:

Name Description
C_1(time) 0.0
T_2(time) 5.0
T_1(time) 6.0
C_3(time) 0.0
T_3(time) 1.0
C_2(time) 0.0

Observables: none

starbuck_wiley_lauffenburger_1990 @ v0.0.1

Starbuck, Wiley, Lauffenburger, 1990

nothing

Parameters:

Name Description
RT nothing
K_DC nothing
kuc nothing
L nothing
kdeg nothing
Kcp nothing
kf nothing
Vvesicle nothing
kt nothing
Nav nothing
kr_ nothing
ku_ nothing
ks nothing
krec_p nothing
kc nothing
K_DT nothing
fr nothing
PT nothing
krec_i nothing
krec_c nothing
kr nothing
PT_RT nothing
Vendosome nothing
lamda nothing
plate nothing
cell nothing

States:

Name Description
Cs(time) nothing
Ts(time) nothing
Cii(time) nothing
Pi(time) nothing
Rii(time) nothing
Ps(time) nothing
Cic(time) nothing
Ric(time) nothing
Lo(time) nothing
Lii(time) nothing
Lic(time) nothing
Ti(time) nothing
Rs(time) nothing

Observables: none

stern_song_sham_yang_boheler_rios_1999 @ v0.0.1

Stern, Song, Sham, Yang, Boheler, Rios, 1999

nothing

Parameters:

Name Description
ko 35.0
ki 0.5
kim 0.005
kom 0.06
Ca 0.0001

States:

Name Description
O(time) 1.0
I(time) 1.0
R(time) 1.0
RI(time) 1.0

Observables: none

stewart_aslanidi_noble_noble_boyett_zhang_2009 @ v0.0.1

Stewart, Aslanidi, Noble, Noble, Boyett, Zhang, 2009

nothing

Parameters:

Name Description
T 310.0
EC 1.5
P_kna 0.03
Km_Ca 1.38
g_bca 0.000592
K_buf_sr 0.3
V_rel 0.102
K_sat 0.1
Km_Nai 87.5
g_f_K 0.0234346
g_to 0.08184
Cm 0.185
V_xfer 0.0038
g_pK 0.0146
P_NaK 2.724
K_mNa 40.0
g_bna 0.00029
g_Ks 0.2352
g_K1 0.065
k3 0.06
K_pCa 0.0005
g_Kr 0.0918
g_sus 0.0227
k1_prime 0.15
V_ss 5.468e-5
Na_o 140.0
K_buf_ss 0.00025
min_sr 1.0
K_up 0.00025
K_mk 1.0
max_sr 2.5
Ca_o 2.0
g_pCa 0.1238
V_sr 0.001094
Buf_ss 0.4
k4 0.005
V_c 0.016404
K_o 5.4
K_buf_c 0.001
Buf_sr 10.0
alpha 2.5
g_Na 130.5744
k2_prime 0.045
Vmax_up 0.006375
V_leak 0.00036
Buf_c 0.2
g_f_Na 0.0145654
gamma 0.35
g_CaL 3.98e-5
K_NaCa 1000.0
R 8314.472
F 96485.3415

States:

Name Description
d(time) 0.000287906256206415
Xr1(time) 0.00550281999719088
V(time) -69.1370441635924
h(time) 0.190678733735145
Ca_ss(time) 0.000446818714055411
f2(time) 0.995474890442185
y(time) 0.0457562667986602
f(time) 0.989328560287987
K_i(time) 136.781894160227
R_prime(time) 0.991580051907845
Xs(time) 0.00953708522974789
Xr2(time) 0.313213286437995
r(time) 0.00103618091196912
j(time) 0.238219836154029
fCass(time) 0.999955429598213
m(time) 0.0417391656294997
Ca_SR(time) 3.10836886659417
Ca_i(time) 0.000101878186157052
s(time) 0.96386101799501
Na_i(time) 8.80420286531673

Observables: none

sthilaire_gronfier_zeitzer_klerman_2007 @ v0.0.1

Sthilaire, Gronfier, Zeitzer, Klerman, 2007

nothing

Parameters:

Name Description
betaIS 0.065
tau_x 24.2
betaCP 0.025
k 0.55
alpha 0.067
I0 9500.0
G 37.0
betaIP 0.047
mu 0.13
beta 0.007
alph_0 0.1
Amax 4.834
m 7.0
betaCS 0.028
lamda 0.588
t_off 29.867
q 0.333333
p 0.6
t_on 21.93

States:

Name Description
H1(time) nothing
xc(time) nothing
H3(time) nothing
A(time) nothing
n(time) nothing
I(time) nothing
x(time) nothing
H2(time) nothing
A_(time) nothing

Observables: none

stilianakis_dietz_schenzle_1997 @ v0.0.1

Stilianakis, Dietz, Schenzle, 1997

nothing

Parameters:

Name Description
X0 1.0e11
b 1.0
mu2 1.0
Kmax 20.0
mu0 0.004
a 1.0
rho 0.5
beta 1000.0
theta 1.0e-6
C1 0.04
C2 1000.0
omega 1.0e-16
lamda 4.0e8
mu1 0.3

States:

Name Description
Z(time) 0.0
K(time) 1.35e-14
V(time) 1.0
X(time) 1.0e11
Y(time) 1.0

Observables: none

Sulman_et_al_2008 @ v0.0.1

Sulman et al. 2008

nothing

Parameters:

Name Description
stim_start 0.06
n_NaK 1.5
alpha_P_lengthening 16.0
length 74.0
d_NaCa 0.0
alpha_2 14.6
flag_ingib 0.0
b_2_on 1000.0
Km_f2ds 0.001
delta_f 0.0001
a_on 70000.0
E_fibro_stretch 0.0
g_Kr1 0.0021
g_fibro 0.0002
K_cyca 0.00015
m_0 0.9
K_mNa 24.2
beta_S_shortening 0.0
g_bna 0.0006
kappa_0 3.0
g_1 0.6
g_Ks 0.0026
beta_Q 5.0
P_Ca_L 0.1
K_srca 0.5
F_afterload 2.0
alpha_G 1.0
Na_o 140.0
V_ds_ratio 0.1
speed_d 3.0
Kdecay 10.0
K_m_rel 10000.0
B_1_tot 0.08
a_off 200.0
pi_min 0.03
b_2_off 3.0
v_max 5.5
kappa 0.705
K_m_Ca_ds 0.01
radius 12.0
beta_CaS 32500.0
K_m_Ca_cyt 0.0005
K_xcs 0.4
isotonic 0.0
P_CaK 0.002
K_mK 1.0
q_4 15.0
speed_f 0.3
alpha_CaS 50000.0
beta_P_shortening 0.0015
stim_amplitude -3.0
alpha_P_shortening 16.0
Km_f2 100000.0
P_CaNa 0.01
c_fibro 1.0e-5
alpha_P 4.0
F 96485.3415
K_b 4.0
T 310.0
g_Kr2 0.0013
P_kna 0.03
k_A 40.0
x_st 0.964285
g_bca 0.00025
g_fibro_stretch 0.0
alpha_up 1.0
S_0 1.14
g_2 0.52
i_NaK_max 0.7
a_tr 15.0
beta_P_lengthening 0.0015
g_to 0.006
Cm 9.5e-5
beta_up 0.03
FRiNaCa 0.001
K_kna 20.0
FrICa 1.0
SRLeak 0.05
beta_2 0.0018
g_K1 0.5
delta_m 1.0e-5
beta_3 0.015
b_1_off 182.0
V_e_ratio 0.4
V_i_ratio 0.49
alpha_S_shortening 39.0
stim_duration 0.0025
g_tos 0.0
A_tot 0.07
n_NaCa 3.0
g_K_Na 0.0
Ca_o 2.0
q_3 17.3
a 0.25
mu 3.0
R_decay 20.0
stim_period 1.0
stim_end 10000.0
l_0 0.525139356105856
alpha_Q 10.0
g_fibro_junct 0.00029
k_mu 0.6
q_1 17.3
K_inh 4.0
K_mk1 10.0
lambda 30.0
V_up_ratio 0.03
b_1_on 100000.0
alpha_3 48.0
V_rel_ratio 0.003
g_Na 2.5
alpha_1 14.6
q_2 259.0
g_pna 0.004
alpha_S_lengthening 46.0
beta_S_lengthening 0.0
CaS_tot 40.0
beta_1 0.84
d_h 0.5
B_2_tot 0.1
gamma 0.5
k_NaCa 0.0005
R 8314.472

States:

Name Description
V_fibro(time) -20.0
l_3(time) 0.088805830771694
xs(time) 0.001
v(time) 0.0
f(time) 1.0
ActFrac(time) 0.001914
ProdFrac(time) 0.2854569
K_o(time) 3.988
m(time) 0.0015
l_1(time) 0.436333342969918
s(time) 0.997044616031121
Na_i(time) 5.18787513289509
w(time) 0.0
d(time) 0.0
xr2(time) 1.53745791069154e-7
Ca_rel(time) 0.989665
l_2(time) 0.436333525334166
h(time) 0.995
V(time) -93.658148
f2(time) 1.0
K_i(time) 139.054
N(time) 7.455e-8
B_1(time) 0.0
Ca_ds(time) 2.55e-6
r(time) 1.63117173173398e-8
B_2(time) 0.0
A(time) 0.00015
xr1(time) 8.88859784542779e-6
Ca_i(time) 6.15e-6
Ca_up(time) 0.994579
f2ds(time) 0.997

Observables: none

surkis_peskin_tranchina_leonard_1998 @ v0.0.1

Surkis, Peskin, Tranchina, Leonard, 1998

nothing

Parameters: none

States: none

Observables: none

sveiczer_csikasznagy_gyorffy_tyson_novak_2000 @ v0.0.1

Sveiczer, Csikasznagy, Gyorffy, Tyson, Novak, 2000

nothing

Parameters:

Name Description
Jmikr 0.15
Vwee 10.0
epsilon_p 0.025
kaa_ 0.01
Vpyp 0.07
k25 1.0
V2_ 0.02
V25_ 0.05
kai 0.1
k25r_ 0.4
kir 0.5
k6_ 0.1
Jwee 0.2
kad 0.1
kwr 1.0
kste9r_ 0.03
kmr 5.0
Vmik 2.0
kste9r 8.0
Y 0.0
Jmik 0.15
k3 0.1
km 1.0
epsilon 0.05
Jste9r 0.01
K 0.06
kpp 100.0
kwr_ 0.4
kmr_ 0.01
Vwee_ 0.08
Jweer 0.2
Pyp3 1.0
J25r 0.05
mu 0.00462
V2c 0.5
V2 1.0
ki 50.0
k6 5.0
Vmik_ 0.04
J25 0.05
ks 0.1
kpp_ 1.0
k25r 2.0
kp 100.0
V2c_ 0.02
kaa 0.1
V4 1.0
kj 400.0
k1 0.02
kste9 5.0
Jste9 0.01
kw 2.0
kas 0.1
SK 0.018
V25 10.0
k5 0.1
V4_ 0.01
kjr 1.0

States:

Name Description
Inh(time) 0.0
Cdc25(time) 0.0
R_dna(time) 1.0
Mik1(time) 0.0
Rum1(time) 0.0
preMPF(time) 1.0
Wee1(time) 0.0
Slp1(time) 0.0
Rum1P(time) 0.0
CRP(time) 0.0
Slp1_a(time) 0.0
PI(time) 0.2
mass(time) 1.0
MPF(time) 0.0
Ste9(time) 0.0
CR(time) 0.0

Observables: none

SVP_Templates200906 @ v0.0.1

Standard Virtual Parts Template Models v200906

Templates for the Standard Virtual Parts Library, v200906

Parameters: none

States: none

Observables: none

swanson_true_lin_buhler_vessella_murray_2001 @ v0.0.1

Swanson, True, Lin, Buhler, Vessella, Murray, 2001

nothing

Parameters:

Name Description
beta_h 0.0
Vo 20.0
Vh 0.0
gamma 1.2896
beta_c 1.721
rho 0.0655

States:

Name Description
p(time) 0.0

Observables: none

swat_2004 @ v0.0.1

Bifurcation analysis of the regulatory modules of the mammalian G1/S transition

MOTIVATION: Mathematical models of the cell cycle can contribute to an understanding of its basic mechanisms. Modern simulation tools make the analysis of key components and their interactions very effective. This paper focuses on the role of small modules and feedbacks in the gene-protein network governing the G1/S transition in mammalian cells. Mutations in this network may lead to uncontrolled cell proliferation. Bifurcation analysis helps to identify the key components of this extremely complex interaction network. RESULTS: We identify various positive and negative feedback loops in the network controlling the G1/S transition. It is shown that the positive feedback regulation of E2F1 and a double activator-inhibitor module can lead to bistability. Extensions of the core module preserve the essential features such as bistability. The complete model exhibits a transcritical bifurcation in addition to bistability. We relate these bifurcations to the cell cycle checkpoint and the G1/S phase transition point. Thus, core modules can explain major features of the complex G1/S network and have a robust decision taking function.

Parameters:

Name Description
j13 0.002
k76 0.1
Fm 0.0
k25 0.9
j18 0.6
km1 0.5
j12 5.0
phi_pRBpp 0.04
j11 0.5
phi_CycDi 0.023
a 0.04
j15 0.001
k89 0.07
phi_pRB 0.005
phi_E2F1 0.1
phi_pRBp 0.06
k61 0.3
km4 0.3
phi_CycDa 0.03
k67 0.7
j61 5.0
k98 0.01
j68 7.0
kp 0.05
k23 0.3
phi_CycEi 0.06
k16 0.4
km9 0.005
k43 0.01
k1 1.0
j62 8.0
j65 6.0
k3 0.05
k28 0.06
km2 4.0
phi_CycEa 0.05
phi_AP1 0.01
j63 2.0
k2 1.6
k34 0.04

States:

Name Description
pRBp(time) 0.0
CycEa(time) 0.0
E2F1(time) 0.0
CycDa(time) 0.0
pRBpp(time) 0.0
CycDi(time) 0.0
pRB(time) 0.0
AP1(time) 0.0
CycEi(time) 0.0

Observables: none

SystemsModelTutorial1 @ v0.0.1

Tutorial on Constructing a Systems Model from SVPs

nothing

Parameters: none

States: none

Observables: none

T


tabak_mascagni_bertram_2010 @ v0.0.1

Tabak, Mascagni and Bertram 2010

nothing

Parameters:

Name Description
wi 0.0
ka -0.05
n 0.01
w 0.8
taus 250.0
th0 0.17
ths 0.2
ks 0.05

States:

Name Description
a(time) 0.1
s(time) 0.3

Observables: none

tabak_toporikova_freeman_bertram_2007 @ v0.0.1

Tabak, Toporikova, Freeman, Bertram, 2007

nothing

Parameters:

Name Description
sh 5.0
C 10.0
VK -75.0
vn -5.0
gSK 1.7
lambda 0.7
sm 12.0
ks 0.5
gK 4.0
tau_h 20.0
tau_n 30.0
kc 0.16
alpha 0.0015
gA 25.0
fc 0.01
sn 10.0
vh -60.0
gCa 2.0
kPRL 1.0
sf 5.6
va -20.0
vm -20.0
sa 10.0
gBK 0.2
vf -20.0
VCa 50.0

States:

Name Description
V(time) -60.0
n(time) 0.1
h(time) 0.1
Ca(time) 0.1

Observables: none

tentusscher_noble_noble_panfilov_2004 @ v0.0.1

Tentusscher, Noble, Noble, Panfilov, 2004

nothing

Parameters:

Name Description
T 310.0
stim_start 10.0
P_kna 0.03
Km_Ca 1.38
c_rel 0.008232
g_bca 0.000592
K_buf_sr 0.3
K_sat 0.1
Km_Nai 87.5
tau_g 2.0
a_rel 0.016464
g_to 0.073
Cm 0.185
g_pK 0.0146
P_NaK 1.362
K_mNa 40.0
g_bna 0.00029
b_rel 0.25
g_Ks 0.245
g_K1 5.405
K_pCa 0.0005
g_Kr 0.096
Na_o 140.0
stim_duration 1.0
K_up 0.00025
K_mk 1.0
Ca_o 2.0
g_pCa 0.825
stim_period 1000.0
V_sr 0.001094
V_c 0.016404
K_o 5.4
K_buf_c 0.001
Buf_sr 10.0
alpha 2.5
g_Na 14.838
Vmax_up 0.000425
stim_amplitude 52.0
V_leak 8.0e-5
Buf_c 0.15
gamma 0.35
g_CaL 0.000175
K_NaCa 1000.0
R 8314.472
F 96485.3415

States:

Name Description
d(time) 0.0
g(time) 1.0
Xr1(time) 0.0
V(time) -86.2
h(time) 0.75
f(time) 1.0
K_i(time) 138.3
Xs(time) 0.0
fCa(time) 1.0
Xr2(time) 1.0
r(time) 0.0
j(time) 0.75
m(time) 0.0
Ca_SR(time) 0.2
Ca_i(time) 0.0002
s(time) 1.0
Na_i(time) 11.6

Observables: none

tentusscher_noble_noble_panfilov_2006 @ v0.0.1

Tentusscher, Noble, Noble, Panfilov, 2006

nothing

Parameters:

Name Description
T 310.0
P_kna 0.03
Km_Ca 1.38
c_rel 0.008232
g_bca 0.000592
K_buf_sr 0.3
K_sat 0.1
Km_Nai 87.5
tau_g 2.0
a_rel 0.016464
g_to 0.073
Cm 0.185
g_pK 0.0146
P_NaK 1.362
IstimPulseDuration 1.0
K_mNa 40.0
g_bna 0.00029
b_rel 0.25
g_Ks 0.245
g_K1 5.405
K_pCa 0.0005
g_Kr 0.096
Na_o 140.0
K_up 0.00025
K_mk 1.0
Ca_o 2.0
g_pCa 0.825
V_sr 0.001094
V_c 0.016404
K_o 5.4
K_buf_c 0.001
Buf_sr 10.0
IstimAmplitude -52.0
alpha 2.5
g_Na 14.838
Vmax_up 0.000425
IstimEnd 50000.0
V_leak 8.0e-5
Buf_c 0.15
IstimPeriod 1000.0
gamma 0.35
g_CaL 0.000175
K_NaCa 1000.0
IstimStart 100.0
R 8314.472
F 96485.3415

States:

Name Description
d(time) 0.0
g(time) 1.0
Xr1(time) 0.0
V(time) -86.2
h(time) 0.75
f(time) 1.0
K_i(time) 138.3
Xs(time) 0.0
fCa(time) 1.0
Xr2(time) 1.0
r(time) 0.0
j(time) 0.75
m(time) 0.0
Ca_SR(time) 0.2
Ca_i(time) 0.0002
s(time) 1.0
Na_i(time) 11.6

Observables: none

tentusscher_panfilov_2006 @ v0.0.1

Tentusscher, Panfilov, 2006

nothing

Parameters:

Name Description
T 310.0
stim_start 10.0
EC 1.5
P_kna 0.03
Km_Ca 1.38
g_bca 0.000592
K_buf_sr 0.3
V_rel 0.102
K_sat 0.1
Km_Nai 87.5
g_to 0.294
Cm 0.185
V_xfer 0.0038
g_pK 0.0146
P_NaK 2.724
K_mNa 40.0
g_bna 0.00029
g_Ks 0.392
g_K1 5.405
k3 0.06
K_pCa 0.0005
g_Kr 0.153
k1_prime 0.15
V_ss 5.468e-5
Na_o 140.0
stim_duration 1.0
K_buf_ss 0.00025
min_sr 1.0
K_up 0.00025
K_mk 1.0
max_sr 2.5
Ca_o 2.0
g_pCa 0.1238
stim_period 1000.0
V_sr 0.001094
Buf_ss 0.4
k4 0.005
V_c 0.016404
K_o 5.4
K_buf_c 0.001
Buf_sr 10.0
alpha 2.5
g_Na 14.838
k2_prime 0.045
Vmax_up 0.006375
stim_amplitude 52.0
V_leak 0.00036
Buf_c 0.2
gamma 0.35
g_CaL 3.98e-5
K_NaCa 1000.0
R 8314.472
F 96485.3415

States:

Name Description
d(time) 3.373e-5
Xr1(time) 0.00621
V(time) -85.23
h(time) 0.7444
Ca_ss(time) 0.00036
f2(time) 0.9755
f(time) 0.7888
K_i(time) 136.89
R_prime(time) 0.9073
Xs(time) 0.0095
Xr2(time) 0.4712
r(time) 2.42e-8
j(time) 0.7045
fCass(time) 0.9953
m(time) 0.00172
Ca_SR(time) 3.64
Ca_i(time) 0.000126
s(time) 0.999998
Na_i(time) 8.604

Observables: none

terkildsen_niederer_crampin_hunter_smith_2008 @ v0.0.1

Terkildsen, Niederer, Crampin, Hunter, Smith, 2008

nothing

Parameters:

Name Description
c 0.01
T 295.0
K_m_K 1.5
A_1 -29.0
B_CMDN 0.05
alpha_2 0.13
i_NaK_max 9.5e-5
K_L 0.00022
k_on 100.0
d 100.0
k_Ref_off 0.2
g_B_K 1.38e-7
Cm 0.0001
theta_R 0.012
alpha_r2 0.00175
k_sat 0.1
K_mNa 87.5
eta 0.35
J_L 0.000913
V_L -2.0
J_R 0.02
V_myo 25850.0
g_K1 2.4e-5
del_VL 7.0
K_mCa 1.38
A_3 129.0
alpha_0 0.008
tau_R 2.43
a_endo 0.583
T_ref 56.2
phi_R 0.05
Na_o 140.0
Ca_50ref 0.00105
stim_duration 10.0
E_Ca 65.0
n_Hill 3.0
z_p 0.85
b 14.0
g_B_Na 8.015e-8
g_ss 7.0e-6
Ca_o 1.2
K_z 0.15
V_SR 2098.0
g_pCa 3.5e-6
K_mpCa 0.0005
a 0.0625
k_CMDN 0.002382
g_D 0.065
stim_period 1000.0
b_endo 0.417
N 50000.0
alpha_r1 0.002
f_Na 0.2
K_o 5.4
g_NCX 0.0385
A_2 138.0
beta_0 4.9
K_m_Na 10.0
n_Rel 3.0
alpha_3 0.625
K_SERCA 0.0005
g_t 3.5e-5
g_SERCA 0.00045
V_SR_uL 2.098e-6
Ca_TRPN_Max 0.07
g_Na 0.0008
g_B_Ca 3.24e-5
gamma_trpn 2.0
g_f 1.45e-6
alpha_1 0.03
stim_amplitude -0.0006
tau_L 650.0
K_RyR 0.041
phi_L 2.35
beta_1 -4.0
g_CaB 2.6875e-8
g_SRl 1.8951e-5
R 8314.5
t_L 1.0
F 96487.0
V_myo_uL 2.585e-5

States:

Name Description
z_1(time) 0.98794
y(time) 0.0026369
z_2(time) 0.00887
s_slow(time) 0.42756
j(time) 0.60876276
Q_3(time) 0.0
z_3(time) 0.003156
m(time) 0.0054828
s(time) 0.8823
Na_i(time) 11.28
V(time) -78.8
TRPN(time) 0.0661796
h(time) 0.6095126
r_ss(time) 0.0033545
s_ss(time) 0.266596
z(time) 0.020023
K_i(time) 138.7225
Q_2(time) 0.0
r(time) 0.002542
Ca_SR(time) 0.72196
Ca_i(time) 0.00011423
Q_1(time) 0.0

Observables: none

testing_Sed_ML_nesting @ v0.0.1

Some test SED-ML to play with the nested proposal

A place to store and track SED-ML documents which demonstrate various aspects of the various proposals to extend SED-ML with nested tasks and/or simulations.

Parameters: none

States: none

Observables: none

teusink_passarge_reijenga_esgalhado_vanderweijden_schepper_walsh_bakker_vandam_westerhoff_snoep_2000 @ v0.0.1

Teusink, Passarge, Reijenga, Esgalhado, Vanderweijden, Schepper, Walsh, Bakker, Vandam, Westerhoff, Snoep, 2000

nothing

Parameters: none

States: none

Observables: none

tham_2008 @ v0.0.1

Tham 2008

nothing

Parameters: none

States: none

Observables: none

thomas_2000 @ v0.0.1

Thomas, 2000

nothing

Parameters:

Name Description
sigma_GLU 0.5
b 4.0
sigma_LAC 0.5
Km 0.1
ksh 1.213
L 4.0
PGLU 1.2
PLAC 33.93
VolFract 0.3
GlyFract 0.2
c_DVR_GLU_0 10.0
N_0 128.0

States:

Name Description
F_AVR_GLU(x) 0.01
F_DVR_v(x) 3.75
F_DVR_GLU(x) 0.01
F_AVR_v(x) 0.01
F_DVR_LAC(x) 0.01
F_AVR_LAC(x) 0.01

Observables: none

thomsen_neubig_1989 @ v0.0.1

Thomsen, Neubig, 1989

nothing

Parameters:

Name Description
GDP nothing
k4_ nothing
k1 nothing
k3_ nothing
GTP nothing
k2_ nothing
k4 nothing
k3 nothing
k6 nothing
k5 nothing
k1_ nothing
k2 nothing

States:

Name Description
DR(time) nothing
DRG_GDP(time) nothing
G_GDP(time) nothing
DRG_GTP(time) nothing
DRG(time) nothing
R(time) nothing
D(time) nothing
Gstar_GTP(time) nothing

Observables: none

tolic_mosekilde_sturis_2000 @ v0.0.1

Tolic, Mosekilde, Sturis, 2000

nothing

Parameters:

Name Description
C3 1000.0
Rm 210.0
td 36.0
a1 300.0
Gin 216.0
Ub 72.0
alpha 0.29
C4 80.0
E 0.2
Um 940.0
beta 1.77
C1 2000.0
C2 144.0
tp 6.0
ti 100.0
U0 40.0
Vp 3.0
C5 26.0
Vg 10.0
Rg 180.0
Vi 11.0

States:

Name Description
Ii(time) 243.2865183
x3(time) 104.5878705
G(time) 12342.61665
x2(time) 112.7601171
Ip(time) 93.36441699
x1(time) 110.420253

Observables: none

tomida_hirose_takizawa_shibasaki_iino_2003 @ v0.0.1

Tomida, Hirose, Takizawa, Shibasaki, Iino, 2003

nothing

Parameters:

Name Description
stim_duration 0.5
k3 0.06
k4 0.035
stim_wavelength 3.0
k1_unstim 0.0
k1_stim 0.359
k2 0.147
time_before_stim 1.0

States:

Name Description
NFAT_cyt(time) 0.0
NFAT_nuc(time) 0.0
NFATP_cyt(time) 5000.0

Observables: none

topp_promislow_devries_miura_finegood_2000 @ v0.0.1

Topp, Promislow, Devries, Miura, Finegood, 2000

nothing

Parameters:

Name Description
SI 0.72
sigma 43.2
r1 0.00084
r2 2.4e-6
d0 0.06
alpha 2000.0
k 432.0
R0 846.0
EG0 1.44

States:

Name Description
G(time) 600.0
I(time) 0.0
beta(time) 0.0

Observables: none

tran_2009 @ v0.0.1

Tran 2010

A metabolite-sensitive, thermodynamically-constrained model of cardiac cross-bridge cycling: Implications for force development during ischemia, Kenneth Tran, Nicolas P. Smith, Denis S. Loiselle and Edmund J. Crampin, 2010, Biophysical Journal, 98, 267-276. PubMed ID: 20338848

Parameters:

Name Description
koffH 0.025
kn_p 0.5
SEon 1.0
perm50 0.5
koffL 0.25
hb 0.4
hfmdc 5.0
gslmod 6.0
hbmdc 0.0
kMgATP 1.54e10
pH 7.15
fapp 0.5
Qgapp 2.5
len_hbare 0.1
MgATP_cons 5000.0
len_thick 1.65
kdADP 4.0
kp_n 0.05
Qkn_p 1.6
kon 0.05
sigman 1.0
hf 2.0
KSE 1.0
SLrest 1.85
Cai 200.0
Qkon 1.5
Qkp_n 1.6
Qhf 6.25
PCon_t 0.002
MgATP 5000.0
PCon_c 0.02
SLset 1.9
xPi_cons 2000.0
sigmap 8.0
gapp 0.07
gxb 0.07
len_thin 1.2
Qkoff 1.3
PExp_c 70.0
MgADP_cons 36.0
xPi 2000.0
nperm 15.0
SL_c 2.25
MgADP 36.3
TmpC 299.0
Qgxb 6.25
x_0 0.007
koffmod 1.0
Trop_conc 70.0
kdHCa 0.02
xPsi 2.0
m 1.0
Qhb 6.25
xbmodsp 0.2
Qfapp 6.25
PExp_t 10.0

States:

Name Description
P(time) 0.999997834540066
TRPNCaL(time) 0.0147730085063734
P_NoXB(time) 4.07437173988636e-8
TRPNCaH(time) 0.13066096561522
SL(time) 2.2
xXBprer(time) 3.41212828972468e-8
XBprer(time) 3.0494964880038e-7
N_NoXB(time) 0.999999959256274
xXBpostr(time) 0.00700005394873882
XBpostr(time) 1.81017564383744e-6
intf(time) -4.5113452510363e-6

Observables: none

tran_smith_loiselle_crampin_2009 @ v0.0.1

Tran, Smith, Loiselle, Crampin, 2009

nothing

Parameters:

Name Description
P_i 1.0
ATP 5.0
kdh1 1.09e-5
k_m1 2.0
k_m2 67200.0
Ca_sr 1.0
Ca_i 0.001
H_i 0.0001
k_p3 20.5
kdcasr 2.24
k_p1 25900.0
k_p2 2540.0
k_m3 149.0
kdhsr 1.05e-8
kdh 7.24e-5
kdcai 0.9
ADP 0.02
kdhi 0.00354
n 2.0

States:

Name Description
Ca_sr(time) 0.0
ATP(time) 0.01

Observables: none

tyson_1991 @ v0.0.1

Tyson, 1991

nothing

Parameters:

Name Description
k4_ 0.018
k9 100.0
P 1.0
k4 180.0
k7 0.6
k6 1.0
aa 1.0
k2 0.0

States:

Name Description
pM(time) 0.001
CP(time) 0.001
M(time) 0.001
YP(time) 0.001
Y(time) 0.001
C2(time) 0.001

Observables: none

tyson_hong_thron_novak_1999 @ v0.0.1

Tyson, Hong, Thron, Novak, 1999

nothing

Parameters:

Name Description
vp 0.5
kp3 0.1
km 0.1
kp1 10.0
vm 1.0
Jp 0.05
Pcrit 0.1
Keq 200.0
kp2 0.03

States:

Name Description
M(time) 0.0
Pt(time) 0.0

Observables: none

U


ueda_hagiwara_kitano_2001 @ v0.0.1

Ueda, Hagiwara, Kitano, 2001

nothing

Parameters:

Name Description
V3 1.63
B1 0.0
L8 0.2
r 4.0
T4 0.52
V1 1.45
T3 1.63
S4 0.48
L6 0.2
D2 0.44
S2 0.48
D7 0.54
R1 1.02
K4 2.0
A3 0.8
D6 0.29
T2 0.72
A1 0.45
D1 0.94
K1 2.0
L1 0.3
L5 0.2
C3 0.0
K2 2.0
B2 0.0
L4 0.2
a 1.0
L2 0.2
D9 0.6
C2 0.0
C1 0.0
S1 1.45
B3 0.6
A2 0.45
L3 0.3
V2 1.45
D4 0.44
L9 0.2
S5 1.63
D10 0.3
S3 1.45
V4 1.63
Cyc_c 1.0
Dbt_c 1.0
L7 0.13
T1 1.73
D3 0.94
R3 0.89
D8 0.6
L10 0.2
S6 0.47
D5 0.44
D0 0.012
R2 1.02
K3 2.0

States:

Name Description
Per_c(time) 0.6
PT_c(time) 0.9
CC_c(time) 0.3
Tim_c(time) 0.8
Clk_c(time) 0.2
Clk_m(time) 0.1
Per_m(time) 0.5
CC_n(time) 0.4
PT_n(time) 1.0
Tim_m(time) 0.7

Observables: none

V


vanbeek_2007 @ v0.0.1

Vanbeek, 2007

nothing

Parameters:

Name Description
PS_tot_ADP 13.3
V_max_syn 15040.0
J_hyd_basis_1 486.5
Kia 750.0
Vmax_MM_f 11440.0
Kic 204.8
PS_tot_PCr 155.0
KPi 800.0
nb_of_cycles_1 5.0
Kb 5200.0
Kd 500.0
Vmax_MM_b 48040.0
PS_tot_Pi 194.0
Vmax_Mi_b 3704.0
PS_tot_Cr 155.0
J_hyd_basis_2 627.6
freq_1 135.0
PS_tot_ATP 13.3
Kid 1600.0
Vmax_Mi_f 882.0
V_cyt 0.75
KADP 25.0
Kib 28800.0
V_ims 0.0625
freq_2 220.0

States:

Name Description
PCr_ims(time) 5000.0
ATP_ims(time) 5912.77
Pi_ims(time) 910.0
ADP_ims(time) 39.0
ATP_cyt(time) 5912.77
Cr_ims(time) 10500.0
ADP_cyt(time) 64.0
PCr_cyt(time) 5000.0
Cr_cyt(time) 10500.0
Pi_cyt(time) 913.0

Observables: none

vancapelle_durrer_1980 @ v0.0.1

Vancapelle, Durrer, 1980

nothing

Parameters:

Name Description
T 50.0
C 0.01
cf 0.2531834
df 2.356256
bf 0.00584649
Vm -78.6
af 3.837854e-5

States:

Name Description
Y(time) 0.07

Observables: none

vanderpol_vandermark_1928 @ v0.0.1

Vanderpol, Vandermark, 1928

nothing

Parameters:

Name Description
epsilon 1.0

States:

Name Description
x(time) -2.0
y(time) 0.0

Observables: none

vangoor_lebeau_krsmanovic_sherman_catt_stojilkovic_2000 @ v0.0.1

Vangoor, Lebeau, Krsmanovic, Sherman, Catt, Stojilkovic, 2000

nothing

Parameters:

Name Description
tau_h 22.0
i_app 15.0
g_M 4.0
g_ir 1.71
g_d 0.044
g_Na 60.0
Vh 40.0
k1 0.3
V_K -80.0
g_K_dr 20.0
k2_ 0.01
V_Ca 100.0
g_Ca_L 1.3
g_Ca_T 0.94
V_Na 60.0
Cm 14.0
k1_ 0.03
k2 0.001

States:

Name Description
D_(time) 0.0
A(time) 1.0
n(time) 0.0
h(time) 0.0
m(time) 0.0
V(time) -60.0
D(time) 0.0
A_(time) 0.0

Observables: none

vasalou_henson_2010 @ v0.0.1

Vasalou and Henson 2010

nothing

Parameters:

Name Description
v_Cl2 19.0
KmB 0.4
v_Cl1 15.5
K_D 0.08
V2PC 0.1
kdnc 0.12
kf 0.001
K_Ca 22.0
beta_IP3 0.5
v_PK 1.9
Cl0 1.0
E_Na_0 45.0
K_A 0.67
v_v0 0.09
Ca_ex 5.0
ksC 1.6
vdPCN 0.7
V_MK 5.0
K_VIP 15.0
v_sP0 1.0
K_ex2 1.0
k3 0.4
E_ex 0.0
V3PC 0.4
v_M2 149.5
v_ex1 105.0
vdCC 0.7
kd_VIP 0.5
nCl -0.2
vmB 0.8
k_q 8.75e-5
KmP 0.31
v_gk 10.0
K_Cl2 1.0
K_gk 10.0
GABA0 0.2
nkk 0.1
E_L_0 -29.0
Kd 0.3
k6 0.2
vdPCC 0.7
V2C 0.1
V4B 0.2
K_GABA 3.0
k_MK 2.9
nd_VIP 0.2
npk -2.0
Cl_ex 114.5
kdmb 0.01
V1P 0.4
k_b 2.0
K_kk 0.02
ksB 0.12
m 2.0
Na_ex 145.0
K_ex1 5.7405e8
P_Cl 0.3
k2 0.2
n 4.0
vdBC 0.5
F 96485.0
K_v0 4.5
vdIN 0.8
T 37.0
P_Na 0.036
V_R 0.41
V_theta 20.0
k8 0.1
vP 1.0
V2P 0.3
V3B 0.5
V4PC 0.1
v_M1 0.0003
K2CB 0.01
vmP 1.1
v_GABA 19.0
V1C 0.6
K_2 5.0
KmC 0.4
Cm 5.0
KAP 0.6
V1B 0.5
kdn 0.01
WT 1.0
KAC 0.6
v_kk 3.3
n_VIP 1.9
vmC 1.0
V_b 2.0
V1PC 0.4
nex2 -1.0
K_Cl1 4.0
K_R 34.0
vsC 1.1
vsB 1.0
T_room 22.0
nex1 2.5
v_Ca 12.3
E_K_0 -97.0
K1CB 0.01
v_M3 400.0
kdmp 0.01
K_PK 1.0
ksP 0.6
V2B 0.1
v_VIP 0.5
C_T 1.6
kdmc 0.01
Kdp 0.1
K_ex 1.0
k4 0.2
v_KCa 3.0
vdPC 0.7
v 2.0
g_K0 9.7
K_KCa 0.16
P_Ca 0.05
g_Na 36.0
nkca -1.0
Kp 0.1
nv0 4.5
k1 0.45
g_inhib 12.3
nca 2.2
K_C 0.15
KIB 2.2
k7 0.5
v_ex2 4.4
vdBN 0.6
k5 0.4
R 8.314
p 4.2
T_abs 273.15

States:

Name Description
IN(time) 0.05
BC(time) 2.41
PCNP(time) 0.091
BN(time) 1.94
PCCP(time) 0.2
PC(time) 0.4
CB(time) 0.12
BCP(time) 0.48
MP(time) 2.8
CCP(time) 9.0
VIP(time) 0.0
Ca_store(time) 0.1
PCN(time) 0.16
CC(time) 12.0
PCP(time) 0.13
PCC(time) 1.26
Ca_in(time) 0.1
MB(time) 7.94
MC(time) 2.0
BNP(time) 0.32

Observables: none

vaseghi_baumeister_rizzi_reuss_1999 @ v0.0.1

Vaseghi, Baumeister, Rizzi, Reuss, 1999

nothing

Parameters:

Name Description
K_NADP_2 1.848
rmax_PKDA 0.004
rmax_Ru5PE 0.85
Ki_MgATP_2 0.109
rmax_G6PDH 44.19
K_PKDA 0.0032
K_RPPK 0.0034
rmax_TAL 3.0
rmax_TKL1 3.24
K_NADP_1 0.116
Ki_MgATP_1 0.33
Ki_NADPH_2 0.055
mu 1.0
C_GAP 0.064
rmax_R5PI 0.57
rmax_6PGDH 0.654
Ki_NADPH_1 1.702
rmax_TKL2 10.5
rmax_RPPK 0.003

States:

Name Description
C_Ru5P(time) 0.033
C_R5P(time) 0.118
C_G6P(time) 0.9
C_MgATP(time) 2.3
C_E4P(time) 0.029
C_NADPH(time) 0.168
C_S7P(time) 0.082
C_NADP(time) 0.168
C_X5P(time) 0.041
C_6PG(time) 0.25

Observables: none

vempati_karagiannis_popel_2007 @ v0.0.1

Vempati, Karagiannis, Popel, 2007

nothing

Parameters:

Name Description
kon_pM9T1M3 34000.0
koff_M3pM9 0.001
kon_M9T1_star 5.6e6
kon_TrpM9 10000.0
koff_M3pM9T1 0.001
koff_pM9T1M3 7.48e-5
koff_M9T1 0.00025
kon_M3_pM9T1 1.9e6
kon_M3T1 1.9e6
kon_pM9T1 34000.0
koff_TrpM9T1M3 0.007
koff_M3_pM9T1 0.000126
koff_M9T1_star 1.6e-5
kon_M9_M3T1 7.48e-5
koff_M9_M3T1 34000.0
kon_M3pM9T1M3 10000.0
kact_M3pM9 0.0019
kact_TrpM9T1 0.0006
koff_M3T1 0.000126
kon_TrpM9T1 10000.0
koff_TrpM9T1 0.007
koff_pM9T1 7.48e-5
kon_M3pM9 10000.0
kon_M9T1 0.00063
kon_TrpM9T1M3 10000.0
kact_M3pM9T1 0.00057
kon_M3pM9T1 10000.0
koff_TrpM9 0.007
koff_M3pM9T1M3 0.001
kact_TrpM9T1M3 0.0006
kact_M3pM9T1M3 0.00057
kact_M9T1M3 0.000126
kact_TrpM9 0.002

States:

Name Description
M9_T1_M3(time) 0.0
pM9_T1(time) 0.0
pM9_T1_M3(time) 0.0
M3_pM9(time) 0.0
M3(time) 5.0e-8
Tr_pM9(time) 0.0
M9_T1(time) 0.0
Tr_pM9_T1(time) 0.0
M3_pM9_T1_M3(time) 0.0
M9_T1_star(time) 0.0
pM9(time) 3.0e-7
Tr(time) 1.0e-7
M3_pM9_T1(time) 0.0
Tr_pM9_T1_M3(time) 0.0
M9(time) 0.0
M3_T1(time) 0.0
T1(time) 3.0e-7

Observables: none

vendelin_kongas_saks_2000 @ v0.0.1

Vendelin, Kongas, Saks, 2000

nothing

Parameters: none

States: none

Observables: none

vilar_2006 @ v0.0.1

Vilar 2006

nothing

Parameters:

Name Description
ka 1.0
kr 0.033333333
p_RII 4.0
ki 0.333333333
kcd 0.0277777778
klid 0.25
alpha 1.0
p_RI 8.0

States:

Name Description
RII(time) 20.0
l_RI_RII_endo(time) 40.0
RII_endo(time) 0.0
l_RI_RII(time) 0.0
RI(time) 20.0
RI_endo(time) 0.0

Observables: none

vilar_kueh_barkai_leibler_2002 @ v0.0.1

Vilar, Kueh, Barkai, Leibler, 2002

nothing

Parameters:

Name Description
Delta_1 1.0
Delta_4 10.0
Delta_3 0.2
Thetha_1 50.0
Delta_2 1.0
Gamma_1 2.0
Delta_5 0.5
Alpha_2 500.0
Gamma_2 1.0
Gamma_3 1.0
BetaR_1 5.0
Alpha_1 50.0
Alpha_3 0.01
BetaA_1 50.0
Alpha_4 50.0
Theta_2 100.0

States:

Name Description
DR(time) 1.0
DA(time) 1.0
MR(time) 0.0
A(time) 0.0
R(time) 0.0
DRP(time) 1.0
MA(time) 0.0
C(time) 0.0
DAp(time) 0.0

Observables: none

vinnakota_kemp_kushmerick_2006 @ v0.0.1

Vinnakota, Kemp and Kushmerick, 2006

nothing

Parameters:

Name Description
T1 298.15
R 0.008314

States:

Name Description
PEP(time) 1.0e-9
G6P(time) 1.0e-9
Pi(time) 0.035
G3P(time) 1.0e-9
Mg(time) 0.0004913450725
Gly(time) 0.04
Cr(time) 0.029999999
AMP(time) 1.0e-9
P3G(time) 1.0e-9
ATP(time) 0.005
pH_calc(time) 7.3
F6P(time) 1.0e-9
FBP(time) 1.0e-9
G1P(time) 1.0e-9
ADP(time) 1.0e-9
BPG(time) 1.0e-9
PCr(time) 1.0e-9
PYR(time) 1.0e-9
GAP(time) 1.0e-9
NAD(time) 0.0005
protonload(time) 0.0
DHAP(time) 1.0e-9
LAC(time) 1.0e-9
P2G(time) 1.0e-9
NADH(time) 1.0e-9

Observables: none

vinnakota_rusk_palmer_shankland_kushmerick_2010 @ v0.0.1

Vinnakota, Rusk, Palmer, Shankland and Kushmerick, 2010

nothing

Parameters:

Name Description
clamp 1.0

States:

Name Description
PEP(time) 1.0e-9
G6P(time) 1.0e-9
Pi(time) 0.0054
G3P(time) 1.0e-9
mg(time) 0.001
Gly(time) 0.02
Cr(time) 0.0075
AMP(time) 1.0e-8
HCO3_cy(time) 0.015
P3G(time) 1.0e-9
HCO3_ec(time) 0.03
ATP(time) 0.0055
pH_ec(time) 7.439766507222684
pH_calc(time) 7.14
F6P(time) 1.0e-9
FBP(time) 1.0e-9
G1P(time) 1.0e-9
ADP(time) 1.0e-5
BPG(time) 1.0e-9
CO2_ec(time) 0.001564425
PCr(time) 0.0145
PYR(time) 1.0e-9
CO2_cy(time) 0.001564425
GAP(time) 1.0e-9
NAD(time) 0.000406654344
DHAP(time) 1.0e-9
LAC(time) 1.0e-9
MOPS(time) 0.0
MOPSH(time) 0.0
P2G(time) 1.0e-9
LAC_ec(time) 0.0
NADH(time) 4.06654344e-8

Observables: none

virtualbacterialphotography @ v0.0.1

Virtual Bacterial Photography

nothing

Parameters: none

States: none

Observables: none

viswanathan_shaw_rudy_1999 @ v0.0.1

Viswanathan, Shaw, Rudy, 1999

nothing

Parameters:

Name Description
nicholsarea 5.0e-5
preplength 0.001
gamma_Cai 1.0
gamma_Cao 0.341
hATP 2.0
stim_start 100.0
Tn_max 0.07
T 310.0
P_Na 6.75e-7
Km_Ca 0.0006
PNaK 0.01833
P_K 1.93e-7
K_mup 0.00092
G_rel_max 60000.0
d_NaCa 0.001
delta_Ca_ith 0.00018
Ko 4.5
gamma_Nao 0.75
Logicthresh 0.98
CMDN_max 0.05
delta_m 1.0e-5
tau_tr 0.18
Ca_NSR_max 15.0
kATP 0.00025
stim_duration 2.0
n_NaCa 3.0
Cao 1.8
g_Nab 0.004
K_mpCa 0.0005
gamma_Nai 0.75
stim_period 1000.0
stim_end 9.9999e7
K_mCSQN 0.8
K_mCMDN 0.00238
radius 0.00011
gamma_Ki 0.75
K_m_ns_Ca 0.0012
A_cap 1.434e-7
I_pCa 1.15
I_NaK 2.0
Nao 132.0
ATPi 3.0
K_mNai 10.0
P_Ca 0.00054
g_Na 16.0
I_up 5.0
g_Cab 0.003016
g_Kp 0.00552
stim_amplitude -25.5
G_rel_overload 4000.0
K_mrel 0.0008
CSQN_max 10.0
gamma_Ko 0.75
g_CaT 0.05
K_mTn 0.0005
nATP 0.24
gamma 0.5
K_mKo 1.5
CSQNthresh 0.7
K_NaCa 0.002
F 96485.0
R 8314.0

States:

Name Description
OVRLDtrack3(time) 2.2645e-282
xr(time) 0.0007500578
Ca_NSR(time) 2.7872629
OVRLDtrack2(time) -2.5e-323
f(time) 0.995259
Cainfluxtrack(time) 1.660129e-87
APtrack2(time) 2.07066e-86
xs1(time) 0.0421517
j(time) 0.99511469
m(time) 0.0008601
xs2(time) 0.08866
Nai(time) 14.177596
APtrack3(time) 0.01924195
APtrack(time) 3.7458e-87
zdv(time) 0.01198974
d(time) 3.538268e-6
g(time) 0.9341828
OVRLDtrack(time) 2.0e-323
V(time) -88.5004
h(time) 0.992806
ydv(time) 0.97497
Ca_JSR(time) 0.8204291
Ki(time) 138.37949
b(time) 0.0010301
Cai(time) 0.00034209

Observables: none

VPH_MIP @ v0.0.1

VPH-MIP case study on CellML

Models used in the VPH-MIP standards and ontologies module for the CellML case study.

Parameters: none

States: none

Observables: none

W


Walmsley_Rodriguez_2013 @ v0.0.1

mRNA expression levels in failing human hearts predict cellular electrophysiological remodeling: A population-based simulation study

mRNA expression levels in failing human hearts predict cellular electrophysiological remodeling: A population-based simulation study. This is an example of a model that uses parameter uncertainty, which is specified in terms of probability density functions.

Parameters: none

States: none

Observables: none

wanant_quon_2000 @ v0.0.1

Wanant, Quon, 2000

nothing

Parameters:

Name Description
k1 1.0e6
k1_ 0.0004
k5_ 0.004
k4_ 0.0004
k3 1.0e6
k4 1.0e6
k5 1.0e7
k3_ 0.0004
k2 1.0e6
k2_ 0.04

States:

Name Description
x4(time) 1.0
x6(time) 1.0
x3(time) 1.0
x9(time) 1.0
x5(time) 1.0
x7(time) 1.0
x8(time) 1.0
x2(time) 0.1
x1(time) 10.0

Observables: none

wang_cirit_haugh_2009 @ v0.0.1

Wang, Cirit and Haugh 2009

nothing

Parameters:

Name Description
Kph 4.64
kd_x2 2.85
Vmax_x12_KM_x12 4.71
KDL 1.5
L 1.0
KM_x21 21.6
Vmax_zph2_KM_zph2 0.228
KM_zph2 31.5
kd_w 0.0333
Vmax_y2_KM_y2 31.9
K_GR 495.0
KM_yph2 12.7
ke 0.2
Vmax_y1_KM_y1 11.8
kappa_PI3K 0.3
K_GP 5.09
Vmax_x21_KM_x21 0.405
k_FB_f 0.976
k_minusx 0.07
kd_x1 0.745
k_FB_ph 2.34
Wph 0.385
kxR0 0.3
KM_zph1 14.0
K_x2 6.77
KM_y2 8.81
kt 0.005
Zf 0.272
KM_y1 31.9
k_Ras 1.0
Vmax_x11_KM_x11 1.18
Vmax_yph1_KM_yph1 4.4
Kf 3.76
alpha_PI3K 80.0
KM_x12 45.5
KM_x11 30.3
Vmax_zph1_KM_zph1 0.451
KM_x22 15.7
gamma 0.1
KM_yph1 44.0
Vmax_yph2_KM_yph2 6.77
k_3PI 1.0
Vmax_x22_KM_x22 2.41
p 1.98
n 1.03

States:

Name Description
e_ph(time) 1.0
zpp(time) 0.0
x2(time) 0.0
m_3PI(time) 0.0
y(time) 1.0
m_Ras(time) 0.0
z(time) 1.0
f_GEF(time) 1.0
c2(time) 0.0
r(time) 0.5
ypp(time) 0.0
w(time) 0.0
x1(time) 0.0

Observables: none

wang_huang_huang_2006 @ v0.0.1

Wang, Huang, Huang, 2006

A quantitative kinetic model for ATP-induced intracellular Ca2+ oscillations.

Parameters:

Name Description
n 4.0
K_C2 2.0
k_5 0.12
k_4 1.2
K_D 0.01
K_S 0.025
k_0 0.0001
k_2 4.0
lambda 0.001
k_8 10.5
w 3.0
C_PLC_T 0.01
K_P 0.004
k_3 4.5
k_11 0.26
beta 0.05
rho 0.2
k_7 2.0
K_C1 1.0
k_10 3.0
m 2.0
K_G 0.025
K_R 0.2
k_6 14.0
k_9 0.6
K_ER 0.075
k_1 3.4

States:

Name Description
G(time) 0.001
C_cyt(time) 0.2
C_ER(time) 1.0
IP_3(time) 0.001
APLC(time) 0.001

Observables: none

wang_li_kuang_2007 @ v0.0.1

Wang, Li, Kuang, 2007

nothing

Parameters:

Name Description
C3 1000.0
alpha 0.29
Ub 72.0
C4 80.0
di 0.0107
Um 940.0
beta 1.77
C2 144.0
ti 100.0
U0 40.0
Vp 3.0
C5 26.0
Vg 10.0
Rg 180.0
Vi 11.0

States:

Name Description
G(time) 150.0
I(time) 5.0

Observables: none

wang_lin_lin_wu_2008 @ v0.0.1

Wang, Lin, Lin, Wu, 2008

nothing

Parameters:

Name Description
b_bar 0.28
C_m 0.009
I_mag 2.0
g_KCa 0.5
E_K -70.0
V_beta_n 40.0
E_m -42.0
k_2 0.011
V_alpha_m 10.0
beta_h_max 3.382
d_2 1.0
a_bar 0.48
kd 0.18
g_K 0.415
alpha_n_max 0.0229
k_pmca 0.2
E_Na 50.0
RT 2577.0
g_Ca0 0.05
V_beta_m 18.0
E_h -41.0
E_Ca 50.0
f_cyt 0.01
k_serca 0.4
f_er 0.01
V_beta_h 7.6
alpha_h_max 0.0156
alpha_m_max 0.208
t_1 6.0
E_L -75.0
alpha 4.5e-6
g_Na 0.45
p_leak 0.0005
v_cytver 5.0
V_alpha_h 14.7
E_n -40.0
beta_n_max 0.09616
R_s 15.0
C_t 0.04
d_1 0.84
beta_m_max 2.081
g_Lmax 0.0024
V_alpha_n 7.0
t_0 5.0
k_1 0.18

States:

Name Description
d(time) 0.0
o(time) 0.15
h(time) 1.0
n(time) 0.0
m(time) 0.0
c(time) 0.15
cer(time) 200.0
V_m(time) -75.0
V_T(time) -70.0

Observables: none

wang_sobie_2008 @ v0.0.1

Wang, Sobie, 2008

nothing

Parameters:

Name Description
Vss 3.0734e-8
Kpc_max 0.23324
Clo 132000.0
R 8.314
T 298.0
stim_start 20.0
E_CaT 50.0
Km_CSQN 800.0
Kpcb 0.0005
k_minus_htrpn 3.2e-5
Km_Nai 21000.0
k_plus_a 0.00608
kf 0.023761
Cli 30000.0
Km_Cl 4.0
Ko 5400.0
i_NaK_max 0.88
Cm 1.0
v3 0.09
Km_CMDN 0.238
g_Kto_f 0.1017
k_sat 0.1
K_mNa 87500.0
eta 0.35
LTRPN_tot 35.0
g_Ks 0.046
n_ClCa 3.0
i_CaL_max 7.0
tau_tr 20.0
g_Kr 1.17
g_K1 0.235
K_mCa 1380.0
Acap 1.541e-5
Km_pCa 0.5
k_minus_a 0.07125
stim_duration 0.5
k_minus_b 0.965
v1 0.45
i_pCa_max 0.2
Cao 1000.0
Vmyo 2.2826e-6
Km_up 0.5
g_Nab 0.0026
tau_xfer 8.0
Kpc_half 20.0
Km_Ko 1500.0
stim_period 2000.0
stim_end 500000.0
k_minus_ltrpn 0.0196
kb 0.036778
k_plus_b 0.00405
CSQN_tot 15000.0
CMDN_tot 25.0
E_CaL 63.0
Nao 140000.0
P_ClCa 2.74e-7
HTRPN_tot 70.0
g_Na 10.0
VJSR 1.2e-9
k_plus_c 0.009
g_Cab 0.00025
stim_amplitude -80.0
VNSR 2.098e-7
m 3.0
g_Kss 0.015
v2 2.088e-5
k_minus_c 0.0008
g_CaT 0.055
g_CaL 0.19019
k_plus_ltrpn 0.0327
g_Kur 0.0048
k_NaCa 907.68
k_plus_htrpn 0.00237
F 96.5
n 4.0

States:

Name Description
O_K(time) 0.0021
ato_f(time) 0.0032
P_C2(time) 0.1003
C2(time) 0.00016996
HTRPN_Ca(time) 66.0407
C3(time) 1.1754e-8
C_K2(time) 0.00083641
O(time) 4.4776e-12
I2(time) 6.4226e-8
j(time) 0.9744
P_RyR(time) 2.8603e-14
nKs(time) 0.0026
C4(time) 6.1239e-10
m(time) 0.0032
Nai(time) 21747.0
ito_f(time) 0.753
Cass(time) 0.1867
g(time) 0.902
V(time) -80.6475
h(time) 0.9606
LTRPN_Ca(time) 8.922
CaJSR(time) 705.5417
C_K1(time) 0.0011
aur(time) 0.00052471
iur(time) 0.9866
P_O1(time) 0.0011
Ki(time) 136450.0
b(time) 0.0047
I_K(time) 0.00043522
CaNSR(time) 703.3063
I3(time) 6.5201e-7
Cai(time) 0.2049
P_O2(time) 2.9799e-8
aKss(time) 0.85
I1(time) 1.545e-9

Observables: none

warashina_ogura_2004 @ v0.0.1

Warashina, Ogura, 2004

nothing

Parameters:

Name Description
tau_m nothing
T nothing
a1 nothing
E_l nothing
L nothing
diameter nothing
n_SK nothing
beta_k nothing
E_K nothing
tau_s nothing
Vmax nothing
DCa nothing
g_l nothing
E_rev nothing
vol0 nothing
FCaDy nothing
Cm nothing
tau1 nothing
a3 nothing
D nothing
Dyi2 nothing
k1b nothing
vol_i nothing
g_K nothing
TBu nothing
tau2 nothing
Ai2 nothing
Ca_rest nothing
Cac nothing
E_Na nothing
b1 nothing
Cai nothing
PCa nothing
Fm nothing
Nc nothing
a2 nothing
Cao nothing
Kex nothing
Fr nothing
Ff nothing
k1d nothing
k2b nothing
TDy nothing
g_SK nothing
A nothing
F0 nothing
k2d nothing
g_Na nothing
Fs nothing
Dkd nothing
tau_f nothing
A0 nothing
Ddy nothing
R nothing
F nothing
Ca1 nothing

States:

Name Description
Dy(time) nothing
V(time) nothing
Ca0(time) nothing
CaDy(time) nothing
h(time) nothing
Bu(time) nothing
B(time) nothing
G(time) nothing
n(time) nothing
m(time) nothing
Cai(time) nothing
CaBu(time) nothing

Observables: none

warren_tawhai_crampin_2009 @ v0.0.1

Warren, Tawhai, Crampin, 2009

nothing

Parameters:

Name Description
Ka 0.3722419
P_pm_2 28.0
R 8314.0
Kpm 0.6
Jer0 0.0035
T 310.0
Ca_ext 1300.0
K_rc 0.3
k2 0.5
V_ATP 0.001
beta_4 0.01
Kc 0.0571428
alpha_4 0.06
PIP2_Total 25.0
Beta_2 36.0
K_IP3 0.01
P_pm_1 0.6
V_mech0 1.0
Vm -39.0
Kb 0.636005
z_Ca 2.0
k1_ 0.88
Jryr0 0.0
Vpm 0.072
Beta_1 0.0
alpha_1 40.0
C_4 10.0
volume_i0 1450.0
Kserca 0.04
beta_1 0.8
K_ATP 0.0001
Jipt0 28.0
C_1 2.6
k3 0.5
J_ip3R0 10.0
Vserca 0.09
gamma 4.9
MechanicalStimulation 0.0
k5 0.02
C_2 0.02
F 96485.0
C_3 2.3

States:

Name Description
volume_iIP3(time) -3.28287434380887e-93
O(time) -2.42013500345263e-89
I2(time) 1.01276768045278e-40
volumeCa_i(time) 75.8335890358239
PIP2(time) 1.0
volumeCa_er(time) 1199.73747802144
ATP_e(time) 0.0
I1(time) 2.24343309680416e-81

Observables: none

waugh_sherratt_2006 @ v0.0.1

Waugh, Sherratt, 2006

nothing

Parameters:

Name Description
tau1 -2.47
d1 0.2
alpha 0.8
k1 0.05
tau3 6.41
tau4 1.75
tau2 21.94
k4 0.07
k3 0.002
k2 0.693
d2 9.1

States:

Name Description
T(time) 6.0
phi_I(time) 200.0
phi_R(time) 200.0

Observables: none

waugh_sherratt_2007 @ v0.0.1

Waugh, Sherratt, 2007

nothing

Parameters:

Name Description
k10 0.924
k9 0.0015
k8 0.015
tau4 0.2527
k4 0.07
d6 0.7
k6 0.0004
k11 5.0
tau1 0.0092
d2 9.1
d1 0.2
k12 0.001
tau3 0.6279
k1 0.05
d5 1.5e-5
d3 4.0
tau2 -0.1552
k3 0.002
k7 0.004
d4 2.5
k5 0.0025
k2 0.693

States:

Name Description
P(time) 2.0
H(time) 0.01
T(time) 6.0
phi_I(time) 200.0
C(time) 10.0
F(time) 50.0
phi_R(time) 200.0

Observables: none

webb_sherratt_fish_2002 @ v0.0.1

Webb, Sherratt, Fish, 2002

nothing

Parameters:

Name Description
k10 3110.0
k9 8.73e9
k1 8.38e-10
k8 1.92e10
k4 0.35
k3 5.9413
k7 0.35
k6 2244.0
k5 2.52e-9
k2 0.006
k11 13.9

States:

Name Description
SL(time) 0.0
T(time) 500.0
m(time) 500.0
LT(time) 0.0
Lm(time) 1000.0
Rm(time) 1000.0
RT(time) 10000.0

Observables: none

wein_damato_perelson_1998 @ v0.0.1

Wein, D'Amato, Perelson 1998

nothing

Parameters:

Name Description
c1 3.07
N1 480.1
delta2_M 0.062
m21 3.4e-5
mu 0.0014
Tmax 450.0
N2 475.3
lambda 0.01
s 0.0
c2 3.07
delta1_M 0.062
m12 3.4e-5
m11 1.0
k1 3.43e-8
delta1 0.69
r1 0.9
r2 0.25
N1_M 534.4
k2_M 4.67e-9
N2_M 529.0
p2 0.25
delta2 0.69
lambda_M 2.0
mu_M 0.04
p1 0.99
m22 1.0
k2 3.43e-8
k1_M 4.67e-9

States:

Name Description
T1_star(time) 1.19
M1_star(time) 0.49
V2(time) 450.0
M(time) 49.2
V1(time) 133500.0
T(time) 178.81
M2_star(time) 0.0017
V2_I(time) 450.0
V1_I(time) 133500.0
T2_star(time) 0.004

Observables: none

weinstein_1998 @ v0.0.1

Weinstein, 1998

nothing

Parameters:

Name Description
k7b 2.6e10
P 5.0
k9 1.75
k6a 5.0e7
k8 54.0
k3a 5.3e9
k6_ 5.0e10
k10_ 50.0
k1_ 6.5
k5_ 200.0
k6b 5.0e7
k4_ 2.5e6
k3b_ 660.0
k6a_ 8.0e12
k3 1.3e9
ADP 0.04
k3b 5.3e9
K 20.0
k7b_ 1.5e8
k3a_ 660.0
ATP 2.0
k10 50000.0
k7_ 3.4e7
k7a 2.6e10
k2b_ 73000.0
k2b 8900.0
k9_ 35.0
k2a 8900.0
k4 50.0
k8_ 32.0
k6b_ 8.0e12
k6 5.0e7
k7a_ 1.5e8
H 4.0
k11 500.0
k11_ 5.0
k1 1.3e7
k3_ 500.0
k2_ 40000.0
k2a_ 73000.0
k7 2.0e10
k5 40.0
k2 4000.0

States:

Name Description
K2_E2(time) nothing
H2_E1_ATP(time) nothing
K2_E1(time) nothing
H2_E2_P(time) nothing
K_E2_P(time) nothing
H2_E1_P(time) nothing
H_E1_P(time) nothing
H_E2_P(time) nothing
H_E1_ATP(time) nothing
K_E2_ATP(time) nothing
K_E1(time) nothing
K2_E2_P(time) nothing
K2_E2_ATP(time) nothing
E2_P(time) nothing
E1_ATP(time) nothing
K_E2(time) nothing
K_E1_ATP(time) nothing
K2_E1_ATP(time) nothing

Observables: none

weinstein_2000 @ v0.0.1

Weinstein 2000

A mathematical model of the outer medullary collecting duct of the rat

Parameters:

Name Description
Pc_pp 61.0
Cl_i 29.0
K_I 172.0
Kc_p 50.0
Kb_p 198.0
Kc_pp 50.0
Cl_e 114.0
Kb_pp 198.0
Pb_p 1247.0
HCO3_e 26.0
Pb_pp 135.0
x_Tmax 1.0
Pc_p 562.0

States:

Name Description
HCO3_i(time) 0.0

Observables: none

westermark_lansner_2003 @ v0.0.1

Westermark, Lansner, 2003

nothing

Parameters:

Name Description
Pfba 0.5
dw_per_ml 0.3333
G6P_F6P_init 3.71728
Sgk 8.0
Spfk 4.0
Sfba 0.005
a 1.0
one 1.0
Sgapdh 0.005
Keq_FBA 0.1
h_PFK 2.5
Keq 0.045455
V_GK_min 10.0
hx 2.5
FBP_init 0.00063612
alpha 5.0
Qfba 0.275
min_to_sec 60.0
h_GK 1.7
V_PFK_min 100.0
V_min 25.0
V_GAPDH_min 250.0
Y_init 0.00063612
h_act 1.0
Keq_TPI 0.045455
Keq_GPI 0.3
two 2.0
Xpfk 0.01
DHAP_G3P_init 0.00262966
V_FBA_min 25.0

States:

Name Description
DHAP_G3P(time) 0.00262966
Y(time) 0.00063612
FBP(time) 0.00063612
G6P_F6P(time) 3.71728

Observables: none

wierschem_bertram_2004 @ v0.0.1

Wierschem 2004

nothing

Parameters:

Name Description
v 10.0
f 0.001
s_m 12.0
C_m 5300.0
g_K_ 3000.0
tau_n 16.0
k 20.0
alpha 2.25e-6
v_n -16.0
k_D 0.3
eta 185.0
V_K -75.0
g_KATP_ 350.0
V_Ca 25.0
tau_c 1200.0
k_c 0.1
g_KCa_ 300.0
g_Ca_ 1200.0
v_m -20.0
s_n 5.6

States:

Name Description
V(time) -67.018
n(time) 0.00011
c(time) 0.15666
ATP(time) 2.1047
ADP(time) 0.085817

Observables: none

wilkins_sneyd_1998 @ v0.0.1

Wilkins, Sneyd, 1998

nothing

Parameters:

Name Description
dc_dy2 nothing
Dc nothing
tau_h nothing
c nothing
dc_dx2 nothing
b nothing
k1 nothing
kf nothing
k_mu nothing
gamma nothing
k_gamma nothing
k2 nothing
p nothing

States:

Name Description
h(time) nothing
mu_p(time) nothing

Observables: none

winograd_destexhe_sanchezvives_2008 @ v0.0.1

Winograd, Destexhe, Sanchezvives, 2008

nothing

Parameters:

Name Description
Z 2.0
tau_m 0.02
V_T -55.0
T 296.65
i_stimAmplitude -0.3
E_h -20.0
C_m 0.001
tau_r 0.017
k_4 1.0
Ca_o 2.0
n_Ca 4.0
cac 0.006
E_K -95.0
g_KD 7.0
i_stimStart 5.0
period 9.0
k_2 0.1
P_c 0.01
Ca_inf 0.0001
g_inc 2.0
d 0.0001
V_S 0.0
Ca_c 0.006
P_Ca 0.000276
g_Na 70.0
k 0.1
E_leak -70.0
n_exp 1.0
p_C 0.01
tau_max 4.0
g_hbar 0.02
i_stimEnd 9.0
g_KM 0.004
g_leak 1.0
E_Na 50.0
R 8.314
F 96489.0

States:

Name Description
p_1(time) nothing
p(time) nothing
V(time) nothing
h(time) nothing
m(time) nothing
n(time) nothing
Ca_i(time) nothing
q(time) nothing
o_2(time) nothing

Observables: none

winslow_rice_jafri_marban_ororke_1999 @ v0.0.1

Winslow, Rice, Jafri, Marban, Ororke, 1999

nothing

Parameters:

Name Description
f 300.0
k_a_minus 576.0
K_mEGTA 0.00015
stim_start 0.1
T 310.0
C_sc 0.001
K_SR 1.0
i_Ca_half -0.265
Vmaxr 0.318
k_htrpn_plus 20000.0
K_sat 0.2
omega 10.0
K_mK1 13.0
k_b_minus 1930.0
Ko 4.0
k_htrpn_minus 0.066
V_NSR 2.1e-6
g 2000.0
K_mNa 87.5
eta 0.35
LTRPN_tot 0.07
k_b_plus 4.05e9
g_Ks 0.0027134
k_c_plus 100.0
g_K1 2.8
tau_tr 0.0005747
g_Kr 0.0034
V_myo 2.584e-5
K_mCa 1.38
k_c_minus 0.8
EGTA_tot 0.0
k_a_plus 1.215e13
stim_duration 0.002
fprime 7.0
v1 1800.0
b 2.0
Cao 2.0
V_SS 1.2e-9
g_Nab 0.0031
tau_xfer 0.0267
K_mpCa 5.0e-5
a 2.0
tau_factor 1.0
stim_period 1.0
stim_end 1.0e8
V_JSR 1.6e-7
K_mCSQN 0.8
K_mCMDN 0.00238
K_fb 0.000168
gprime 7000.0
A_cap 0.0001534
k_ltrpn_minus 40.0
I_pCa 0.05
I_NaK 0.693
CSQN_tot 15.0
k_ltrpn_plus 40000.0
Nao 138.0
CMDN_tot 0.05
K_mNai 10.0
N_rb 1.0
N_fb 1.2
HTRPN_tot 0.14
g_to1 0.23815
P_Ca 0.0003125
g_Na 12.8
Vmaxf 0.0813
g_Cab 0.0003842
g_Kp 0.002216
stim_amplitude -21.1268
K_rb 3.29
m 3.0
K_NaCa 0.3
K_mKo 1.5
R 8.314472
P_K 5.79e-7
F 96.4853415
n 4.0

States:

Name Description
X_kr(time) 0.51
P_C1(time) 0.47
Ca_ss(time) 0.00011
Ca_NSR(time) 0.257
P_C2(time) 0.53
C0(time) 0.997208
y(time) 0.798
C2(time) 1.535e-9
C3(time) 1.63909e-14
HTRPNCa(time) 0.98
O(time) 9.84546e-21
j(time) 0.99254
C_Ca0(time) 0.00272826
C_Ca3(time) 2.87031e-15
m(time) 0.0328302
X_to1(time) 2.63
C4(time) 6.56337e-20
Y_to1(time) 0.99
Nai(time) 10.0
LTRPNCa(time) 0.078
X_ks(time) 0.264
C_Ca4(time) 4.59752e-20
V(time) -96.1638
h(time) 0.988354
C_Ca1(time) 6.99215e-7
C1(time) 6.38897e-5
P_O1(time) 0.0
Ki(time) 157.8
Ca_JSR(time) 0.257
O_Ca(time) 0.0
Cai(time) 8.0e-5
P_O2(time) 0.0
C_Ca2(time) 6.71989e-11

Observables: none

wodarz_2003 @ v0.0.1

Wodarz, 2003

nothing

Parameters:

Name Description
k_1 1.0
g 0.01
a_1 0.03
alpha_1 0.1
r 0.5
a_2 1.0
beta_2 1.0
beta_1 1.0
alpha_2 0.1
epsilon 0.1
k_2 1.0
u 0.5
d 0.01

States:

Name Description
P_2(time) 1.0
I_2(time) 0.0
I_21(time) 0.0
R_1(time) 0.0
P_1(time) 1.0
S(time) 100.0
I_1(time) 0.0
R_2(time) 0.0
I_12(time) 0.0
R_12(time) 0.0

Observables: none

wodarz_hamer_2007 @ v0.0.1

Wodarz, Hamer, 2007

nothing

Parameters:

Name Description
c 1.0
k 10.0
alpha 0.2
b 0.1
r 1.0
eta 1.0
a 0.2
delta 0.01
rho 0.3
beta 0.3
epsilon 1.0
phi 1.5
lambda 1.0
xi 0.01
gamma 0.01
u 1.0
p 45.0
d 0.001

States:

Name Description
m_7(time) 0.0
m_4(time) 0.0
m_3(time) 0.0
T(time) 1000.0
I(time) 0.0001
v(time) 0.0001
x(time) 10.0
y(time) 0.0
z(time) 0.0
m_9(time) 0.0
m_0(time) 0.1
m_5(time) 0.0
m_8(time) 0.0
m_1(time) 0.0
m_6(time) 0.0
m_2(time) 0.0
w(time) 0.0

Observables: none

wodarz_jansen_2003 @ v0.0.1

Wodarz, Jansen, 2003

nothing

Parameters:

Name Description
delta_1 0.1
k 10.0
alpha 0.05
r 0.5
eta 2.0
mu 0.1
delta_2 1.5
epsilon 1.0
gamma 1.0
lambda 1.0
q 0.5
d 0.1

States:

Name Description
A(time) 1.0
T(time) 0.1
C(time) 0.015
A_star(time) 2.0

Observables: none

wodarz_nowak_1999 @ v0.0.1

Wodarz, Nowak, 1999

nothing

Parameters:

Name Description
p 1.0
d 0.1
c 0.1
b 0.01
lamda 1.0
q 0.5
a 0.2
h 0.1
beta 0.5

States:

Name Description
x(time) 10.0
y(time) 0.1
w(time) 0.001
z(time) 0.0

Observables: none

wodarz_sierro_klenerman_2007 @ v0.0.1

Wodarz, Sierro, Klenerman, 2007

nothing

Parameters:

Name Description
pa 1.0e-6
a0 0.1
k 1.0
a1 0.2
alpha 0.2
r 1.0
eta 0.01
ba 0.1
beta 0.1
ci 12.0
bi 0.1
phi 0.1
lambda 10.0
xi 0.01
ca 15.5
gamma 0.5
p_i 1.0
u 1.0
d 0.1

States:

Name Description
m_7(time) 0.0
m_4(time) 0.0
m_3(time) 0.0
v(time) 1.0
x(time) 1.0
y1(time) 0.0
L(time) 0.0
m_0(time) 0.0
m_5(time) 0.0
m_8(time) 0.0
m_1(time) 0.0
za(time) 1.0
m_6(time) 0.0
m_2(time) 0.0
zi(time) 0.1
y0(time) 0.0

Observables: none

wolf_heinrich_2000 @ v0.0.1

Wolf, Heinrich, 2000

nothing

Parameters:

Name Description
A 4.0
K_I 0.52
Jo 3.0
k 1.3
k_5 1.28
k_4 100.0
k_3 16.0
N 1.0
kappa 13.0
k_2 6.0
phi 0.1
k_6 12.0
q 4.0
k_1 100.0

States:

Name Description
S3(time) 0.2
S4_ex(time) 0.1
S1(time) 5.8
A3(time) 2.4
N2(time) 0.1
S2(time) 0.9
S4(time) 0.2

Observables: none

wolf_passarge_somsen_snoep_heinrich_westerhoff_2000 @ v0.0.1

Wolf, Passarge, Somsen, Snoep, Heinrich, Westerhoff, 2000

nothing

Parameters:

Name Description
k_1 550.0
k_PGK_plus 76411.1
K_i 1.0
A 4.0
Jo 50.0
k_8 85.7
k_GAPDH_minus 57823.1
k_5 9.7
k_4 80.0
k 375.0
k_7 28.0
k_PGK_minus 23.7
k_GAPDH_plus 323.8
N 1.0
k_2 9.8
phi 0.1
k_6 2000.0
k_9 80.0
n 4.0

States:

Name Description
S6(time) 0.078042624
S6_ex(time) 0.025277594
S3(time) 0.468657507
S5(time) 8.210114438
S1(time) 1.57981839
A3(time) 1.972814237
N2(time) 0.384873894
S4(time) 0.589391932
S2(time) 4.8279999

Observables: none

wolf_sohn_heinrich_kuriyama_2001 @ v0.0.1

Wolf, Sohn, Heinrich, Kuriyama, 2001

nothing

Parameters:

Name Description
k14 10.0
Kc 0.1
KA 1.0
v0 1.6
k18 1.0
k9 10.0
KH 0.5
k15 5.0
A_m 2.0
k8 10.0
k4 0.2
N 2.0
k6 0.12
v10 80.0
k11 10.0
v13 4.0
k12 5.0
alpha 0.1
k16 10.0
A_c 2.0
S 2.0
m 4.0
k3 0.2
k7 10.0
k17 0.02
k5 0.1
k2 0.2
n 4.0

States:

Name Description
sul(time) 0.012871557
aps(time) 0.053366179
hyd(time) 0.159317029
A3_c(time) 1.570847601
eth(time) 10.25246999
oah(time) 5.571685096
aco(time) 1.139360412
A3_m(time) 1.835158493
oxy(time) 6.146549084
pap(time) 0.082791522
cys(time) 0.805117739
S1(time) 1.892468811
N2(time) 1.933616149

Observables: none

wu_jeneson_beard_2006 @ v0.0.1

Wu, Jeneson, Beard, 2006

nothing

Parameters:

Name Description
X_PI2 327.0
k_PIH 0.0002542
mincond 1.0e-6
r 4.559
V_mito 0.056
dG_C4o -122.94
dG_F1o 36.03
n_A 3.0
k_mADP 3.5e-6
mincon 1.0e-9
X_CK 1.0e7
k_PI2 0.0008222
X_AK 1.0e7
X_F1 1000.0
k_PI3 0.0003601
X_Hle 200.0
O2_x 3.48e-5
k_PI4 0.005651
X_MgA 1.0e7
X_KH 5.651e7
NAD_tot 0.00297
k_PI1 0.0001553
X_AtC 0.0
RT 2.5775
K_c 0.15
X_C1 4405.0
K_AK 0.4331
C_IM 6.75e-6
k_O2 0.00012
X_C3 4.887
V_cyto 0.894
Q_tot 0.00135
K_DT 2.4e-5
x_buff 100.0
C_tot 0.0027
X_A 85.0
dG_C3o -32.53
dG_C1o -69.37
pH_C 7.0
X_K 0.0
X_ANT 0.008123
X_C4 6.766e-5
K_DD 0.000347
gamma 5.99
X_DH 0.0866
X_PI1 385000.0
CR_tot 0.0427
K_CK 1.66e9
F 0.096484

States:

Name Description
NADH_x(time) 0.0015723
ATP_mc(time) 0.0079786
ADP_mc(time) 5.1958e-5
Mg_x(time) 0.0010229
K_x(time) 0.14661
Q_x(time) 0.000675
Mg_c(time) 0.001003
pH_x(time) 7.0
PI_i(time) 0.000172
ADP_i(time) 6.5773e-5
ADP_c(time) 6.85e-5
ADP_mi(time) 4.8866e-5
Cox_x(time) 0.00135
ADP_mx(time) 0.0054765
Mg_i(time) 0.0010029
PI_x(time) 0.000172
ADP_x(time) 0.0073343
AMP_c(time) 3.0911e-7
ATP_i(time) 0.0065339
AMP_i(time) 2.8837e-7
ATP_mi(time) 0.0063812
ATP_x(time) 0.0026657
ATP_mx(time) 0.0026046
ATP_c(time) 0.0081312
PCr_c(time) 0.023589
PI_c(time) 0.0087702
deltaPsi(time) 166.67

Observables: none

wu_yang_vinnakota_beard_2007 @ v0.0.1

Wu, Yang, Vinnakota, Beard, 2007

nothing

Parameters:

Name Description
X_mdh 0.077060004692409
dGf1_O2 16.4
KMg_COASH_x 1.0e20
dGf1_ATP -2771.0
dFADH2_x_dt 0.0
K_aADP 0.0001
K_mMAL 0.0001977
K_iSCOA 0.00014
KK_NAD_x 1.0e20
dGf1_COQ 65.17
rho_m 272500.0
KMg_QH2_x 1.0e20
J_AtC 0.0
KH_K_x 1.0e20
X_KH 4.758023126099895e6
K_mMALi 0.0014
K_ir_akgd 6.04e-7
dGf1_Cox -6.52
KK_NADH_x 1.0e20
dGf1_Cred -27.41
KK_K_x 1.0e20
K_iAMP 0.00065
KK_ASP_x 1.0e20
dGf1_QH2 -23.3
n_H 3.0
KH_COQ_x 1.0e20
K_mB 5.5e-5
KK_FADH2_x 1.0e20
dGf1_ACCOA -178.19
k_PIHt 0.00161251709168
dGf1_GLU -692.4
dGf1_GLC -907.21
K_mP 4.7e-5
K_iNADH 4.0e-5
W_x 0.651384
K_mSUC 0.000467
dGf1_FUM -603.32
K_iASPi 2.8e-5
X_pdh 0.205093643103884
X_GLUH 2.725114215177993e8
X_CITMAL 80.43211032286638
X_PIHt 3.335568500871044e7
K_mFUM 0.0012
X_akgd 0.087630003425524
KH_ACCOA_x 1.0e20
F 0.096484
dGf1_PYR -470.82
KMg_NADH_x 1.0e20
zero 0.0
K_ir 1.11e-5
KK_Mg_x 1.0e20
Ki_G6P 1.0e-5
dGf1_CIT -1165.59
KH_PYR_x 1.0e20
theta 0.6
X_isod 0.492047553306503
KMg_FADH2_x 1.0e20
cytC_tot 0.0027
X_Hle 302.092849850504
dGf1_NAD 18.1
X_PiHt 3.335568500871044e7
K_Mg 1.0e20
KK_GLU_x 1.0e20
dGf1_ADP -1903.96
KMg_COQ_x 1.0e20
KH_FADH2_x 1.0e20
CO2_tot_x 0.0214
dAMP_x_dt 0.0
KMg_FAD_x 1.0e20
K_mNAD 9.055e-5
NAD_tot 0.00297
KH_QH2_x 1.0e20
minCon 1.0e-32
dGf1_FAD 19.55
K_mQH2 2.45e-6
V_mf 0.087630003425524
A_tot 0.01
dGf1_GDP -1903.96
dGf1_Pi -1098.27
X_C1 32364.81869934019
KMg_H_x 1.0e20
KH_H_x 1.0e20
X_C3 0.790813746051711
B_x 0.02
dGf1_GTP -2771.0
KMg_CO2_tot_x 1.0e20
KMg_AKG_x 1.0e20
X_ndk 0.025543515147654
X_SUCMAL 96.99561824738987
KK_PYR_x 1.0e20
K_mMALx 0.0007
K_ic 0.002
KK_COQ_x 1.0e20
X_sdh 0.08578867843174
K_aFUM 0.000375
KK_QH2_x 1.0e20
KK_AKG_x 1.0e20
k_PiHt 0.00161251709168
X_C4 0.0001076088893810943
X_MALPI 16.062441848715917
K_iATP 5.0e-5
KK_ACCOA_x 1.0e20
KK_O2_x 1.0e20
k_PI_2 0.003474542589709
X_scoas 0.448520452008943
p_TI 85.0
StateType 2.0
p_PI 327.0
dGf1_AKG -793.41
K_mR 1.11e-5
n_A 3.0
K_iCIT 0.0035
KK_OAA_x 1.0e20
KH_NAD_x 1.0e20
k_mADP 3.5e-6
X_CK 1.0e7
W_i 0.072376
FAD_tot 0.0001
KK_FUM_x 1.0e20
X_AK 1.0e7
KH_AKG_x 1.0e20
dGf1_SCOA -507.55
K_H 1.0e20
p_A 85.0
dGf1_OAA -794.74
KH_Mg_x 1.0e20
X_ASPGLU 5.865621634754698e-5
K_ib 4.7e-5
K_iGDP 0.00033
K_iAKG 0.0166
KH_NADH_x 1.0e20
KMg_FUM_x 1.0e20
X_acon 0.027665411180519
X_got 4.551391837332316
pKa_ASPGLU 6.5
dGf1_ASP -692.26
k_PI_1 3.248913595933763e-5
X_cits 9.82530750761898
K_mAKGi 0.0003
K_mC 2.1e-5
K_mNADH 2.58e-6
k_O2 0.00012
K_iCOASH 6.7e-5
KMg_Mg_x 1.0e20
Q_tot 0.00135
K_ir1 6.010527470838273e-7
dGf1_Cr -252.68
K_ia 0.001
X_ANT 0.007522124149343
m 1.8
dGf1_AMP -1034.66
KK_ICIT_x 1.0e20
CR_tot 0.0427
K_BX 1.0e-7
K_mA 8.0e-5
K_mCOQ 0.00048
dGf1_H2O -235.74
K_iGTP 8.0e-5
K_aSUC 0.00045
ExpType 1.0
K_iq 6.9e-6
K_iOAA 1.5e-6
dGf1_ICIT -1158.94
X_F1 8120.393248498723
X_AKGMAL 0.282091450119444
KK_CO2_tot_x 1.0e20
KK_COASH_x 1.0e20
dGf1_NADH 39.31
dCO2_tot_x_dt 0.0
K_mAKGx 0.00017
dGf1_SUC -690.44
KMg_O2_x 1.0e20
KK_SCOA_x 1.0e20
conversion_factor 1.0
dGf1_CO2_tot -530.71
K_ip 4.7e-5
KMg_NAD_x 1.0e20
dGf1_PI -1098.27
KK_FAD_x 1.0e20
minCond 1.0e-9
dGf1_MAL -842.66
K_iADP 0.0004
KMg_SCOA_x 1.0e20
C_IM 6.75e-6
KMg_ACCOA_x 1.0e20
K_iGLUx 0.0016
dFAD_x_dt 0.0
K_iACCOA 4.02e-5
K_mOAA 6.128e-6
K_iASPx 0.0028
K_ir2 1000.0
KH_OAA_x 1.0e20
KH_O2_x 1.0e20
dGf1_COASH -0.72
KK_H_x 1.0e20
dO2_x_dt 0.0
dGf1_G6P -1758.87
KH_FAD_x 1.0e20
K_mQ 0.001
dGf1_PCr 0.0
X_fum 0.00707728025683
gamma 5.99
K_K 1.0e20
KMg_K_x 1.0e20
dGf1_FADH2 -67.6
X_PYRH 2.996779273769102e8
K_iGLUi 0.00018

States:

Name Description
AKG_c(time) 1.0e-9
G6P_c(time) 1.0e-9
FUM_c(time) 1.0e-9
ASP_x(time) 0.00010217
FUM_x(time) 7.8476e-9
QH2_x(time) 0.0
GLU_c(time) 5.754e-12
ICIT_i(time) 1.0e-9
ADP_i(time) 1.0e-9
ADP_c(time) 1.0e-9
AKG_i(time) 9.9995e-10
SUC_i(time) 1.0e-9
GDP_x(time) 0.005
GLU_i(time) 5.7539e-12
OAA_x(time) 0.00089236
PI_x(time) 0.00029918
ADP_x(time) 0.01
ATP_i(time) 1.0e-9
SCOA_x(time) 6.9627e-10
GLU_x(time) 9.9311e-12
ICIT_c(time) 1.0e-9
PCr_c(time) 1.0e-9
CIT_i(time) 1.0e-9
Cred_i(time) 9.6996e-8
ACCOA_x(time) 2.5507e-12
PYR_i(time) 9.1804e-10
AKG_x(time) 4.7979e-11
NADH_x(time) 8.4842e-21
Mg_x(time) 0.0046388
COASH_x(time) 0.0030107
MAL_i(time) 1.0e-9
K_x(time) 0.086878
H_c(time) 1.0e-7
MAL_c(time) 1.0e-9
dPsi(time) -14.087
Mg_c(time) 0.005
ICIT_x(time) 9.3558e-7
PI_i(time) 0.00011574
PYR_x(time) 1.2076e-11
AMP_x(time) 1.0e-6
PYR_c(time) 1.0e-9
SUC_c(time) 1.0e-9
GLC_c(time) 1.0e-9
CO2_tot_x(time) 0.0214
ASP_i(time) 4.4404e-9
CIT_x(time) 6.8151e-5
FUM_i(time) 1.0e-9
AMP_c(time) 1.0e-9
O2_x(time) 6.5e-5
AMP_i(time) 1.0e-9
ATP_x(time) 1.025e-11
SUC_x(time) 2.1681e-7
CIT_c(time) 1.0e-9
K_c(time) 0.15
ATP_c(time) 1.0e-9
MAL_x(time) 3.2191e-8
GTP_x(time) 2.7157e-10
ASP_c(time) 4.4404e-9
PI_c(time) 0.00011574
H_x(time) 5.7919e-8

Observables: none

Y


yamaguchi_takaki_matsubara_yasuhara_suga_1996 @ v0.0.1

Yamaguchi, Takaki, Matsubara, Yasuhara, Suga, 1996

nothing

Parameters:

Name Description
f 10.0
g 10.0
Ca_max 1.0
L_0 0.0
D_Ca 0.1
L 1.0
CumCB_on_end 1.0
Total_CB 1.0
Total_Tn 1.0
F_max 0.228
epsilon 1.0
phi 1.0
k_2 20.0
s 1.0
k_1 40.0

States:

Name Description
TnCa(t) 0.0
CumCB_off(t) 0.0
CB_on(t) 0.0
FTI(t) 0.0
CumCB_on(t) 0.0

Observables: none

yanagihara_1980 @ v0.0.1

Yanagihara 1980

nothing

Parameters:

Name Description
Cm 1.0

States:

Name Description
d(time) 3.2e-5
V(time) -62.83
h(time) 0.95994
n(time) 0.509494
m(time) 0.047938
f(time) 1.0
q(time) 0.010759

Observables: none

yang_clark_bryan_robertson_2003 @ v0.0.1

Yang, Clark, Bryan, Robertson, 2003

nothing

Parameters:

Name Description
R nothing
Kr2 nothing
K3 nothing
Kr1 nothing
T nothing
fAM nothing
k_1 nothing
P_Na nothing
g_Kb nothing
sigma nothing
fAMp nothing
d_NaCa nothing
lc nothing
B nothing
Km_Nai nothing
K_CaCM nothing
lopt nothing
lx nothing
Cm nothing
vx nothing
Vol_u nothing
k_d nothing
Vol_i nothing
Vol_r nothing
g_NaCa nothing
Am nothing
Ps_infinity nothing
kd nothing
K4 nothing
g_K nothing
Ca_u nothing
tau_Pf nothing
B_F_Ca nothing
ia nothing
tau_tr nothing
g_Ca_L nothing
Kr2_ nothing
S_CM_Ca nothing
tau_rel nothing
Na_o nothing
kx2 nothing
K2 nothing
g_K_Ca nothing
sigma_1_2 nothing
g_Nab nothing
K7 nothing
Ca_o nothing
Km_up nothing
Km_Ko nothing
l0 nothing
I_Ca_P nothing
K_o nothing
G_Ki nothing
ls0 nothing
n_Ki nothing
delta_ls nothing
ks nothing
I_NaK nothing
mu_s nothing
K5 nothing
A nothing
kp nothing
k nothing
kx1 nothing
P_Ca nothing
I_up nothing
k1 nothing
g_Cab nothing
beta nothing
la nothing
Vol_Ca nothing
alpha_s nothing
tau_Ps nothing
gamma nothing
alpha_p nothing
Kr1_ nothing
V_1_2 nothing
P_K nothing
k_sigma nothing
F nothing

States:

Name Description
Mp(time) nothing
P1(time) nothing
R00(time) nothing
ff(time) nothing
R01(time) nothing
AMp(time) nothing
P2(time) nothing
Na_i(time) nothing
d(time) nothing
Pf(time) nothing
M(time) nothing
R10(time) nothing
V(time) nothing
ls(time) nothing
AM(time) nothing
Ps(time) nothing
K_i(time) nothing
S_CM_cal(time) nothing
Ca_r(time) nothing
B_F_cal(time) nothing
Ca_up(time) nothing
Ca_i(time) nothing
R11(time) nothing

Observables: none

yang_tong_mccarver_hines_beard_2006 @ v0.0.1

Yang, Tong, Mccarver, Hines, Beard, 2006

nothing

Parameters:

Name Description
Q 1221.34
K2 0.8532
P 15.61
V 1454.0
Qc 6445.65
Km 198.0
n2 1.0
age 5.0
Va 2148.0
Vv 3431.0
Vmax 0.009433
F 0.48

States:

Name Description
C(time) 0.0
Ca(time) 6.6685

Observables: none

yasamura_suga_1987 @ v0.0.1

Yasumura, Suga, 1988

nothing

Parameters: none

States: none

Observables: none

yates_stark_klein_antia_callard_2007 @ v0.0.1

Yates, Stark, Klein, Antia, Callard, 2007

nothing

Parameters:

Name Description
v 0.5
f 100.0
d1 0.005
kappa 1.0
r 1.0
a 0.03333
p 200.0
mu 0.023

States:

Name Description
x(time) 1.0
y(time) 0.0
z(time) 0.01
w(time) 0.0

Observables: none

yi_fogelson_keener_peskin_2003 @ v0.0.1

Yi, Fogelson, Keener, Peskin, 2003

nothing

Parameters: none

States: none

Observables: none

youm_kim_han_kim_joo_leem_goto_noma_earm_2006 @ v0.0.1

Youm, Kim, Han, Kim, Joo, Leem, Goto, Noma, Earm, 2006

nothing

Parameters:

Name Description
pNaK 79.0
Na_o 140.0
T 309.15
IP3_IP4 0.004
dt_CellML 0.01
Ca_o 1.8
dt 0.2
pleak 0.45
I_ext 0.0
PCaL 5.76
Pup 7728.0
PAI 15.61
Km_Ca_i 0.08
K_o 5.4
pPMCA 927.4
g_Ki 4.32
PNaCa 8.458
Km_Ca_o 0.002
ZNa 1.0
Vi 715.5
kci 0.000849
Km_K_o 0.27
PIP3R 217.2
ZK 1.0
Cm 25.0
Km_Na_o 670000.0
koi 0.02
ptr 20.5
ZCa 2.0
IP3total 0.0033
Km_Na_i 670.0
PIP2_IP4 0.0
R 8.314
F 96.485
PVDDR 7.92

States:

Name Description
Cai_A(time) 0.0035
Ca_rel(time) 13.1
h(time) 0.0
y(time) 0.1
K_i(time) 140.0
Vm(time) -68.0
m(time) 0.0
Ca_up(time) 4.6
PIP2(time) 0.002664
IP3(time) 0.0002682
Na_i(time) 5.4

Observables: none

Z


zager_schlosser_tran_2007 @ v0.0.1

Zager, Schlosser, Tran, 2007

nothing

Parameters:

Name Description
Ppp 0.59
tbasal 0.0865
cv 1.0
cgen 0.06561
kcon_urine 0.0
m_rat 0.25
Prp 1.94
VGI 0.011
Vpp 0.188
Km 0.6231
Pl 3.61
kgen_urine 9.5
Vmax 25.25
Vl 0.0092
epsilon 0.1
VROB 0.2408
ct 1.0107
kbile 111.72
Vrp 0.012

States:

Name Description
Cgen_l(time) 0.0
Cgen_GI(time) 0.0
Cgen_pp(time) 0.0
Ccon_ROB(time) 0.0
Acon_b(time) 0.0
Cgen_rp(time) 0.0
Ccon_l(time) 0.0

Observables: none

zeng_laurita_rosenbaum_rudy_1995 @ v0.0.1

Zeng, Laurita, Rosenbaum, Rudy, 1995

nothing

Parameters:

Name Description
gamma_Cai nothing
gamma_Cao nothing
T nothing
TRPN_max nothing
calcium_overload nothing
P_Na nothing
Km_Ca nothing
delta_Ca_i2 nothing
K_mup nothing
Ca_JSR_old nothing
delta_Ca_ith nothing
K_sat nothing
gamma_Nao nothing
tau_on nothing
CMDN_max nothing
Cm nothing
P_ns_Ca nothing
R_A_V nothing
P_NaK nothing
K_mNa nothing
eta nothing
V_myo nothing
tau_tr nothing
Ca_NSR_max nothing
K_mCa nothing
Cao nothing
g_Nab nothing
K_mpCa nothing
gamma_Nai nothing
Cai_old nothing
K_mCSQN nothing
t nothing
gamma_Ki nothing
I_st nothing
K_m_ns_Ca nothing
K_mCMDN nothing
tau_off nothing
A_cap nothing
I_pCa nothing
I_NaK nothing
Nao nothing
K_mTRPN nothing
K_mNai nothing
P_Ca nothing
g_Na nothing
I_up nothing
V_cleft nothing
g_Cab nothing
CSQN_th nothing
g_Kp nothing
K_mrel nothing
CSQN_max nothing
g_Ca_T nothing
gamma_Ko nothing
K_NaCa nothing
K_mKo nothing
R nothing
P_K nothing
F nothing

States:

Name Description
d(time) nothing
g(time) nothing
delta_Cai(time) nothing
V(time) nothing
h(time) nothing
Ca_NSR(time) nothing
c1(time) nothing
f(time) nothing
b1(time) nothing
Xs(time) nothing
Ko(time) nothing
Ki(time) nothing
b(time) nothing
j(time) nothing
Ca_total(time) nothing
m(time) nothing
Xr(time) nothing
Nai(time) nothing
Ca_foot(time) nothing

Observables: none

zhang_holden_kodama_honjo_lei_varghese_boyett_2000 @ v0.0.1

Zhang, Holden, Kodama, Honjo, Lei, Varghese, Boyett, 2000

nothing

Parameters:

Name Description
Na_i 8.0
T 310.0
K_m_K 0.621
Ca_i 0.0001
d_NaCa 0.0001
dCell 0.0
g_K_r_Centre 0.000797
g_b_Ca_Periphery 4.3e-5
i_Ca_p_max_Centre 0.0
i_Ca_p_max_Periphery 0.0
k_NaCa_Periphery 8.8e-6
g_to_Centre 0.00491
g_K_s_Periphery 0.0104
g_Ca_T_Centre 0.0043
g_f_K_Periphery 0.0069
g_Na_Periphery 1.2e-6
g_Na_Centre 0.0
i_p_max_Periphery 0.16
g_Ca_L_Centre 0.0058
g_b_K_Centre 2.52e-5
g_to_Periphery 0.03649
g_b_Ca_Centre 1.32e-5
Na_o 140.0
g_sus_Periphery 0.0114
K_i 140.0
Ca_o 2.0
g_b_Na_Periphery 0.000189
E_Ca_T 45.0
tau_P_i 0.002
g_Ca_L_Periphery 0.0659
g_K_r_Periphery 0.016
K_o 5.4
K_m_Na 5.64
CmPeriphery 6.5e-5
g_K_s_Centre 0.000518
g_f_Na_Centre 0.000548
g_sus_Centre 6.65e-5
E_Ca_L 46.4
gamma_NaCa 0.5
i_p_max_Centre 0.0478
g_f_Na_Periphery 0.0069
g_f_K_Centre 0.000548
g_b_K_Periphery 8.19e-5
g_b_Na_Centre 5.8e-5
k_NaCa_Centre 2.7e-6
R 8314.0
g_Ca_T_Periphery 0.0139
F 96845.0
CmCentre 2.0e-5

States:

Name Description
d_T(time) 0.42074047435
h2(time) 0.01445216109
V(time) -39.013558536
xs(time) 0.082293827208
y(time) 0.03889291759
f_T(time) 0.038968420558
P_af(time) 0.13034201158
r(time) 0.064402950262
P_i(time) 0.87993375273
f_L(time) 0.48779845203
h1(time) 0.015905380261
d_L(time) 0.04804900895
m(time) 0.092361701692
q(time) 0.29760539675
P_as(time) 0.46960956028

Observables: none

Content