CellMLPhysiome: 1 - G

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1


1ac

1ac @ v0.0.1

Linear 2nd order nonhomogeneous ODE with constant coefficients

Classical example: a linear second order nonhomogeneous ODE IVP with constant coefficients and constant right hand side.

See Wikipedia

Parameters: none

States:

Name Description
v(t) 1.0
u(t) 1.0

Observables: none

1b5

1b5 @ v0.0.1

Cell viability models for tissue exposed to thermal ablation temperatures.

A collection of similar cell death models that can be used to predict cell viability during radio-frequency and microwave ablation. The parameters are derived from cell-culture experiments where the temperature is held constant for a fixed amount of time.

Parameters:

Name Description
A 1.0
c 1.0
T 340.0
E2 128000.0
E 1.0
A2 2.83e17
kf_ 0.00333
kb 0.00777
A1 6.83e36
E1 250000.0
Tk 313.0
R 8.3
p 1.0

States:

Name Description
P0(time) 1.0
P4(time) 0.0
P7(time) 0.0
P6(time) 0.0
P9(time) 0.0
C(time) 1.0
P1(time) 0.0
P8(time) 0.0
P3(time) 0.0
P2(time) 0.0
P5(time) 0.0
X2(time) 0.0
A(time) 0.99
X1(time) 1.0
D(time) 0.0

Observables: none

2


2bb

2bb @ v0.0.1

Synchronized Scene Viewer

A CTK-OpenCMISS ZINC Plugin that can render graphical elements across multiple opengl contexts and synchronize mouse events initiated by the user.

Parameters: none

States: none

Observables: none

2bc

2bc @ v0.0.1

Basket Catheter Emulator

An 64 electrode basket catheter emulator CTK-Plugin.

Parameters: none

States: none

Observables: none

2d5

2d5 @ v0.0.1

Moore, Li, 2004

nothing

Parameters:

Name Description
rc 0.23
alpha_e 0.53
dc 0.68
dn 0.05
eta 43.0
gamma_c 0.047
sn 0.071
gamma_e 0.0077
de 0.12
kn 0.063
Cmax 190000.0
alpha_n 0.56

States:

Name Description
C(time) 9600.0
Te(time) 20.0
Tn(time) 1510.0

Observables: none

2d8

2d8 @ v0.0.1

Alexander and Wahl 2010

nothing

Parameters:

Name Description
sigma1 3.0e-6
f 0.0001
lambdaE 1000.0
v_tilday 0.0025
v 125000.0
k 5.0e7
b3 0.25
muA 0.25
muE 0.25
sigma4 1.2e-5
muG 5.0
beta 200.0
sigma3 3.0e-6
pi3 0.0256
pi4 0.016
b4 1.0
pi1 0.016
gamma 2000.0
muR 0.25
b1 0.25

States:

Name Description
E(time) 0.0
A(time) 1.0
G(time) 1.0e8
R(time) 0.0

Observables: none

2e3

2e3 @ v0.0.1

Benson 2008

nothing

Parameters:

Name Description
prnak 0.01833
iupmax 0.004375
tissue 0.0
KmNao 87.5
Km 0.0015
KmBSR 0.00087
stim_offset 0.0
BSLmax 1.124
ibarpca 0.0575
GNaL 0.0065
kmko 1.5
KmCao 1.3
tbar 0.07
kmpca 0.0005
gitodv 0.1805
Kmto2 0.1502
KmNai 12.3
eta 0.35
l 0.01
FonRT 0.0374358835078
nsrmax 15.0
CTNaClmax 9.8443e-6
dtau_rel_max 10.0
ksat 0.27
kmc 0.00238
NCXmax 5.85
Na_o 140.0
CTKClmax 7.0756e-6
stim_duration 3.0
ibarnak 0.61875
csqnbar 10.0
Kmup 0.00092
Ca_o 1.8
cbar 0.05
a 0.0011
stim_period 1000.0
kmt 0.0005
KmCa 0.000125
KmCaMK 0.15
gacai 1.0
K_o 5.4
gacao 0.341
dKmPLBmax 0.00017
kmnai 10.0
kmcsqn 0.8
KmBSL 0.0087
dJupmax 0.75
pca 0.000243
stim_amplitude -20.0
Cl_o 100.0
PCl 4.0e-7
BSRmax 0.047
GClb 0.000225
KmCai 0.0036
F 96485.0
CaMK0 0.05

States:

Name Description
Cl_i(time) 15.59207157178
xr(time) 7.24074e-6
fca2(time) 0.893052931249
Ca_ss(time) 0.00012271265
fca(time) 0.97836624923
dp(time) 8.98230672628
f(time) 0.999961508634
J(time) 0.991924983076
xs1(time) 0.019883138161
Ca_nsr(time) 1.832822335168
mL(time) 0.001356538159
m(time) 0.001356538159
xs2(time) 0.019890650554
ro(time) 0.0
Ca_jsr(time) 1.737580994071
Na_i(time) 12.972433387269
zdv(time) 0.829206149767
d(time) 1.64013e-6
V(time) -85.781844107117
f2(time) 0.992234519148
ydv(time) 0.013970786703
CaMKtrap(time) 0.021123704774
K_i(time) 135.469546216758
AA(time) 0.000816605172
ydv2(time) 0.99996472752
H(time) 0.987317750543
Ca_i(time) 0.00012131666
ri(time) 0.862666650318
hL(time) 0.26130711759

Observables: none

2f1

2f1 @ v0.0.1

Vasalou and Henson 2010

This workspace contains SED-ML and cellml files that reproduces the results shown in the original paper.

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

3


3e0

3e0 @ v0.0.1

A model for pacemaking in substantia nigra neurons (A simple model based on a spherical geometry)

A simple model of pacemaking using ion transport at the neuronal membrane that would help to analyse the implied energy usage is presented. The model has been used to study the association between repetitive firing pattern of Substantia nigra neurons and cytosolic calcium. With the help of detailed mechanism to describe the functioning of pumps and exchangers at the membrane, this model is capable of describing energy expenditure of these neurons due to the activity at its membrane. The model can also be used to simulate the response of these neurons to channel blockers such as TTX and dihydropyridines.

The original reference is cited below:

Francis F, Garcia MR, Middleton RH (2012) Energetics of ion transport in dopaminergic substantia nigra neurons. In: Wellstead P, Cloutier M, editors, Systems Biology of Parkinson's Disease, Springer New York. pp. 81-109

Parameters:

Name Description
F 96485.30929
Camtot 0.0489
T 310.15
K_xmnao 87.5
zb_hna -1.1868
g_kdr 10.0
g_khcn 10.0
B_hna 0.5296
k_4pc 1.0
cAMP 1.0e-5
za_hna -2.4317
dia 0.003
svr 6.0
k_2pc 0.001
kcal_2 0.002
k_3pc 0.001
kcal_1 10.0
Calbtot 0.002
K_nkki 32.88
A_mna 1.9651
B_mna 0.0424
g_kir 5.0
C_sp 900000.0
delta_xmca 0.68
zb_mna 1.5581
g_cal 1158.2
k_pmca 10.0
g_cat 10.0
fr_cyt 1.0
Na_o 137.0
k_3nk 0.01
K_nknai 4.05
K_pco 2.0
K_nknao 69.8
Ca_o 1.8
delta_xmna 0.32
atp 2.0
k_2nk 0.04
g_nahcn 3.0
K_o 5.4
k_nk 200.0
k_xm 25.0
g_nalk 0.0039
K_xmcao 1.38
k_4nk 0.165
g_ka 0.2234
A_hna 9.566e-5
za_mna 1.7127
kcam_cd 0.003
g_na 395.14
K_xmnai 8.75
g_cah 78.5
K_nkko 0.258
g_ksk 15.0
R 8314.472
K_xmcai 0.00138
kcam_nd 3.0

States:

Name Description
Na_i(t) 6.0
y_xm(t) 0.343
h_cah(t) 0.454
Cam(t) 0.0487
Ca_i(t) 0.00015
p_ka(t) 0.2577
y_nk(t) 0.555
h_na(t) 0.2272
m_cat(t) 0.1099
h_cat(t) 0.5716
m_cah(t) 0.3021
Calb(t) 0.0011
O_hcn(t) 0.0
q_ka(t) 0.827
m_na(t) 0.0758
y_pc(t) 0.001
m_kdr(t) 0.0043
K_i(t) 140.0
m_cal(t) 0.0004

Observables: none

4


4a2

4a2 @ v0.0.1

Tran 2017 - Cross-bridge model of shortening heat

Model of cross-bridge kinetics used to simulate cardiac mechano-energertics in the paper titled: Experimental and modelling evidence of shortening heat in cardiac muscle. DOI: 10.1113/JP274680.

Parameters: none

States: none

Observables: none

4a3

4a3 @ v0.0.1

A model of intracellular pH control

CellML model derived from: Boron WF and De Weer P. Intracellular pH transients in squid giant axons caused by CO2, NH3, and metabolic inhibitors. Journal of General Physiology, Vol. 67, pp 91-112, 1976.

Parameters:

Name Description
P_CO2 6.0e-5
beta -26.0
P_HCO3 5.0e-9
V_m -0.057
RTF 0.0256796
H_Lim 3.98107170553497e-5
k 0.0375
K_A 0.001
rho 8000.0
H_o 1.995262314968879e-5

States:

Name Description
TA_i(t) 0.0
H_i(t) 3.98107170553497e-5

Observables: none

4be

4be @ v0.0.1

Atrial fibroblast model

A novel model of electrophysiology of a single atrial fibroblast (based on experimental data by Wu et al., 2014) was developed. Atrial fibroblasts in the model had higher (more positive) resting potential compared to the previous models of ventricular fibroblasts

(MacCannell et al., 2007). The use of relevant electrophysiological data for the atrial fibroblast model make it more representative of atrial electrophysiology and better suited for the studies of atrial myocyte-fibroblast coupling.

Parameters:

Name Description
Na_i 11.2
K_i 139.0
stim_duration 2.0
K_c 5.4
stim_start 100.0
Na_c 140.0
V_rev -150.0
RToF 26.54
stim_period 5000.0
B -200.0
stim_end 10000.0
stim_amplitude -100.0
g_K1 0.03
i_NaK_max 2.002
k_NaK_K 1.0
g_ns 0.018
g_to 0.01652
g_b_Na 0.00607
g_Kur 0.6
k_NaK_Na 11.0

States:

Name Description
ui(time) 0.0999
oa(time) 0.2488
oi(time) 0.1866
V(time) -80.0
ua(time) 0.9933

Observables: none

4c6

4c6 @ v0.0.1

SED-ML example

Example used in the SED-ML (L1V3) specification.

Parameters:

Name Description
mu 1.0

States:

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

Observables: none

4cd

4cd @ v0.0.1

Hill, 1972 - a model of feto-maternal oxygen exchange

This model is developed based on mathematical model of placental oxygen transfer by Ester Hill and Gordon Power (1972).

Parameters: none

States: none

Observables: none

4e4

4e4 @ v0.0.1

O'Hara-Rudy-CiPA-v1.0 (2017)

A modified version of the O'Hara-Rudy 2011 human ventricular action potential model, with a new hERG formulation that allows kinetic drug binding, and altered channel conductances for improved predictions of drug block.

Parameters:

Name Description
B53 0.004668
zca 2.0
A62 0.3226
bt 4.75
Kki 0.5
Temp 37.0
B61 0.1725
KmBSR 0.00087
BSLmax 1.124
q62 5.0
CaMKo 0.05
A21 5.455e-6
wca 60000.0
GNaL_b 0.019957499999999975
Kxkur 292.0
eP 4.2
i_Stim_Start 10.0
Knai0 9.073
q51 5.0
KmCaAct 0.00015
Knao0 27.78
hssV1 82.9
GKr_b 0.04658545454545456
qna 0.5224
nao 140.0
Ahf 0.99
A3 0.001214
Pnak_b 30.0
k3p 1899.0
kasymm 12.5
GK1_b 0.3239783999999998
qca 0.167
i_Stim_Period 1000.0
A61 0.01241
Khp 1.698e-7
rad 0.0011
Vhalf 1.0
ko 5.4
PKNa 0.01833
B2 -0.004226
trpnmax 0.07
B62 -0.0006575
wnaca 5000.0
MgATP 9.8
mtV3 77.42
mtV1 11.64
k2m 39.4
KmCaMK 0.15
B41 -0.02877
i_Stim_Amplitude -80.0
q21 4.156
wna 60000.0
H 1.0e-7
q1 4.843
celltype 0.0
GpCa 0.0005
A52 0.3181
kcaoff 5000.0
kna1 15.0
Kmgatp 1.698e-7
PCa_b 0.0001007
A51 0.4492
KmCaM 0.0015
bCaMK 0.00068
F 96485.0
A63 0.008978
GNa 75.0
k4p 639.0
n 1.0
Ku 0.0
q61 5.568
Kt 0.0
A53 0.149
B1 4.631e-5
T 310.0
PCab 2.5e-8
Gncx_b 0.0008
L 0.01
cm 1.0
q2 4.23
A4 1.854e-5
Kmax 0.0
zk 1.0
k1p 949.5
Jup_b 1.0
q41 1.459
B4 -0.04641
csqnmax 10.0
q53 2.412
mtD2 8.552
B21 -0.1688
B52 3.613e-8
zna 1.0
Gto_b 0.02
shift_INa_inact 0.0
k1m 182.4
kna3 88.12
kmtrpn 0.0005
k3m 79300.0
q31 4.22
A1 0.0264
cmdnmax_b 0.05
KmCap 0.0005
halfmax 1.0
q63 5.682
B11 1.535e-8
kna2 5.0
B63 -0.02215
GKs_b 0.006358000000000001
Kko 0.3582
Knap 224.0
mssV1 39.57
q11 4.942
q52 4.663
A41 0.001416
i_Stim_End 1.0e17
Jrel_scaling_factor 1.0
txs1_max 817.3
delta -0.155
B3 0.008516
A2 4.986e-6
kmcmdn 0.00238
mtD1 6.765
PNab 3.75e-10
k4m 40.0
cao 1.8
B51 0.008595
k2p 687.2
GKb_b 0.003
mtV2 34.77
kmcsqn 0.8
thL 200.0
MgADP 0.05
A11 0.0007868
KmBSL 0.0087
kcaon 1.5e6
mssV2 9.871
k2n 1000.0
Kmn 0.002
q4 3.769
B31 7.771e-9
aCaMK 0.05
i_Stim_PulseDuration 0.5
mtV4 5.955
A31 0.005509
BSRmax 0.047
R 8314.0
hssV2 6.086
q3 4.962

States:

Name Description
cai(time) 8.6e-5
nca(time) 0.002749414044
IC1(time) 0.999637
Cbound(time) 0.0
iF(time) 0.9995541745
v(time) -88.00190465
nai(time) 7.268004498
fs(time) 0.9102412777
O(time) 0.00015551
mL(time) 0.0001882617273
ki(time) 144.6555918
D(time) 0.0
ap(time) 0.0005100862934
jp(time) 0.6979245865
iFp(time) 0.9995541823
fcafp(time) 0.9999999909
nass(time) 7.268089977
a(time) 0.001001097687
C1(time) 1.80145e-8
iSp(time) 0.6393399482
jca(time) 0.9999738312
xk1(time) 0.9967597594
fcas(time) 0.9998046777
Obound(time) 0.0
hL(time) 0.5008548855
Jrelnp(time) 2.5e-7
fcaf(time) 0.9999999909
ffp(time) 0.9999999909
C2(time) 8.26619e-5
IC2(time) 6.83208e-5
ff(time) 0.9999999909
IObound(time) 0.0
xs1(time) 0.2707758025
j(time) 0.6979908432
hLp(time) 0.2693065357
m(time) 0.007344121102
xs2(time) 0.0001928503426
cansr(time) 1.619574538
kss(time) 144.6555651
cass(time) 8.49e-5
cajsr(time) 1.571234014
d(time) 2.34e-9
hf(time) 0.6981071913
hsp(time) 0.4549485525
CaMKt(time) 0.0125840447
Jrelp(time) 3.12e-7
iS(time) 0.5865061736
IO(time) 5.67623e-5
hs(time) 0.6980895801

Observables: none

4e9

4e9 @ v0.0.1

HH Sodium Current model for estimation task

The standard HH sodium current, to be used in a parameter estimation task.

Parameters:

Name Description
V_new -10.0
g_Na 120.0
E_Na 35.0
V_hold -85.0

States:

Name Description
h(t) 0.6
m(t) 0.05

Observables: none

4f0

4f0 @ v0.0.1

Steady state HMT

The steady state version of the HMT active tension model.

Parameters:

Name Description
T_ref 100.0
Ca_max 1.0
c50 0.5
lambda 1.0
h 3.0
beta 1.45

States:

Name Description
Ca_actn(time) 0.0

Observables: none

5


5b0

5b0 @ v0.0.1

Ni et al. 2017 Human atrial model

Model of the human atrial action potential by Ni et al. 2017

Parameters:

Name Description
Aca_IC50_Ito 9.3
cpumps 0.04
Aca_IC50_IKr 32.4
T 310.0
drug_La 0.1
SLhigh 13.0
kmcalr 1.38
KdBCa 0.00238
DCa 0.78
kmko 1.5
kmnalr 87.5
ksatlr 0.1
dx 1.625
Cm 100.0
icapbar 0.275
LC 0.00028636715
gammalr 0.35
ryr_o_i_tau 5.0
KdCSQN 0.8
DCaSR 0.044
kmcap 0.0005
Aca_hill_IKs 0.8
Aj_nj 2492.324412
k3 0.002314815
BCa 0.024
ryr_c_ss_tau 15.0
KO 0.00019445959
ryr_o_ss_tau 5.0
Na_o 140.0
kSRleak 6.0e-6
Aca_IC50_IKs 81.4
Aca_hill_Ito 0.9
Ca_o 1.8
ical_fca_tau 2.0
KdSLlow 1.1
SLlow 165.0
CSQN 6.7
duration 0.5
gNa 7.8
ryr_a_i_tau 250.0
k4 0.0075
period 1000.0
knacalr 1600.0
conc 1.0e-14
K_o 5.4
pace 0.0
Vi 13668.0
kmnai 10.0
LO 0.00029099869
xj_nj 0.8225
ZLC 0.83707302269
ryr_a_ss_tau 250.0
offset 10.0
drug_concen 0.0
KC 0.00247871659
Aca_hill_IKr 0.9
k1 7500.0
K_Q10 3.0
gK1 0.09
KdSLhigh 0.013
drug_Li 0.01
ErL 65.0
R 8.3143
F 96.4867
k2 0.00046875

States:

Name Description
SERCACass(time) 0.009386941118
Ca_SRi(time) 0.9892411621
xr(time) 0.00157418133
a_i(time) 0.2977219443
Ca_ss(time) 0.0001313595105
xs(time) 0.02225979641
fca(time) 0.7270823666
f(time) 0.9354212881
o_ss(time) 0.000456694441
j(time) 0.9380183564
o_i(time) 0.0003667999273
Ca_SRss(time) 0.9779168037
BI(time) 0.0
m(time) 0.005631819916
BO(time) 2.355477517e-16
c_i(time) 0.9790238698
s(time) 0.8849139842
Na_i(time) 10.30397012
SERCACa(time) 0.00958584702
d(time) 0.0002267161277
BC(time) 3.062722822e-15
a_ss(time) 0.1419271573
V(time) -77.13255836
i(time) 0.9517278864
h(time) 0.9168420281
a(time) 0.0002417881801
K_i(time) 131.867138
c_ss(time) 0.9571976502
BA(time) 0.0
r(time) 0.01223706011
Ca_i(time) 0.0001403133065

Observables: none

5bb

5bb @ v0.0.1

Fenton, Karma, 1998

nothing

Parameters:

Name Description
tau_v_plus 10.0
tau_v2_minus 18.2
u_c 0.13
tau_w_plus 1020.0
IstimAmplitude -0.2
k 10.0
tau_r 130.0
tau_w_minus 80.0
IstimPulseDuration 1.0
g_fi_max 5.8
tau_v1_minus 18.2
IstimEnd 50000.0
tau_si 127.0
u_csi 0.85
IstimPeriod 1000.0
V_0 -85.0
tau_0 12.5
V_fi 15.0
IstimStart 100.0
Cm 1.0
u_v 0.0

States:

Name Description
u(time) 0.0
v(time) 1.0
w(time) 1.0

Observables: none

5d7

5d7 @ v0.0.1

A computational human cardiac Purkinje electrophysiological model

The present computational model reproduces the electrophysiology of human cardiac Purkinje cells. Model design, calibration, optimization, and validation is presented (open access) in: C. Trovato, E. Passini, N. Nagy, et al., Human Purkinje in silico model enables mechanistic investigations into automaticity and pro-arrhythmic abnormalities, Journal of Molecular and Cellular Cardiology (2019)

Parameters:

Name Description
cmdnmax 0.1125
dkmplbbar 0.00017
zca 2.0
GK1 0.0455
Kki 0.5
KmBSR 0.00087
BSLmax 0.4777
CaMKo 0.05
wca 60000.0
Pnak 32.4872
trpnmaxsl 0.0035
Kxkur 292.0
Gsus 0.0301
Knao0 27.78
eP 4.2
Knai0 9.073
KmCaAct 0.00015
hssV1 78.5
GfK 0.0232
qna 0.5224
greekpi 3.14159265
nao 140.0
GfNa 0.0116
GKr 0.0342
kasymm 12.5
k3p 1899.0
Ahf 0.99
Khp 1.698e-7
qca 0.167
Gto 0.192
rad 0.00175
ko 5.4
PKNa 0.01833
PCa 7.7677e-5
trpnmax 0.0315
wnaca 5000.0
MgATP 9.8
mtV3 77.42
mtV1 11.64
k2m 39.4
KmCaMK 0.15
sstau 0.2
wna 60000.0
H 1.0e-7
GpCa 0.0005
amp -40.0
kcaoff 5000.0
kna1 15.0
k0a 9.6
Gncx 0.00095709
Kmgatp 1.698e-7
KmCaM 0.0015
bCaMK 0.00068
F 96485.0
cm 1.0
k2 1800.0
k4p 639.0
GNa 39.4572
T 310.0
PCab 2.5e-8
tauip3 3.7
L 0.0164
gaptau 12.0
zk 1.0
k1p 949.5
kmup 0.00028
GNaL 0.0189
csqnmax 2.88
cmdnmaxsl 0.0125
GCaT 0.0754
mtD2 8.552
k0 96000.0
zna 1.0
csqnmaxsl 1.2
k1m 182.4
kna3 88.12
kmtrpn 0.0005
k3m 79300.0
KmCap 0.0005
Knap 224.0
kna2 5.0
nsrbar 15.0
Kko 0.3582
mssV1 48.4264
k1a 16.5
delta -0.155
GKs 0.0029
dqupcamkbar 0.75
IP3 0.0001
k2a 0.21
duration 1.0
kmcmdn 0.00238
mtD1 6.765
PNab 9.375e-10
k4m 40.0
cao 1.8
k2p 687.2
kmcsqn 0.8
mtV2 34.77
thL 200.0
MgADP 0.05
KmBSL 0.0087
mssV2 7.5653
kcaon 1.5e6
k1 150000.0
Kmn 0.002
k2n 1000.0
aCaMK 0.05
mtV4 5.955
BSRmax 0.019975
R 8314.0
hssV2 6.22

States:

Name Description
cai(time) 4.36004404734282e-5
nca(time) 0.00547252500964926
v(time) -86.6814002878592
nai(time) 8.23183964616932
Jrel1(time) 0.000108240945806962
y(time) 0.233119011214908
fs(time) 0.926692153319136
casl(time) 0.000102004317781147
u(time) 0.466236137183558
mL(time) 0.000241925773627233
cacsr(time) 1.26516959198518
ki(time) 143.767359809132
g(time) 0.994214357917907
jp(time) 0.790947058236417
fcafp(time) 0.999999968278239
nass(time) 8.23154325237268
a(time) 0.000272851144435704
b(time) 0.000304250912559619
jca(time) 0.999978907334662
xk1(time) 0.997084813729909
fcas(time) 0.999999905741936
hL(time) 0.463574582508218
fcaf(time) 0.99999996819573
ffp(time) 0.999999968365903
ff(time) 0.999999968230738
xs1(time) 0.191165248085394
j(time) 0.790474358603666
hLp(time) 0.240216198686475
ksl(time) 143.767769906216
m(time) 0.00632661703915808
xs2(time) 0.000222677365291219
cansr(time) 1.26350902016858
xrs(time) 0.568716473334161
kss(time) 143.767768218104
cass(time) 0.000101777993438818
cajsr(time) 1.24811940209535
d(time) 6.97735089296892e-9
hf(time) 0.788611739889677
hsp(time) 0.579693514309867
nasl(time) 8.23153516580562
i2(time) 0.989965695822495
CaMKt(time) 0.00505983330678751
xrf(time) 0.000331691184084272
i1(time) 0.649604795721571
hs(time) 0.788545979951331
Jrel2(time) 1.25045800437317e-69

Observables: none

5e1

5e1 @ v0.0.1

A computational human ventricular electrophysiological model

The present computational model reproduces the electrophysiology of human cardiac ventricular cells. Model design, calibration, optimization, and validation is presented (open access) in:

Tomek, Jakub, et al. "Development, calibration, and validation of a novel human ventricular myocyte model in health, disease, and drug block." Elife 8 (2019). DOI: 10.7554/eLife.48890

Parameters:

Name Description
ICaL_fractionSS 0.8
zcl -1.0
zca 2.0
bt 4.75
Kki 0.5
KmBSR 0.00087
Jrel_b 1.5378
BSLmax 1.124
Fjunc 1.0
CaMKo 0.05
wca 60000.0
GNaL_b 0.0279
Kxkur 292.0
Knao0 27.78
eP 4.2
Knai0 9.073
KmCaAct 0.00015
vShift 0.0
KdClCa 0.1
i_Stim_Start 0.0
cli 24.0
GKr_b 0.0321
qna 0.5224
nao 140.0
INaCa_fractionSS 0.35
kasymm 12.5
Pnak_b 15.4509
k3p 1899.0
GK1_b 0.6992
Khp 1.698e-7
qca 0.167
gkatp 4.3195
i_Stim_Period 1000.0
rad 0.0011
tauK 2.0
ko 5.0
PKNa 0.01833
trpnmax 0.07
tauNa 2.0
wnaca 5000.0
MgATP 9.8
k2m 39.4
KmCaMK 0.15
i_Stim_Amplitude -53.0
wna 60000.0
H 1.0e-7
celltype 2.0
offset 0.0
GpCa 0.0005
kcaoff 5000.0
kna1 15.0
Kmgatp 1.698e-7
GClCa 0.2843
EKshift 0.0
PCa_b 8.3757e-5
KmCaM 0.0015
bCaMK 0.00068
K_atp 0.25
F 96485.0
GNa 11.7802
k4p 639.0
A_atp 2.0
PCab 5.9194e-8
T 310.0
Gncx_b 0.0034
L 0.01
tjca 75.0
zk 1.0
k1p 949.5
Jup_b 1.0
cajsr_half 1.7
csqnmax 10.0
Aff 0.6
fkatp 0.0
tauCa 0.2
zna 1.0
clo 150.0
Gto_b 0.16
k1m 182.4
kna3 88.12
kmtrpn 0.0005
k3m 79300.0
KmCap 0.0005
cmdnmax_b 0.05
Knap 224.0
GKs_b 0.0011
kna2 5.0
Kko 0.3582
i_Stim_End 1.0e17
K_o_n 5.0
delta -0.155
kmcmdn 0.00238
PNab 1.9239e-9
k4m 40.0
cao 1.8
k2p 687.2
GKb_b 0.0189
kmcsqn 0.8
thL 200.0
MgADP 0.05
alpha_1 0.154375
KmBSL 0.0087
kcaon 1.5e6
Kmn 0.002
k2n 500.0
dielConstant 74.0
beta_1 0.1911
aCaMK 0.05
i_Stim_PulseDuration 1.0
BSRmax 0.047
GClb 0.00198
R 8314.0

States:

Name Description
cai(time) 8.166e-5
iF(time) 0.9996
v(time) -89.1704
nai(time) 15.0038
C3(time) 0.9979
fs(time) 0.92
O(time) 0.00054206
mL(time) 0.00015079
hp(time) 0.6838
ki(time) 143.0403
ap(time) 0.00047143
nca_ss(time) 0.00051399
jp(time) 0.8358
iFp(time) 0.9996
fcafp(time) 1.0
nass(time) 15.0043
a(time) 0.00092527
C1(time) 0.0006956
Jrel_p(time) 0.0
iSp(time) 0.6261
jca(time) 1.0
fcas(time) 0.9998
hL(time) 0.5327
fcaf(time) 1.0
nca_i(time) 0.0012
ffp(time) 1.0
I(time) 1.8784e-5
C2(time) 0.00082672
ff(time) 1.0
xs1(time) 0.2653
j(time) 0.8363
hLp(time) 0.2834
m(time) 0.00073818
xs2(time) 0.00016921
cansr(time) 1.9557
kss(time) 143.0402
Jrel_np(time) 0.0
cass(time) 6.5781e-5
cajsr(time) 1.9593
d(time) 0.0
h(time) 0.8365
CaMKt(time) 0.0192
iS(time) 0.5671

Observables: none

5f5

5f5 @ v0.0.1

McIntyre, Richardson, Grill, 2001

Modeling the excitability of mammalian nerve fibers: influence of afterpotentials on the recovery cycle

Parameters:

Name Description
g_Naf 3.0
C_n 0.002
stim_duration 0.5
g_Kf 0.0
stim_amplitude 0.05
E_K -90.0
g_Ks 0.08
E_Lk -90.0
E_Na 50.0
g_Nap 0.01
g_Lk 0.007

States:

Name Description
s(t) 0.00997371545602793
h(t) 0.841520865130776
p(t) 0.0969864645712442
n(t) 0.000886041197111556
V_m(t) -88.5901439103062
m(t) 0.0302964457761589

Observables: none

2


25d

25d @ v0.0.1

Models for the OpenCOR and PMR tutorial by Peter Hunter

We provide here a collection of the models used in the OpenCOR and PMR tutorial written by Peter Hunter. The tutorial itself is available under https://www.cellml.org/getting-started/tutorials

Parameters:

Name Description
beta_y 2.0
b 2.0
V 0.0
g_y 36.0
a 1.0
mu 1.0
Ki 140.0
sigma 10.0
Ko 2.5
Cm 12.0
A 0.2645
Nao 140.0
E_L -60.0
g_Na 120.0
g_L 0.075
g_Na_max 400.0
rho 28.0
Nai 30.0
g_K 36.0
alpha_y 1.0
beta 2.66667
RTF 25.0
E_y -85.0
gamma 4.0
E_Na 35.0

States:

Name Description
h(t) 0.8
n(t) 0.01
m(t) 0.01
z(t) 1.0
x(t) -2.0
y(t) 0.0
V(t) -85.0

Observables: none

25e

25e @ v0.0.1

Faber, Rudy, 2000 and Tong, Ghouri, Taggart, 2014

nothing

Parameters:

Name Description
preplength 0.1
stim_start 10.0
Tn_max 0.07
CMDN_max 0.05
c2 0.0001
tau_tr 120.0
Ca_NSR_max 15.0
kATP 0.00025
Cao 1.8
gamma_Nai 0.75
K_relss 1.0
radius 0.011
i_K_ATP_on 1.0
I_pCa 1.15
I_NaK 2.25
Nao 140.0
ATPi 3.0
g_Kp 0.00552
stim_amplitude -80.0
K_mrel 0.0008
CSQN_max 10.0
nKNa 2.8
K_mKo 1.5
CSQNthresh 0.7
F 96485.0
nicholsarea 5.0e-5
gamma_Cao 0.341
qn 9.0
T 310.0
P_Na 6.75e-7
Km_Ca 0.0006
tau 4.75
K_mup 0.00092
G_Ks 0.433
stim_period 300.0
stim_end 9.0e6
kdKNa 66.0
K_mCSQN 0.8
K_mTRPN 0.0005
P_Ca 0.00054
I_up 0.00875
G_rel_overload 4.0
K_mTn 0.0005
R 8314.0
TRPN_max 0.07
G_rel_max 60.0
Ko 5.4
gamma_Nao 0.75
Logicthresh 0.98
c1 0.00025
g_Nab 0.004
G_Kr 0.02614
kappa 0.125
K_m_ns_Ca 0.0012
K_mNai 10.0
G_K1 0.75
gamma_Cai 1.0
hATP 2.0
PNaK 0.01833
delta_Ca_ith 0.00018
delta_m 1.0e-5
stim_duration 0.5
g_K_Na 0.12848
K_mpCa 0.0005
K_mCMDN 0.00238
gamma_Ki 0.75
A_cap 0.0001534
g_Na 16.0
g_Cab 0.003016
gamma_Ko 0.75
g_CaT 0.056
nATP 0.24
gamma 0.15
P_K 1.93e-7

States:

Name Description
OVRLDtrack3(time) 0.0
NSR(time) 3.35408001677624
xr(time) 0.0068050628191769
Ca_NSR(time) 1.74647588622419
OVRLDtrack2(time) 0.0
f(time) 0.983904806551856
Cainfluxtrack(time) 2.82367737273297e-196
APtrack2(time) 5.84534012971144e-195
xs1(time) 0.053484483308799
j(time) 0.988104917040651
m(time) 0.00176916305136317
xs2(time) 0.0915338818524544
Nai(time) 17.6117490445233
APtrack3(time) 0.000129513799736416
APtrack(time) 1.05741719313009e-195
zdv(time) 0.0153950987302045
d(time) 6.86847510834054e-6
g(time) 0.592188823541168
OVRLDtrack(time) 0.0
V(time) -84.1873796338053
h(time) 0.981794631652901
ydv(time) 0.931914460539262
Ca_JSR(time) 1.10786985002835
Ki(time) 136.516534944494
b(time) 0.00107239754072387
JSR(time) 7.64464040842916
CaT(time) 0.0354676562409019
Cai(time) 0.000115992251742132
i_rel(time) 0.000948968144034608

Observables: none

3


35a

35a @ v0.0.1

Goldbeter Dupont Berridge 1990

This workspace contains both SED-ML and cellML files with reproduces the results as shown in the original paper.

Parameters:

Name Description
v_1 7.3
W_T 1.0
K_A 0.9
K_a 2.5
k 10.0
v_P 5.0
V_MK 40.0
k_f 1.0
V_M2 65.0
v_0 1.0
beta 0.301
m 2.0
V_M3 500.0
K_1 0.1
K_R 2.0
K_2 1.0
p 4.0
n 2.0

States:

Name Description
W_star(time) 0.0
Z(time) 0.5
Y(time) 1.75

Observables: none

35c

35c @ v0.0.1

A single compartment model of pacemaking in dissasociated Substantia nigra neurons with hyperbolic tetrahedral geometry

A model is developed to study the membrane oscillations of a dissociated substantia nigra neuron, by describing its geometry based on a hyperbolic tetrahedron. The model demonstrates the dependance of these neurons on the L-type calcium channel for its autonomous pacemaking activity. Existence of stable limit cycles for important state variables establishes the robustness of the system.

Parameters:

Name Description
Camtot 0.0235
T 310.15
zb_hna -1.1868
g_kdr 31.237
B_hna 0.5296
k_4pc 1.0
cAMP 1.0e-5
vol_pmu 5.0
za_hna -2.4317
k_2pc 0.001
kcal_2 0.002
k_3pc 0.001
kcal_1 10.0
Calbtot 0.005
K_nkki 32.88
A_mna 1.9651
B_mna 0.0424
g_kir 13.816
C_sp 900000.0
zb_mna 1.5581
g_cal 2101.2
k_pmca 2.233
fr_cyt 0.5
Na_o 137.0
k_3nk 0.01
K_nknai 4.05
K_pco 2.0
K_nknao 69.8
Ca_o 1.8
atp 2.0
k_2nk 0.04
g_nahcn 51.1
K_o 5.4
k_nk 1085.7
k_xm 0.0166
g_nalk 0.0053
del 0.35
k_4nk 0.165
A_hna 9.566e-5
za_mna 1.7127
kcam_cd 0.003
g_na 907.68
SVR_pmu 16667.0
K_nkko 0.258
g_ksk 2.2515
R 8314.472
F 96485.30929
kcam_nd 3.0

States:

Name Description
Na_i(t) 4.6876
Cam(t) 0.0222
Ca_i(t) 0.000188
y_nk(t) 0.6213
Calb(t) 0.0026
h_na(t) 0.1848
O_hcn(t) 0.003
V(t) -49.42
m_na(t) 0.0952
y_pc(t) 0.483
m_kdr(t) 0.0932
K_i(t) 126.05893
m_cal(t) 0.006271

Observables: none

35e

35e @ v0.0.1

Aguda, B, 1999

nothing

Parameters:

Name Description
k14 0.0005
kn7 0.01
k21 0.01
k20 0.1
k18 1.0
k9 1.0
k13 1.0
kn2 0.01
k10 0.0
k15 0.01
kn3_ 0.0
Chk1_T 1.0
kn23 1.0
k8 0.1
kPlk1_ 0.0
k9_ 0.0
k14_ 1.0
k4 0.0
k8_ 0.0
k22 0.1
k6 0.01
kex 1.0
k11 1.0
kn1 10.0
kn9 1.0
k12 0.1
kctak1_ 0.0
kn18 0.01
kctak1 0.0
k16 0.0002
k23 0.1
k1 1.0
k3_ 100.0
k2_ 0.1
kPlk1 0.0
k7 1.0
V_in 1.0e-5
k17 0.1
k5 1.0
k2 0.1
kn8 0.01

States:

Name Description
iCdc25Ps216(time) 2.0e-5
p21(time) 0.0
preMPF(time) 1.0e-6
Wee1(time) 0.001
Chk1P(time) 1.0e-6
Rad3(time) 0.0
aCdc25Ps216(time) 0.0
p53(time) 0.0
aCdc25(time) 1.0e-6
Wee1P(time) 0.0
iCdc25(time) 1.0e-6
p21_MPF(time) 0.0
MPF(time) 1.0e-8
iCdc25Ps216_protein1433(time) 0.03
protein1433(time) 2.0

Observables: none

35f

35f @ v0.0.1

Gupta, Maurya, Stephens, Dennis and Subramaniam, 2009

nothing

Parameters:

Name Description
k_21 0.034
k_18 0.054
k_19 0.029
k_22 0.116
PIP_2 1.0
k_5 1.0e-15
k_4 1.0e-15
k_15 0.061
k_16 1.0e-15
DG 0.0
k_2 1.0e-15
k_12 0.098
k_8 0.007
k_20 0.014
k_13 0.204
k_14 1.0e-15
k_3 1.0e-15
k_11 0.111
GPCho 1.0
k_7 1.0e-15
k_10 0.024
k_6 0.33
k_9 0.187
k_17 3.116
k_1 355.637

States:

Name Description
dPGD_2(time) 0.0
dPGJ_2(time) 0.0
PGH_2(time) 0.0
PGF_2a(time) 0.0
HETE(time) 0.0
PGJ_2(time) 0.0
AA(time) 25.0
PGD_2(time) 0.0
PGE_2(time) 0.0

Observables: none

4


43c

43c @ v0.0.1

Testing RDF linking across CellML, SED-ML, and SVG

A workspace to play with ideas about linking SVG entities to other resources in the workspace. Using trivial CellML models and SED-ML simulation experiments to put emphasis on linkages without needing to think about the other stuff.

Parameters: none

States: none

Observables: none

44c

44c @ v0.0.1

A 0D model of the Heart

A simplified "0D" version of our 3D Cardiac Electromechanical Model based on the Bestel-Clément-Sorine equations of myocardial tissue, Mooney-Rivlin equations of passive material and Windkessel model for cardiac afterload.

Parameters:

Name Description
APD 0.3
P_at_t1 0.005
R_0 0.028
dt 1.0e-5
AV_delay 0.12
K_iso 1.0e-13
P_at_Lower 1000.0
QRS_duration 0.085
HeartPeriod 0.8
mu 70.0
P_ar_Lower 10000.0
R_p 2.0e7
P_at_t2 0.1
k_0 100000.0
c_1 800.0
c_2 800.0
E_s 3.0e7
w 1.0
Tau 0.8
alpha 1.5
katp 30.0
P_at_Upper 1500.0
eta 100.0
K_at 0.0001
d_0 0.014
rho 1070.0
K_ar 1.0e-6
n_0 1.0
krs 30.0
sigma_0 50000.0
Z_c 8.0e6

States:

Name Description
e_c(t) 0.0
tau_c(t) 0.0
phase(t) 0.0
k_c(t) 0.0
P_ar(t) 13500.0
x(t) 0.0
y(t) 0.0

Observables: none

47c

47c @ v0.0.1

Varela - Canine Atrial Cell Models

These are the four regional models for canine atrial myocytes. The regions are: right atrium, left atrium, Bachmann's bundle/crista terminalis, pulmonary veins. There are also options for adding electrophysiological remodelling and anti-arrhythmic drugs to the model. The models are completely characterised in the Supplementary Text of Varela et al, PLoS Comp Bio, 2016.

Parameters:

Name Description
g_Ca_L 0.58
Na_o 140.0
stim_duration 2.0
T 310.0
TRPN_max 0.35
stim_start 50.0
K_up 0.0006
K_rel 8.0
Ca_o 1.8
g_B_Na 1.0e-5
Ca_up_max 27.0
g_K_Ach 0.0045
V_cell 20100.0
stim_period 1000.0
stim_end 50000.0
K_sat 0.1
i_NaK_max 0.6
K_o 5.4
I_up_max 0.0035
g_to 0.096
CMDN_max 0.045
Cm 100.0
g_B_Cl 0.0008
Km_K_o 1.5
i_CaP_max 0.275
g_Na 7.8
g_B_Ca 1.0e-5
K_mNa 87.5
stim_amplitude -2000.0
g_Ks 0.052
g_K1 0.1
CSQN_max 10.0
tau_tr 180.0
Cl_o 132.0
g_Kr 0.00899
I_NaCa_max 1600.0
Km_Na_i 10.0
g_Kur 0.0115
K_mCa 1.38
gamma 0.35
F 96.4867
R 8.3143

States:

Name Description
Ca_CMDN(time) 0.001856
oa(time) 0.07164
oi(time) 0.9992
Cl_i(time) 29.26
xr(time) 7.433e-7
v(time) 1.0
xs(time) 0.01791
f(time) 0.9999
ui(time) 0.9987
u(time) 0.0
j(time) 0.9869
m(time) 0.001972
w(time) 0.9993
Na_i(time) 11.75
d(time) 4.757e-6
Ca_rel(time) 1.502
V(time) -85.53
h(time) 0.9791
xa(time) 1.0e-5
ua(time) 0.05869
Ca_TRPN(time) 0.007022
Ca_CSQN(time) 6.432
K_i(time) 138.4
f_Ca(time) 0.7484
Ca_up(time) 1.502
Ca_i(time) 0.0001024

Observables: none

49e

49e @ v0.0.1

Noble 1962 model for Physiome article

This is a workspace for testing out a Physiome article based on the Noble 1962 model.

Parameters: none

States: none

Observables: none

5


58f

58f @ v0.0.1

Loewe-Lutz-Fabbri-Severi human sinus node cellular electrophysiology model

Loewe et al., Biophysical Journal 2019,

https://doi.org/10.1016/j.bpj.2019.07.037

Axel Loewe, Yannick Lutz, Deborah Nairn, Alan Fabbri, Norbert Nagy, Noemi Toth, Xiaoling Ye, Doris H. Fuertinger, Simonetta Genovesi, Peter Kotanko, Jochen G. Raimann, Stefano Severi

"Hypocalcaemia-Induced Slowing of Human Sinus Node Pacemaking"

Loewe et al., Proceedings of the 41st IEEE Engineering in Medicine and Biology Conference (2019), Berlin

"Inter-Species Differences in the Response of Sinus Node Cellular Pacemaking to Changes of Extracellular Calcium"

Parameters: none

States: none

Observables: none

59a

59a @ v0.0.1

A Model of Cardiac Electrical Activity Incorporating Ionic Pumps and Concentration Changes, DiFrancesco, Noble, 1985

This model reproduces the results as shown in the original paper, and also contains semantically relevant annotations.

Parameters: none

States: none

Observables: none

6


61a

61a @ v0.0.1

Generic human heart scaffold

Annotated heart scaffold for human available for registration of segmented neural anatomical-functional mapping of cardiac neural circuits. See SPARC portal for more details

Parameters: none

States: none

Observables: none

61d

61d @ v0.0.1

Generic mouse lung scaffold

Annotated lung scaffold for mouse available for registration of segmented neural anatomical-functional mapping of pulmonary neural circuits. See SPARC portal for more details.

Parameters: none

States: none

Observables: none

62b

62b @ v0.0.1

Generic human lung scaffold

Annotated lung scaffold for human available for registration of segmented neural anatomical-functional mapping of pulmonary neural circuits.

Parameters: none

States: none

Observables: none

62f

62f @ v0.0.1

rat flatmap

Files for the rat flatmap. Uses mapmaker to generate map datasets for a flatmap server and viewer.

Parameters: none

States: none

Observables: none

63a

63a @ v0.0.1

Rat whole body scaffold

In this workspace we have the Scaffold Maker workflow and configuration files needed to produce the rat whole body scaffold for the SPARC project.

Parameters: none

States: none

Observables: none

2


239

239 @ v0.0.1

Combine Archive Example

nothing

Parameters:

Name Description
IstimPeriod 1000.0
IstimAmplitude 0.5
C 0.01
g_s 0.0009
g_Na 0.04
IstimPulseDuration 1.0
g_Nac 3.0e-5
E_Na 50.0
IstimStart 10.0
IstimEnd 50000.0

States:

Name Description
d(time) 0.003
j(time) 0.975
V(time) -84.624
h(time) 0.988
m(time) 0.011
Cai(time) 0.0001
f(time) 0.994
x1(time) 0.0001

Observables: none

261

261 @ v0.0.1

Tong, Choi, Kharche, Holden, Zhang, Taggart, 2011

nothing

Parameters:

Name Description
I_hold 0.0
tinyamount 1.0e-8
test_end 3000.0
inaca_sign -1.0
jnaca_sign -1.0
conversion 1000.0
I_test -0.5
test_start 1000.0

States:

Name Description
cai(time) 0.0001161881607214449
k2(time) 0.9968408069904307
v(time) -53.90915441282156
c(time) 0.0003764413740731269
x(time) 0.08785242843398365
y(time) 0.002604864867063448
p(time) 0.1174074734567931
r1(time) 0.1922244113609531
m(time) 0.1253518889572223
s(time) 0.0307583106982354
q(time) 0.2060363247740295
w(time) 0.2345238135343783
d(time) 0.01036961357784695
g(time) 0.03582573962705717
r2(time) 0.1932803618375963
xab(time) 0.002220456569762898
f2(time) 0.9065967263076083
h(time) 0.404599170710196
xa(time) 0.0003569126518797985
f1(time) 0.9065941499695301
b(time) 0.508117603077852
k1(time) 0.996838577027165

Observables: none

262

262 @ v0.0.1

Tong, Tribe, Smith, Taggart, 2014

nothing

Parameters:

Name Description
I_hold 0.0
tinyamount 1.0e-8
test_end 50000.0
inaca_sign -1.0
jnaca_sign -1.0
conversion 1000.0
I_test -0.25
test_start 1000.0

States:

Name Description
cai(time) 0.0001235555354004079
k2(time) 0.9944827384537837
v(time) -50.80774403486136
c(time) 0.0006695090454068198
x(time) 0.06162789823439722
y(time) 0.001821587846781853
p(time) 0.1358747732875166
nq5s(time) 0.2618890409031491
r1(time) 0.1261674553968813
nq5f(time) 0.2618890409031491
m(time) 0.166998688814229
nq4(time) 0.1081102112425531
s(time) 0.04562272513582834
q(time) 0.22560249352574
w(time) 0.2768302028689621
d(time) 0.01605749091924106
g(time) 0.02817518341064734
r2(time) 0.1261674420211442
xab(time) 0.002673927875795617
hn1(time) 0.02498997383730429
f2(time) 0.8617233295451014
h(time) 0.3156075507278521
xa(time) 0.0003575122973592095
wq1(time) 0.9230513956601629
f1(time) 0.861723329545759
sq1(time) 0.7426740827665872
sq5(time) 0.6280622663818354
b(time) 0.5857399935992883
nq1s(time) 0.09043683263784785
nq1f(time) 0.09043683263784785
k1(time) 0.9944827384537837
hs(time) 0.5292140214748325
wq5(time) 0.9230513956601629
sq4(time) 0.6280622663818354
hn2(time) 0.02498997383730429

Observables: none

285

285 @ v0.0.1

Gattoni 2016

Models from Sara Gattoni at Kings College London. Rat ventricular myocyte electrophysiology and calcium dynamics.

Parameters: none

States: none

Observables: none

3


314

314 @ v0.0.1

Novak, Tyson, 1993

This workspace contains SED-ML and CellML files that reproduce results seen in the paper.

Parameters:

Name Description
ka 0.01
kcak 0.25
V2__ 1.0
Vwee_ 0.1
K_c 0.01
Vwee__ 1.0
kd_antiIE 0.095
kbPPase 0.125
Cdc2_T 100.0
K_d 0.01
V2_ 0.015
V25_ 0.1
Wee1_T 1.0
K_e 0.3
K_f 0.3
Cdc25_T 1.0
K_h 0.01
kfPPase 0.1
kc 0.1
K_a 0.1
khPPase 0.087
kinh 0.025
ke 0.0133
k1AA 1.0
IE_T 1.0
k3 0.01
K_g 0.01
V25__ 2.0
UbE_T 1.0
K_b 0.1
kg 0.0065

States:

Name Description
cyclin(time) 1.0
Wee1_P(time) 0.0
Tyr15P_dimer(time) 0.0
UbE(time) 0.0
MPF_pre(time) 0.0
Cdc25_P(time) 0.0
IE_P(time) 0.0
MPF_active(time) 0.0
cyclin_Cdc2(time) 0.0

Observables: none

354

354 @ v0.0.1

Cui, Kaandorp, 2006

This workspace contains both SED-ML and cellML files that recreate the results shown in the paper.

Parameters:

Name Description
Kx 500.0
f 0.1
kc 10.0
V3 10000.0
K2 0.1
kM_minus 100.0
alpha 0.006
Caex 1.0
kN_minus 5.0
K1 4.3
CaMtotal 25.0
Vx 1000.0
kN_plus 5.0
kM_plus 500.0
V1 30000.0
CaNtotal 25.0
V2 100.0
N 13.0
lamda 5.0
K3 100.0
d 0.4

States:

Name Description
h(time) 0.0
m(time) 0.0
x(time) 0.0
z(time) 1.0e-8

Observables: none

361

361 @ v0.0.1

Arresting the mitotic oscillator and the control of cell proliferation: insights from a cascade model for cdc2 kinase activation

We consider a minimal cascade model previously proposed for the mitotic oscillator driving the embryonic cell division cycle. The model is based on a bicyclic phosphorylation-dephosphorylation cascade involving cyclin and cdc2 kinase. By constructing stability diagrams showing domains of periodic behavior as a function of the maximum rates of the kinases and phosphatases involved in the two cycles of the cascade, we investigate the role of these converter enzymes in the oscillatory mechanism. Oscillations occur when the balance of kinase and phosphatase rates in each cycle is in a range bounded by two critical values. The results suggest ways to arrest the mitotic oscillator by altering the maximum rates of the converter enzymes. These results bear on the control of cell proliferation.

Parameters:

Name Description
V_4 0.5
v_i 0.05
k_d 0.01
K_c 0.5
v_d 0.25
V_2 1.5
K_d 0.02
V_M1 3.0
K_3 0.01
K_1 0.01
V_M3 1.0
K_2 0.01
K_4 0.01

States:

Name Description
M(time) 0.1
X(time) 0.1
C(time) 0.1

Observables: none

362

362 @ v0.0.1

Aslanidi 2009

nothing

Parameters:

Name Description
gamma_Cai 1.0
gamma_Cao 0.341
rcg 2.0
km_b_SR 0.00087
T 310.0
TRPN_max 0.07
stim_start 0.0
p_Cl 4.0e-7
p_Ca 0.000243
CT_Na_Cl_max 9.8443e-6
dq_up_Ca_MK_max 0.75
g_NaK 0.61875
length 0.01
g_K_b 0.005
q_leak_max 0.004375
i_NaCa_max 4.5
b_SL_max 1.124
Vol_cell 0.3454
km_Na_i_2 10.0
km_Ca_p 0.0005
CMDN_max 0.05
km_to_2 0.1502
Cm 1.0
z_Cl -1.0
p_Ca_b 1.995084e-7
km_CMDN 0.00238
km_Ca_MK 0.15
tau_ro 3.0
km_Ca_i 0.0036
dkm_plb_max 0.00017
k_sat 0.27
g_K_p 0.00276
g_Cl_b 0.000225
km_K_o 1.5
km_b_SL 0.0087
g_Ca_L 0.3392328
tau_tr 120.0
km_TRPN 0.0005
km_up 0.00092
b_SR_max 0.047
beta_Ca_MK 0.00068
Na_o 140.0
g_to_1 0.14135944
Ca_MK_0 0.05
Ca_o 1.8
CT_K_Cl_max 7.0756e-6
X_NaCa 0.4
stim_end 1.0
radius 0.0011
km_Ca_o 1.3
K_o 5.4
q_up_max 0.004375
z_Ca 2.0
tau_ss 0.2
km_CSQN 0.8
X_q_up 0.5
km_Na_i_1 12.3
g_Na 8.0
NSR_max 15.0
r_NaK 0.01833
stim_amplitude -80.0
i_Ca_p_max 0.0575
tau_Ca_MK_max 10.0
CSQN_max 10.0
g_Ca_T 0.13
Cl_o 100.0
alpha_Ca_MK 0.05
g_Na_L 0.037375
g_Na_b 0.0025
km_Na_o 87.5
R 8314.0
F 96485.0
km_Ca_act 0.000125

States:

Name Description
h_L(time) 0.8946968372659203
Cl_i(time) 18.904682470140408
xr(time) 0.07084939408222911
Ca_NSR(time) 1.2132524695849454
Ca_MK_trap(time) 8.789168284782809e-6
f(time) 0.9985607329462358
m_L(time) 0.002003390432234504
xs1(time) 0.0011737654433043125
j(time) 0.09866447258167589
f_Ca2(time) 0.868690796671854
m(time) 0.002003390432234504
ro(time) 1.2785734760674763e-9
xs2(time) 0.001179442867470093
Na_i(time) 9.927155552932733
d(time) 2.322223865147363e-6
g(time) 0.9720432601848331
V(time) -83.43812846286808
f2(time) 0.8173435436674658
h(time) 0.9786390933308567
i(time) 0.9990935802459496
a(time) 0.0004238729429342389
i2(time) 0.9777368439681764
K_i(time) 141.9670801746057
Ca_JSR(time) 1.1433050636518596
b(time) 0.0002563937630984438
f_Ca(time) 0.9610551285529658
Ca_r(time) 0.00022418117117903934
Ca_i(time) 0.00022355433459434943
ri(time) 0.7802870066567904

Observables: none

363

363 @ v0.0.1

Bagci 2008

nothing

Parameters:

Name Description
k_1NO 1.0
k_09 0.5
k_17NO 66.0
k_18NO 1.0
k_f8 0.1
k_20NO 66.0
Cyt_c 400.0
O_2 35.0
k_12aNO 6.0e-6
k_22NO 66.0
k_8NO 0.058
k_15b 5.0
k_13 10.0
k_6NO 0.00135
u 0.006
k_07 0.0035
k_14b 5.0
k_04 0.5
k_f6b 0.1
k_13NO 1600.0
k13 10.0
k_f3 0.1
GSH_0 10000.0
P_Pro9 0.0003
GPX 5.8
k_15 5.0
k_16b 10.0
k_15NO 100.0
k_01b 0.5
P_Pro3 0.0003
k_03 0.5
k11 10.0
k_f9 0.1
k_15c 5.0
k_06 0.5
k_10 10.0
k_16NO 1.21
FeLn_0 0.05
k14 10.0
k_m 50.0
k_02 0.5
k_17bNO 0.0002
k_19 10.0
P_oBcl_2 8.0e-5
k_05 0.0035
k_18 10.0
CO_2 1000.0
P_Cytc_mito 0.0003
k_9NO 0.025
p53 0.0066
k_2NO 0.1
k_10NO 0.0006
k_16 10.0
p53_thresh 0.004
k_4NO 6700.0
k_11NO 66.0
k_12 10.0
k_05b 0.0035
u_Bax 0.006
k_11 5.0
k12b 10.0
k_f0 0.1
P_Apaf_1 0.0003
k_06b 0.5
k_f6 0.001
u_Bcl_2 0.006
k_08 0.5
SOD 10.0
P_oBax 3.0e-5
k_7NO 2.0
k_00 0.5
k_21NO 66.0
k_01 0.5
k_19NO 10.0
k_05c 0.0035
k_12bNOp 1100.0
k12a 10.0
P_IAP 3.0e-5
k_12bNOm 81000.0
k_04b 0.5
k_14 5.0
P_Bid 3.0e-5
k_5NO 2400.0
PTPC_0 0.0
k_14NO 0.0002
k_11b 50000.0
v_m 320.0
k_17 5.0
p 4.0
k_1 1.0

States:

Name Description
IAP(time) 0.004
Casp3IAP(time) 0.0
Bcl_2(time) 0.004
FeLnNO(time) 0.0
NO_2(time) 0.0
Casp9IAP(time) 0.0
ApopCasp9_2Pro3(time) 0.0
NO(time) 0.0
ApopCasp9(time) 0.0
O_2m(time) 35.0
Casp9Pro3(time) 0.0
Apop(time) 0.0
Bax_2(time) 0.0
tBid(time) 0.0
Casp8(time) 0.0
FeLn(time) 0.05
Casp3(time) 0.0
GSH(time) 10000.0
PTPC(time) 0.0
ApopPro9_2(time) 0.0
ONOO_m(time) 0.0
ApopPro9(time) 0.0
tBid_mito(time) 0.0
tBidBax(time) 0.0
Cytc(time) 0.0
ApopCasp9IAP(time) 0.0
Casp8Bid(time) 0.0
CcOX(time) 0.1
Casp3Bcl_2(time) 0.0
CytcApaf_1(time) 0.0
Casp9(time) 0.0
ApopCasp9_2(time) 0.0
Pro9(time) 0.004
GSNO(time) 0.0
ApopCasp9_2IAP(time) 0.0
Casp3Bid(time) 0.0
Bid(time) 0.004
Pro3(time) 0.004
Cytc_mito(time) 0.004
N2O3(time) 0.0
Bax(time) 0.004
Apaf_1(time) 0.004

Observables: none

364

364 @ v0.0.1

Barberis, Klipp, Vanoni, Alberghina, 2007

nothing

Parameters:

Name Description
k_37 4363.6
k_25 0.55
k_1 0.03523
k_22 0.01
k_18 0.0008
k_29 0.55
k_19 0.01
k_5 4.2e-5
k_28 2.82
k_16 0.03
k_44 0.005
k_2 0.03523
k_39 1.0
k_30 42300.0
k_12 0.1
k_13 0.35
k_40 1.0
k_3 0.32
k_53 0.001
k_11 0.12
k_33 0.55
k_50 0.6
k_49 0.001
k_45 0.005
k_52 0.005
k_36 4363.6
k_21 0.0
k_4 0.32
k_15 0.01
k_32 84.6
k_46 0.1
k_43 0.005
k_23 0.01
k_41 1.0
k_24 2.82
k_27 0.55
k_20 0.01
k_42 0.005
k_8 4.0e-5
k_51 0.6
k_14 0.01
k_38 4363.6
k_7 0.01
k_10 0.12
k_47 1.0
k_growth 0.0051
k_48 0.012
k_31 0.55
k_6 1.0e-5
k_35 0.0005
k_9 5.0e-5
k_17 0.01
k_26 2.82
k_34 8.46

States:

Name Description
whi5p_c(time) 0.0
far1_c(time) 0.0037926
cdk1cln3far1_n(time) 0.0
sic1_c(time) 0.039234
sbfwhi5_n(time) 0.025544
cdk1cln2_c(time) 0.0
v_c(time) 0.5
cdk1clb5sic1_n(time) 0.0
cln3_c(time) 0.000485
cln3_n(time) 0.0
cdk1cln3far1p_n(time) 0.0
sbf_n(time) 0.0
cdk1cln3_n(time) 0.0
cdk1clb5_n(time) 0.0
cdk1clb5_c(time) 0.0
far1P_n(time) 0.0
far1_n(time) 0.0
cdk1cln2_n(time) 0.0
cdk1clb5sic1_c(time) 0.0
v_n(time) 0.5
sbfwhi5p_n(time) 0.0
mcln2_n(time) 0.0
mclb5_n(time) 0.0
cdk1_n(time) 0.0074127
whi5_c(time) 0.073564
cln2_c(time) 0.0
mclb5_c(time) 0.0
cdk1_c(time) 0.333333
whi5p_n(time) 0.0
clb5_c(time) 0.0
whi5_n(time) 0.0
mcln2_c(time) 0.0
sic1P_n(time) 0.0
cdk1clb5sic1p_n(time) 0.0

Observables: none

366

366 @ v0.0.1

Bental, 2006

nothing

Parameters:

Name Description
P_w 47.0
V_T 0.41
V_D 0.151
sigma_c 3.3e-5
L 1.712e8
r_2 0.12
K_T 10000.0
P_m 760.0
E 2.5
sigma 1.4e-6
D_o 1.56e-5
omega 1.256637
T_h 0.002
f_om 0.21
K_R 3.6e6
V_c 0.071
l_2 164000.0
R 1.0
D_c 3.16e-5
f_cm 0.0

States:

Name Description
P_A(time) 760.0
f_o(time) 0.1368
f_c(time) 0.05263
p_o(time) 40.0
p_c(time) 46.0
z(time) 4.4219e-7
V_A(time) 1.0

Observables: none

369

369 @ v0.0.1

Chen, Calzone, Csikasznagy, Cross, Novak, Tyson, 2004

This workspace contains a SED-ML file for the original model as shown in the paper.

Parameters:

Name Description
ks_bud 0.2
Ji_tem 0.1
epsilon_sbf_n2 2.0
ks_n2__ 0.15
epsilon_sbf_n3 10.0
ka_apc 0.1
kd_b2__ 0.4
kd_swi 0.08
kas_esp 50.0
kas_rent 200.0
ki_mcm 0.15
Ja_apc 0.1
kdi_rentp 2.0
kd_net 0.03
epsilon_f6_k2 0.03
ks2_pds__ 0.055
kd3_c1 1.0
Jspn 0.14
kas_f5 0.01
Kez2 0.2
ks_b2__ 0.04
C0 0.4
kd1_pds_ 0.01
Ji_apc 0.1
epsilon_c1_n2 0.06
epsilon_cdh_n2 0.4
epsilon_f6_n2 0.06
ks_20__ 0.6
kd1_c1 0.01
Cdc15_T 1.0
kg 0.007702
ks_f6___ 0.004
ka_15_ 0.002
kd_b5__ 0.16
kpp_c1 4.0
epsilon_c1_n3 0.3
ka_cdh_ 0.01
J20_ppx 0.15
ks_f6_ 0.024
ks_c1_ 0.012
ks_ori 2.0
epsilon_ori_b5 0.9
Ja_tem 0.1
epsilon_sbf_b5 2.0
epsilon_f6_b5 0.1
epsilon_bud_n2 0.25
kpp_f6 4.0
ks_swi__ 0.08
ks_b2_ 0.001
ks_swi_ 0.005
ka_cdh__ 0.8
ks_20_ 0.006
kkp_net__ 0.6
epsilon_cdh_b2 1.2
Tem1_T 1.0
epsilon_bud_n3 0.05
kas_b2 50.0
kd_20 0.3
kd_n2 0.12
epsilon_c1_b2 0.45
ka_mcm 1.0
ks_b5_ 0.0008
ks1_pds__ 0.03
Ji_mcm 0.1
ka_20__ 0.2
ks_cdh 0.01
ks_net 0.084
ks_c1__ 0.12
epsilon_f6_n3 0.3
Ji_cdh 0.03
ki_15 0.5
epsilon_c1_b5 0.1
ks_pds_ 0.0
ka_swi 2.0
kd_14 0.1
Jd2_f6 0.05
ka_sbf 0.38
ki_cdh_ 0.001
Esp1_T 1.0
kas_b5 50.0
kas_rentp 1.0
ki_sbf_ 0.6
kd_ppx_ 0.17
kd2_f6 1.0
kpp_net_ 0.05
ki_sbf__ 8.0
kd2_pds__ 0.2
ki_apc 0.15
epsilon_bud_b5 1.0
ks_n2_ 0.0
Kez 0.3
kd_ppx__ 2.0
ks_spn 0.1
kkp_net_ 0.01
epsilon_cdh_b5 8.0
kdi_f2 0.5
kd3_pds__ 0.04
kd_b5_ 0.01
kdi_b5 0.06
kd1_f6 0.01
kd2_c1 1.0
kdi_f5 0.01
ka_15__ 1.0
Ja_cdh 0.03
Ji_sbf 0.01
Jpds 0.04
Jd2_c1 0.05
epsilon_c1_k2 0.03
epsilon_ori_b2 0.45
ki_cdh__ 0.08
kd_ori 0.06
Dn3 1.0
kpp_net__ 3.0
Ja_sbf 0.01
ki_swi 0.05
ks_14 0.2
kd_spn 0.06
kd_b2p 0.15
kdi_b2 0.05
kas_f2 15.0
epsilon_f6_b2 0.55
Jn3 6.0
kd3_f6 1.0
kd_b2_ 0.003
ka_20_ 0.05
kd_cdh 0.01
epsilon_cdh_n3 0.25
Ja_mcm 0.1
kd_bud 0.06
B0 0.054
ka_15___ 0.001
ks_f6__ 0.12
kdi_rent 1.0
kdi_esp 0.5
ks_b5__ 0.005
ks_ppx 0.1

States:

Name Description
Swi5(time) 0.9562
Clb5(time) 0.0518
Cdc14_T(time) 2.0
Cdh1_T(time) 1.0
Net1(time) 0.0186
Net1_T(time) 2.8
Sic1P(time) 0.0064
C2(time) 0.2384
Cdh1(time) 0.9305
Pds1(time) 0.0256
C2P(time) 0.024
Sic1(time) 0.0229
F2P(time) 0.0274
Swi5_T(time) 0.9765
Cdc15(time) 0.6565
F5(time) 7.2e-5
mass(time) 1.206
Cln2(time) 0.0652
BUD(time) 0.0085
C5P(time) 0.0069
C5(time) 0.0701
Cdc20_A(time) 0.4443
Cdc6(time) 0.1076
RENT(time) 1.0495
APC_P(time) 0.1015
SPN(time) 0.0305
ORI(time) 0.0009
PPX(time) 0.1232
Clb2(time) 0.1469
Esp1(time) 0.3013
F5P(time) 7.9e-6
Cdc6P(time) 0.0155
Tem1(time) 0.9039
F2(time) 0.2361
Cdc20_T(time) 1.9163
Cdc14(time) 0.4683

Observables: none

394

394 @ v0.0.1

Kholodenko, Demin, Moehren, Hoek, 1999

nothing

Parameters:

Name Description
k14 6.0
k18 0.3
k25 1.0
k9 0.003
k15_ 0.0009
k6_ 0.05
k12_ 0.0001
k21_ 0.1
k10_ 0.06
K16 340.0
k1_ 0.06
k5_ 0.2
V8 1.0
k12 0.0015
K4 50.0
K8 100.0
k3 1.0
k17 0.003
k22_ 0.064
k20 0.12
k21 0.003
k10 0.01
k13 0.09
k18_ 0.0009
k7_ 0.006
k15 0.3
V16 1.7
k23_ 0.021
k20_ 0.00024
k19 0.01
k9_ 0.05
k14_ 0.06
k22 0.03
k13_ 0.6
k6 1.0
k11 0.03
k23 0.1
V4 450.0
k11_ 0.0045
k17_ 0.1
k3_ 0.01
k1 0.003
k2_ 0.1
k7 0.3
k24_ 0.0429
k25_ 0.03
k19_ 0.0214
k5 0.06
k24 0.009
k2 0.01

States:

Name Description
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

Observables: none

4


486

486 @ v0.0.1

Computational analysis of the human sinus node action potential: model development and effects of mutations

nothing

Parameters:

Name Description
C 5.7e-5
Km_fCa 0.000338
Km_Kp 1.4
EC50_SR 0.45
Ko 5.4
Nai_clamp 1.0
t_holding 0.5
Qco 0.0
V_nsr_part 0.0116
kf_TMM 2277.0
blockade_NaCa 0.0
Kco 3.663
clamp_mode 0.0
kf_CM 1.642e6
kim 5.0
tau_tr 0.04
g_Kr 0.00424
kf_CQ 175.4
V_i_part 0.46
ACh 0.0
P_CaL 0.4578
CQ_tot 10.0
K_up 0.000286113
Cao 1.8
Mgi 2.5
Ki 140.0
Qn 0.4315
koCa 10000.0
K3no 4.663
K2ni 2.289
ks 1.480410851e8
kb_CQ 445.0
Qci 0.1369
Nao 140.0
HSR 2.5
alpha 0.5927
g_f 0.00427
kb_TMC 7.51
g_KACh 0.00345
L_cell 67.0
P_CaT 0.04132
R_cell 3.9
F 96485.3415
Iso_1_uM 0.0
K3ni 26.44
T 310.0
slope_up 5.0e-5
TC_tot 0.031
kf_TC 88800.0
Km_Nap 14.0
K1ni 395.3
blockade 0.0
i_NaK_max 0.08105
MaxSR 15.0
Kcni 26.44
L_sub 0.02
g_to 0.0035
alpha_fCa 0.0075
t_test 0.5
shift_fL 0.0
kb_TC 446.0
P_up_basal 5.0
V_holding -45.0
TMC_tot 0.062
delta_m 1.0e-5
ACh_on 1.0
y_shift 0.0
k_dL 4.3371
k_fL 0.0
K1no 1628.0
kb_CM 542.0
Km_f 45.0
K2no 561.4
tau_dif_Ca 5.469e-5
kb_TMM 751.0
kom 660.0
kf_TMC 227700.0
MinSR 1.0
kiCa 500.0
Kci 0.0207
g_Na 0.0223
offset_fT 0.0
V_jsr_part 0.0012
V_dL -16.4508
CM_tot 0.045
g_Kur 0.0001539
K_NaCa 3.343
V_test -35.0
g_Ks_ 0.00065
R 8314.472
g_Na_L 0.0

States:

Name Description
paS(time) 0.283185
paF(time) 0.011068
V_ode(time) -47.787168
dT(time) 0.268909
I(time) 4.595622e-10
piy(time) 0.709051
y(time) 0.009508
s_Kur(time) 0.845304
fT(time) 0.020484
fCQ(time) 0.138975
O(time) 6.181512e-9
Ca_nsr(time) 0.435148
fTC(time) 0.017929
Ca_sub(time) 6.226104e-5
fCMs(time) 0.158521
n(time) 0.1162
fTMC(time) 0.259947
m(time) 0.447724
q(time) 0.430836
Ca_jsr(time) 0.409551
RI(time) 0.069199
Nai_(time) 5.0
fTMM(time) 0.653777
h(time) 0.003058
a(time) 0.00277
r_Kur(time) 0.011845
fCa(time) 0.844449
fCMi(time) 0.217311
r(time) 0.014523
R(time) 0.9308
dL(time) 0.001921
Cai(time) 9.15641e-6
fL(time) 0.846702

Observables: none

496

496 @ v0.0.1

BG Mica models

Bond graph models for teaching physics in the context of Mica instrumentation

Parameters:

Name Description
E_2 2.0
omega_ref 1.0
R_2 0.4
E_1 0.0
L_1 0.0
Bl 10.0
L_2 0.018
R_1 0.0
amplitude_ref 1.0
phase_ref 1.0

States:

Name Description
omega(t) 0.1

Observables: none

5


593

593 @ v0.0.1

paci_hyttinen_aaltosetala_severi_2013

nothing

Parameters:

Name Description
nifed_10nM 0.0
T 310.0
c_rel 8.232
PNaK 1.841424
Buf_C 0.25
Chromanol_iKs70 0.0
i_stim_Amplitude 5.5e-10
Kbuf_SR 0.3
tau_g 0.002
a_rel 16.464
Ko 5.4
nifed_30nM 0.0
g_to 29.9038
Cm 9.87109e-11
E4031_100nM 0.0
Chromanol_iKs90 0.0
TTX_3uM 0.0
Chromanol_iKs50 0.0
KmNai 87.5
tau_fCa 0.002
b_rel 0.25
TTX_10uM 0.0
g_Ks 2.041
VmaxUp 0.56064
i_stim_PulseDuration 0.005
g_K1 28.1492
g_Kr 29.8667
Kup 0.00025
E_f -0.017
Kbuf_C 0.001
Km_Na 40.0
L0 0.025
g_b_Ca 0.69264
Q 2.3
Cao 1.8
KPCa 0.0005
V_SR 583.73
Ki 150.0
KmCa 1.38
i_stim_frequency 60.0
g_b_Na 0.9
nifed_100nM 0.0
i_stim_End 800.0
Vc 8800.0
Buf_SR 10.0
Ksat 0.1
PkNa 0.03
Nao 151.0
i_stim_Start 0.0
alpha 2.8571432
E4031_30nM 0.0
g_Na 3671.2302
g_f 30.10312
nifed_3nM 0.0
g_PCa 0.4125
V_leak 0.00044444
kNaCa 4900.0
Chromanol_iKs30 0.0
Km_K 1.0
TTX_30uM 0.0
g_CaL 8.635702e-5
gamma 0.35
stim_flag 0.0
R 8.314472
F 96485.3415

States:

Name Description
d(time) 8.96088425225182e-5
g(time) 0.999999981028517
Xr1(time) 0.00778547011240132
h(time) 0.786926637881461
f2(time) 0.999965815466749
f1(time) 0.970411811263976
Xs(time) 0.0322944866983666
fCa(time) 0.998925296531804
Xr2(time) 0.432162576531617
r(time) 0.00573289893326379
j(time) 0.253943221774722
Xf(time) 0.100615100568753
Vm(time) -0.0743340057623841
m(time) 0.102953468725004
Ca_SR(time) 0.2734234751931
Cai(time) 1.80773974140477e-5
Nai(time) 10.9248496211574
q(time) 0.839295925773219

Observables: none

595

595 @ v0.0.1

Grandi et al. 2011 Atrial Action Potential and Ca2+ Model

Atrial AP model by Eleonora Grandi, Sandeep V. Pandit, Niels Voigt, Antony J. Workman, Dobromir Dobrev, José Jalife, and Donald M. Bers

Parameters: none

States: none

Observables: none

6


612

612 @ v0.0.1

Generic mouse colon scaffold

Annotated colon scaffold for mouse available for registration of segmented neural anatomical-functional mapping of enteric neural circuits. See SPARC portal for more details

Parameters: none

States: none

Observables: none

613

613 @ v0.0.1

Generic pig colon scaffold

Annotated colon scaffold for pig available for registration of segmented neural anatomical-functional mapping of enteric neural circuits. See SPARC portal for more details

Parameters: none

States: none

Observables: none

614

614 @ v0.0.1

Generic human colon scaffold

Annotated colon scaffold for human available for registration of segmented neural anatomical-functional mapping of enteric neural circuits. See SPARC portal for more details

Parameters: none

States: none

Observables: none

615

615 @ v0.0.1

Generic rat stomach scaffold

Annotated stomach scaffold for rat available for registration of segmented neural anatomical-functional mapping of enteric neural circuits. See SPARC portal for more details

Parameters: none

States: none

Observables: none

616

616 @ v0.0.1

Generic rat heart scaffold

Annotated heart scaffold for rat available for registration of segmented neural anatomical-functional mapping of cardiac neural circuits. See SPARC portal for more details

Parameters: none

States: none

Observables: none

617

617 @ v0.0.1

Generic rat bladder scaffold

Annotated bladder scaffold for rat available for registration of segmented neural anatomical-functional mapping of LUT neural circuits. See SPARC portal for more details

Parameters: none

States: none

Observables: none

618

618 @ v0.0.1

Generic cat bladder scaffold

Annotated bladder scaffold for cat available for registration of segmented neural anatomical-functional mapping of LUT neural circuits. See SPARC portal for more details

Parameters: none

States: none

Observables: none

619

619 @ v0.0.1

Generic pig heart scaffold

Annotated heart scaffold for pig available for registration of segmented neural anatomical-functional mapping of cardiac neural circuits. See SPARC portal for more details

Parameters: none

States: none

Observables: none

630

630 @ v0.0.1

Koivumäki, Korhonen, Tavi 2011 Atrial AP model

Model of the human atrial AP by Koivumäki, Korhonen & Tavi, 2011

Parameters:

Name Description
cpumps 0.04
T 306.15
SLhigh 13.0
gam 0.45
tau_act 0.01875
KdBCa 0.00238
tau_inactss 0.015
DCa 780.0
Ko 5.4
PNa 0.0018
fCaNCX 1.0
dx 1.625
gKs 1.0
Cm 0.05
kNaKNa 11.0
DCaBm 25.0
kNaKK 1.0
DNa 0.12
rjunct 6.5
KdCSQN 0.8
DCaSR 44.0
gCab 0.0952
kCaP 0.0005
BCa 0.024
kCan 2.0
ECa_app 60.0
tau_actss 0.005
kSRleak 0.006
tau_inact 0.0875
SERCAKmr 1.8
INaKmax 70.8253
gKr 0.5
Cao 1.8
kCa 0.001
ical_fca_tau 0.002
KdSLlow 1.1
KdBNa 10.0
SLlow 165.0
CSQN 6.7
duration 0.001
gCaL 25.3125
k4 7.5
period 1.0
SERCAKmf 0.00025
lcell 122.051
tau_adapt 1.0
Nao 130.0
dNaCa 0.0003
offset 0.01
gNab 0.060599
pi 3.141592653589793
ICaPmax 2.0
gIf 1.0
kNaCa 0.0084
Vss 4.99232e-5
KdSLhigh 0.013
R 8314.0
F 96487.0

States:

Name Description
o1(time) 9.478514e-5
Cai4(time) 0.0001561844
o2(time) 7.765503e-5
fca(time) 0.9744374
Cai2(time) 0.0001381421
y(time) 0.05620665
c2(time) 0.9995086
a3(time) 0.004326409
css(time) 0.9999717
Cai1(time) 0.0001354965
o3(time) 5.674947e-5
n(time) 0.004109751
Cai3(time) 0.0001442087
m(time) 0.002775812
Nai(time) 9.28686
s(time) 0.954338
CaSR2(time) 0.6076289
Cass(time) 0.0001619377
a1(time) 0.004638565
d(time) 1.060917e-5
pa(time) 4.189417e-5
CaSR1(time) 0.6189225
h2(time) 0.9039673
CaSR3(time) 0.5905266
f2(time) 0.9988624
V(time) -75.42786
c1(time) 0.9993722
CaSR4(time) 0.5738108
f1(time) 0.9988566
Ki(time) 134.6313
r(time) 0.0009594258
oss(time) 3.975097e-5
h1(time) 0.90391
ass(time) 0.004250445
Nass(time) 8.691504
c3(time) 0.9995604
a2(time) 0.004512078

Observables: none

633

633 @ v0.0.1

Voigt, Heijman et al. 2013 human atrial AP model

Model of the human atrial action potential by Voigt, Heijman et al.

Parameters:

Name Description
nu 0.35
pNaK 0.01833
C 1.381e-10
koff_myoca 0.00046
kon_tncl 32.7
koff_tnchmg 0.00333
KmCao 1.3
KdClCa 0.1
kon_tnchca 2.37
Bmax_myosin 0.14
koff_na 0.001
koff_tnchca 3.2e-5
kim 0.005
ksat 0.27
gNaB 0.000597
koff_sr 0.06
Na_o 140.0
Constitutive_Frac 0.0
fcaCaMSL 0.0
KmNaip 11.0
IK1_Fact 2.1
gNa 23.0
KmPCa 0.0005
gKp 0.002
ks 25.0
Bmax_Na_sl 1.65
gClCa 0.0548
Fjn_CaL 0.9
Kmr 1.7
offset 50.0
koff_slh 0.03
kon_na 0.0001
pi 3.141592653589793
kon_myoca 13.8
hillSRCaP 1.787
KmCai 0.00359
F 96485.0
Bmax_Na_jn 7.561
T 310.0
KmNao 87.5
Q10CaL 1.8
IbarNaK 1.26
kon_slh 100.0
kon_sr 100.0
koff_csqn 65.0
Mg_i 1.0
AF 0.0
Q10SRCaP 2.6
inal_hl_tau 600.0
gCaB 0.00060643
kon_cam 34.0
KmKo 1.5
MaxSR 15.0
fcaCaj 0.0
KmNai 12.29
ec50SR 0.45
koff_myomg 5.7e-5
Bmax_TnClow 0.07
IbarSLCaP 0.0471
Bmax_CaM 0.024
Ca_o 1.8
duration 0.5
kon_sll 100.0
Kdact 0.000384
Fjn 0.11
Bmax_TnChigh 0.14
period 1000.0
kom 0.06
K_o 5.4
MinSR 1.0
Vmax_SRCaP 0.0053114
Q10NCX 1.57
kon_tnchmg 0.003
Cl_i 15.0
kiCa 0.5
koff_sll 1.3
gClB 0.009
CCh 0.0
kon_csqn 100.0
cell_length 100.0
cell_radius 10.25
kon_myomg 0.0157
Cl_o 150.0
koff_tncl 0.0196
koff_cam 0.238
R 8314.0
Q10SLCaP 2.35

States:

Name Description
NaB_sl(time) 0.7910872172521405
Myoc(time) 0.0037960884452301414
SRB(time) 0.0043138341336658535
Na_sl(time) 9.205596316266082
SLL_sl(time) 0.02051310458749874
SLH_jn(time) 0.10075493394087875
x(time) 0.004424059763108028
y(time) 0.9523962844989157
f(time) 0.9987600221985378
hl(time) 0.05181171143249535
j(time) 0.8925014414924747
Na_jn(time) 9.204849700722741
SLH_sl(time) 0.1860552421436766
m(time) 0.007974267944916322
Ca_jn(time) 0.00030733308537360534
TnCHm(time) 0.005911067986333375
s(time) 0.9629504586432251
ml(time) 0.007974267944905819
Na_i(time) 9.20582356442187
TnCL(time) 0.01773055279803314
Ca_sl(time) 0.00022313421414786036
d(time) 1.677502822734765e-5
Ca_sr(time) 0.48578449149189934
NaB_jn(time) 3.6252756041992815
fCaB_jn(time) 0.042406684547122694
SLL_jn(time) 0.012812216114372279
o(time) 1.7337771060382367e-6
i(time) 4.163512356558445e-7
V(time) -74.97388771859164
h(time) 0.8709554637486303
K_i(time) 120.0
fCaB_sl(time) 0.03137179897719969
Csqn(time) 1.1120413257676331
CaM(time) 0.000673710089221737
r(time) 0.00032887242349569686
Myom(time) 0.13569148958168384
Ca_i(time) 0.00020205482525225072
TnCHc(time) 0.12740593502976583

Observables: none

A


acikgoz_2009 @ v0.0.1

Two compartment model of diazepam biotransformation in an organotypical culture of primary human hepatocytes

Drug biotransformation is one of the most important parameters of preclinical screening tests for the registration of new drug candidates. Conventional existing tests rely on nonhuman models which deliver an incomplete metabolic profile of drugs due to the lack of proper CYP450 expression as seen in human liver in vivo. In order to overcome this limitation, we used an organotypical model of human primary hepatocytes for the biotransformation of the drug diazepam with special reference to metabolites in both the cell matrix phase and supernatant and its interaction of three inducers (phenobarbital, dexamethasone, aroclor 1254) in different time responses (1, 2, 4, 8, 24 h).

This model runs in OpenCell to reproduce the results in figure 3 of the published paper. There are four model versions: control (a), aroclor (b), dexamethasone (c) and phenobarbital (d). Initial values were taken from the published graphs.

Parameters:

Name Description
p4 0.050607
p5 5.119458
p10 0.162463
p7 1.224656
p3 0.006932
p6 7.986374
p12 3.018396
p9 0.188594
p15 2.0e-6
p13 0.097796
p14 0.35925
p2 0.08547
p8 1.488771
p1 0.097884
p11 2.527205

States:

Name Description
c11(time) 9000.0
c51(time) 0.0
c32(time) 0.0
c22(time) 0.0
c31(time) 0.0
c21(time) 0.0
c41(time) 0.0
c12(time) 10000.0
c42(time) 0.0
c52(time) 0.0

Observables: none

adrian_chandler_hodgkin_1970 @ v0.0.1

Adrian, Chandler, Hodgkin, 1970

nothing

Parameters:

Name Description
EL -95.0
EK -70.0
v_beta_h 7.6
v_beta_m 18.0
ENa 50.0
En -40.0
v_alpha_m 10.0
gL_max 0.0024
alpha_m_max 0.208
alpha_h_max 0.0156
v_alpha_n 7.0
v_alpha_h 14.7
beta_h_max 3.382
Cm 0.009
Eh -41.0
Em -42.0
v_beta_n 40.0
IstimAmplitude 0.5
Rs 15.0
Am 200.0
IstimPulseDuration 1.0
gK_max 0.415
IstimEnd 50000.0
beta_n_max 0.09616
IstimPeriod 1000.0
beta_m_max 2.081
gNa_max 1.8
alpha_n_max 0.0229
IstimStart 10.0
Ct 0.04

States:

Name Description
Vm(t) -95.0
h(t) 1.0
n(t) 0.0
m(t) 0.0
Vt(t) -95.0

Observables: none

aguda_b_1999 @ v0.0.1

Aguda, B, 1999

nothing

Parameters:

Name Description
k14 0.0005
kn7 0.01
k21 0.01
k20 0.1
k18 1.0
k9 1.0
k13 1.0
kn2 0.01
k10 0.0
k15 0.01
kn3_ 0.0
Chk1_T 1.0
kn23 1.0
k8 0.1
kPlk1_ 0.0
k9_ 0.0
k14_ 1.0
k4 0.0
k8_ 0.0
k22 0.1
k6 0.01
kex 1.0
k11 1.0
kn1 10.0
kn9 1.0
k12 0.1
kctak1_ 0.0
kn18 0.01
kctak1 0.0
k16 0.0002
k23 0.1
k1 1.0
k3_ 100.0
k2_ 0.1
kPlk1 0.0
k7 1.0
V_in 1.0e-5
k17 0.1
k5 1.0
k2 0.1
kn8 0.01

States:

Name Description
iCdc25Ps216(time) 2.0e-5
p21(time) 0.0
preMPF(time) 1.0e-6
Wee1(time) 0.001
Chk1P(time) 1.0e-6
Rad3(time) 0.0
aCdc25Ps216(time) 0.0
p53(time) 0.0
aCdc25(time) 1.0e-6
Wee1P(time) 0.0
iCdc25(time) 1.0e-6
p21_MPF(time) 0.0
MPF(time) 1.0e-8
iCdc25Ps216_protein1433(time) 0.03
protein1433(time) 2.0

Observables: none

aguda_tang_1999 @ v0.0.1

Aguda, Tang, 1999

nothing

Parameters:

Name Description
k20 0.01
k21 0.1
k18 0.0001
k9 2.0
k25 0.01
kn2 1.0
k10 0.035
k26 0.01
V_23 0.2
k29 0.001
k8 2.0
k19 0.05
k22 0.001
V_6 0.018
k1_ 0.5
kn1 0.001
V_4 1.0e-6
V_27 0.01
V_7 0.0001
kn4 0.016
k1 0.1
k3_ 0.0
k1__ 0.5
k26_ 0.1
k28 0.01
k3 1.42
k17 3.5
kn6 5.0
k5 0.02
k24 0.1
k2 0.1
k25_ 0.02

States:

Name Description
a_CyclinE_Cdk2(time) 0.0
i_CyclinE_Cdk2(time) 0.01
E2F(time) 0.0
pRB_E2F(time) 1.95
pRB_P(time) 0.01
p16(time) 5.0
CycE_Cdk2_p27(time) 1.0
CycD_Cdk4(time) 0.0
p27(time) 5.0
pRB(time) 0.05
CycD_Cdk4_p27(time) 0.0

Observables: none

albrecht_colegrove_friel_2002 @ v0.0.1

Albrecht, Colegrove, Friel, 2002

nothing

Parameters:

Name Description
EC50_extru nothing
n_extru nothing
v_ER nothing
v_i nothing
I_Ca nothing
Pmax_RyR nothing
Ca_o nothing
Vmax_SERCA nothing
k_ER nothing
k_i nothing
EC50_SERCA nothing
n_SERCA nothing
n_RyR nothing
EC50_RyR nothing
k_leak_pm nothing
P_basal nothing
Vmax_extru nothing
F nothing

States:

Name Description
Ca_i(time) nothing
Ca_ER(time) nothing

Observables: none

albrecht_colegrove_hongpaisan_pivovarova_andrews_friel_2001 @ v0.0.1

Albrecht, Colegrove, Hongpaisan, Pivovarova, Andrews, Friel, 2001

nothing

Parameters:

Name Description
EC50_extru nothing
n_extru nothing
v_ER nothing
v_i nothing
k_leak nothing
I_Ca nothing
Pmax_RyR nothing
Ca_o nothing
Vmax_SERCA nothing
k_ER nothing
k_i nothing
EC50_SERCA nothing
n_SERCA nothing
n_RyR nothing
EC50_RyR nothing
Vmax_extru nothing
P_basal nothing
F nothing

States:

Name Description
Ca_i(time) nothing
Ca_ER(time) nothing

Observables: none

alexander_wahl_2010 @ v0.0.1

Alexander and Wahl 2010

nothing

Parameters:

Name Description
sigma1 3.0e-6
f 0.0001
lambdaE 1000.0
v_tilday 0.0025
v 125000.0
k 5.0e7
b3 0.25
muA 0.25
muE 0.25
sigma4 1.2e-5
muG 5.0
beta 200.0
sigma3 3.0e-6
pi3 0.0256
pi4 0.016
b4 1.0
pi1 0.016
gamma 2000.0
muR 0.25
b1 0.25

States:

Name Description
E(time) 0.0
A(time) 1.0
G(time) 1.0e8
R(time) 0.0

Observables: none

aon_cortassa_2002 @ v0.0.1

Aon, Cortassa, 2002

nothing

Parameters:

Name Description
PO 4.0
KATP_r 0.06
KDPG_m 0.002
gr_PK 0.1
V_ALD_max 2.5
KFDP_m 0.5
KNAD 0.18
cAMP 0.019
KPy__m 0.169
kf 3.0
Cn 9.0
G_o 1.0
V_HK_max 13.0
V_PFK_max 30.0
GDP 0.05
KpH 9.5e-9
NADP 1.0
V_PGK_max 3.0
cATP 1.0
KPEP_r 1.0
V_ADH_max 0.5
KPy_m 0.329
gr 10.0
NAD 1.0
Lo 25000.0
KTUB 0.4
K1 1.1
KG6P 0.05
K2 1.5
KADP_r 0.06
cFDP 0.01
n1 2.0
gt_PK 1.0
KATP 5.0
AMP 0.5
KG_in 0.001
CMTP 0.9
KG3P 0.0025
GTP 0.95
V_IN_max 10.0
KNADP 0.05
Ke_in 12.0
k4 0.02
V_GAPDH_max 10.0
kb 2.5
V_PKt_max 25.0
V_ALD_max_r 1.0
Lo_PK 1000.0
KG_m 0.11
KNADP_ 0.05
H 3.2e-8
V_TCA_max 10.0
KATP_m 0.1
NADH 0.01
V_G6PDH_max 1.6
cADP 1.0
C_PK 0.01
V_PKp_max 50.0
KAMP_r 0.025
KFDP_r 0.025
V_G6PDH_max_II 1.0
KNADH_i 0.0003
KG3P_m 20.0
KG_s 0.0062
kp3 0.05
cPEP 0.02
kdp 0.0025
kpol 10.0
cG6P 0.0005
KG6P_r 1.0
kp2 10.0
K3 2.5

States:

Name Description
PEP(time) 0.01
G6P(time) 0.01
CP(time) 1.2
G3P(time) 0.01
PKp(time) 0.005
ATP(time) 1.4
FDP(time) 0.01
DPG(time) 0.01
G(time) 0.01
Py(time) 0.01
CT(time) 0.2

Observables: none

Aorta_Brown_Shi_et_al_2012 @ v0.0.1

Workflows for analysis of valvular and aortic disease

Original data made available with permission of original authors. FieldML v0.4 and 0.5 representation created by Auckland Bioengineering Institute. This is a aortic coarctation model with four vessel branches in the aortic arch: namely the right subclavian artery, right common carotid artery, left common carotid artery and the left subclavian artery. The coarctation index (area ratio of the narrowest section to the normal section of the vessel) is 0.41. Clinical measurement gave a systolic peak to peak pressure gradient of 20.86mmHg, while our CFD simulation predicted a gradient of 24.04mmHg, which agreed well with the clinical data.

The figure shows a coarse mesh for demonstration purpose. In the CFD calculation we used a much dense mesh with 375695 nodes, 555027 tetrahedral elements and 543720 prism elements.

Parameters: none

States: none

Observables: none

aslanidi_atrial_model_2009 @ v0.0.1

Aslanidi Atrial Model 2009

nothing

Parameters:

Name Description
KmK1 0.59
T 308.0
stim_start 0.01
P_Na 1.4e-6
Mg_i 2.5
d_NaCa 0.0003
alpha_rel 200.0
k_NaK_K 1.0
i_NaK_max 0.06441
I_up_max 2.8
g_to 0.050002
k_CaP 0.0002
Cm 5.0e-5
shiftK1 -3.6
Ca_c 2.5
Vol_rel 4.4e-8
Vol_i 1.26e-5
k_rel 0.0003
Vol_up 3.969e-7
g_Ks 0.0025
g_K1 0.00508
k_xcs 0.4
tau_tr 0.01
g_Kr 0.0035
g_Ca_L 0.004
steepK1 1.393
stim_duration 0.0002
Na_c 140.0
g_B_Na 6.4e-5
E_Ca_T 38.0
stim_period 0.5
stim_end 100.0
PM 0.0
k_NaK_Na 11.0
k_srca 0.5
i_CaP_max 0.009509
Vol_c 2.5e-6
g_B_Ca 3.1e-5
stim_amplitude -20.0
k_cyca 0.0003
Vol_Ca 5.884e-6
CT 1.0
E_Ca_app 50.0
g_Ca_T 0.006
gamma 0.45
k_NaCa 2.0e-5
k_F3 0.815
R 8314.0
F 96487.0

States:

Name Description
O_TC(time) 0.014071
F3(time) 0.612697
s2(time) 0.39871
O_Calse(time) 0.465921
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) 0.029108
d_T(time) 0.00046
Ca_rel(time) 0.726776
h2(time) 0.61493
O_TMgMg(time) 0.693565
V(time) -80.0
K_c(time) 5.0
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) 0.288039
f_L(time) 0.99981
h1(time) 0.706
Ca_up(time) 0.730866
Ca_i(time) 7.1e-5
F2(time) 0.002262
O_TMgC(time) 0.214036

Observables: none

Aslanidi_etal_2010 @ v0.0.1

Aslanidi_etal_2010

Aslanidi, Sleiman, Boyett, Hancox, Zhang, 2010

Ionic mechanisms for electrical heterogeneity between rabbit Purkinje fiber and ventricular cells

Parameters: none

States: none

Observables: none

aslanidi_purkinje_model_2009 @ v0.0.1

Aslanidi 2009

nothing

Parameters:

Name Description
gamma_Cai 1.0
gamma_Cao 0.341
rcg 2.0
km_b_SR 0.00087
T 310.0
TRPN_max 0.07
stim_start 0.0
p_Cl 4.0e-7
p_Ca 0.000243
CT_Na_Cl_max 9.8443e-6
dq_up_Ca_MK_max 0.75
g_NaK 0.61875
length 0.01
g_K_b 0.005
q_leak_max 0.004375
i_NaCa_max 4.5
b_SL_max 1.124
Vol_cell 0.3454
km_Na_i_2 10.0
km_Ca_p 0.0005
CMDN_max 0.05
km_to_2 0.1502
Cm 1.0
z_Cl -1.0
p_Ca_b 1.995084e-7
km_CMDN 0.00238
km_Ca_MK 0.15
tau_ro 3.0
km_Ca_i 0.0036
dkm_plb_max 0.00017
k_sat 0.27
g_K_p 0.00276
g_Cl_b 0.000225
km_K_o 1.5
km_b_SL 0.0087
g_Ca_L 0.3392328
tau_tr 120.0
km_TRPN 0.0005
km_up 0.00092
b_SR_max 0.047
beta_Ca_MK 0.00068
Na_o 140.0
g_to_1 0.14135944
Ca_MK_0 0.05
Ca_o 1.8
CT_K_Cl_max 7.0756e-6
X_NaCa 0.4
stim_end 1.0
radius 0.0011
km_Ca_o 1.3
K_o 5.4
q_up_max 0.004375
z_Ca 2.0
tau_ss 0.2
km_CSQN 0.8
X_q_up 0.5
km_Na_i_1 12.3
g_Na 8.0
NSR_max 15.0
r_NaK 0.01833
stim_amplitude -80.0
i_Ca_p_max 0.0575
tau_Ca_MK_max 10.0
CSQN_max 10.0
g_Ca_T 0.13
Cl_o 100.0
alpha_Ca_MK 0.05
g_Na_L 0.037375
g_Na_b 0.0025
km_Na_o 87.5
R 8314.0
F 96485.0
km_Ca_act 0.000125

States:

Name Description
h_L(time) 0.8946968372659203
Cl_i(time) 18.904682470140408
xr(time) 0.07084939408222911
Ca_NSR(time) 1.2132524695849454
Ca_MK_trap(time) 8.789168284782809e-6
f(time) 0.9985607329462358
m_L(time) 0.002003390432234504
xs1(time) 0.0011737654433043125
j(time) 0.09866447258167589
f_Ca2(time) 0.868690796671854
m(time) 0.002003390432234504
ro(time) 1.2785734760674763e-9
xs2(time) 0.001179442867470093
Na_i(time) 9.927155552932733
d(time) 2.322223865147363e-6
g(time) 0.9720432601848331
V(time) -83.43812846286808
f2(time) 0.8173435436674658
h(time) 0.9786390933308567
i(time) 0.9990935802459496
a(time) 0.0004238729429342389
i2(time) 0.9777368439681764
K_i(time) 141.9670801746057
Ca_JSR(time) 1.1433050636518596
b(time) 0.0002563937630984438
f_Ca(time) 0.9610551285529658
Ca_r(time) 0.00022418117117903934
Ca_i(time) 0.00022355433459434943
ri(time) 0.7802870066567904

Observables: none

asthagiri_lauffenburger_2001 @ v0.0.1

Asthagiri, Lauffenburger, 2001

nothing

Parameters:

Name Description
kP3_plus 6.0e8
kP2_minus 30.0
kcat_P4 6.0
kP2_plus 6.0e8
A2_T 10000.0
kf_12 3.0e8
kcat_P3 6.0
k3_plus 6.0e8
kf 1.0e7
kc_12 3.0e8
kP5_minus 30.0
k4_minus 30.0
kP3_minus 30.0
k1_plus 6.0e8
kcat_5 6.0
k3_minus 30.0
kcat_z 6.0
kc 6.0e7
kx_plus 6.0e8
k2_minus 30.0
kcat_P5 6.0
R0 100000.0
kr 0.3
kc_minus 5.0
kc_plus 50.0
kcat_2 6.0
kcat_P2 6.0
kP1_plus 6.0e8
k1_minus 30.0
k2_plus 6.0e8
k4_plus 6.0e8
A1_T 10000.0
E5_T 10000.0
E4_T 10000.0
kx_minus 30.0
k5_plus 6.0e8
P3_T 5000.0
P1_T 5000.0
kP4_minus 30.0
kcat_3 6.0
kcat_P1 6.0
E3_T 10000.0
kcat_4 6.0
P2_T 5000.0
kcat_x 6.0
kz_plus 6.0e8
kf_2 3.0e8
E2_T 10000.0
P4_T 5000.0
kz_minus 30.0
kf_1 3.0e8
kcat_1 6.0
ku 60.0
kP4_plus 6.0e8
kP1_minus 30.0
k5_minus 30.0
kP5_plus 6.0e8
E1_T 10000.0
P5_T 5000.0

States:

Name Description
e1_star(time) 0.0
a1a2(time) 0.0
e5_star(time) 0.0
c(time) 0.0
e2_minus(time) 0.0
e2_star(time) 0.0
c2(time) 0.0
e1_star_p1(time) 0.0
e3_star(time) 0.0
e3_e2_star(time) 0.0
e4_e3_star(time) 0.0
e0_star_e4_star(time) 0.0
e1_e0_star(time) 0.0
e5_e4_star(time) 0.0
e5_star_p5(time) 0.0
e0_star(time) 0.0
c_star(time) 0.0
e2_e1_star(time) 0.0
c_star_a1(time) 0.0
e2_star_p2(time) 0.0
e4_star_p4(time) 0.0
e3_star_p3(time) 0.0
e4_star(time) 0.0
a2_minus(time) 0.0
e2_star_e4_star(time) 0.0

Observables: none

B


bagci_2006 @ v0.0.1

Bagci 2006

nothing

Parameters:

Name Description
k14 10.0
k_02 0.5
k_18 10.0
k_19 10.0
P_oBcl_2 8.0e-5
k_05 0.0035
k_09 0.5
k_f8 0.1
P_Cytc_mito 0.0003
p53 0.0066
k_16 10.0
p53_thresh 0.004
k_12 10.0
k_05b 0.0035
k_15b 5.0
k_13 10.0
u_Bax 0.006
k_11 5.0
k12b 10.0
k_f0 0.1
P_Apaf_1 0.0003
k_06b 0.5
u 0.006
k_07 0.0035
k_14b 5.0
k_04 0.5
k_f6b 0.1
k_f6 0.001
u_Bcl_2 0.006
k_08 0.5
k13 10.0
k_f3 0.1
P_Pro9 0.0003
P_oBax 3.0e-5
k_15 5.0
k_00 0.5
k_16b 10.0
k_01b 0.5
k_01 0.5
P_Pro3 0.0003
k_05c 0.0035
k_03 0.5
k11 10.0
k12a 10.0
P_IAP 3.0e-5
k_f9 0.1
k_15c 5.0
k_04b 0.5
k_14 5.0
k_06 0.5
P_Bid 3.0e-5
k_10 10.0
k_11b 50000.0
k_17 5.0
p 4.0

States:

Name Description
IAP(time) 0.004
Casp3IAP(time) 0.0
Bcl_2(time) 0.004
Casp9IAP(time) 0.0
ApopCasp9_2Pro3(time) 0.0
Casp9Pro3(time) 0.0
ApopCasp9(time) 0.0
Apop(time) 0.0
Bax_2(time) 0.0
tBid(time) 0.0
Casp8(time) 0.0
ApopPro9_2(time) 0.0
Casp3(time) 0.0
ApopPro9(time) 0.0
tBidBax(time) 0.0
tBid_mito(time) 0.0
Cytc(time) 0.0
ApopCasp9IAP(time) 0.0
Casp8Bid(time) 0.0
Casp3Bcl_2(time) 0.0
ApopCasp9_2IAP(time) 0.0
Pro9(time) 0.004
ApopCasp9_2(time) 0.0
CytcApaf_1(time) 0.0
Casp9(time) 0.0
Casp3Bid(time) 0.0
Bid(time) 0.004
Pro3(time) 0.004
Cytc_mito(time) 0.004
Apaf_1(time) 0.004
Bax(time) 0.004

Observables: none

bagci_2008 @ v0.0.1

Bagci 2008

nothing

Parameters:

Name Description
k_1NO 1.0
k_09 0.5
k_17NO 66.0
k_18NO 1.0
k_f8 0.1
k_20NO 66.0
Cyt_c 400.0
O_2 35.0
k_12aNO 6.0e-6
k_22NO 66.0
k_8NO 0.058
k_15b 5.0
k_13 10.0
k_6NO 0.00135
u 0.006
k_07 0.0035
k_14b 5.0
k_04 0.5
k_f6b 0.1
k_13NO 1600.0
k13 10.0
k_f3 0.1
GSH_0 10000.0
P_Pro9 0.0003
GPX 5.8
k_15 5.0
k_16b 10.0
k_15NO 100.0
k_01b 0.5
P_Pro3 0.0003
k_03 0.5
k11 10.0
k_f9 0.1
k_15c 5.0
k_06 0.5
k_10 10.0
k_16NO 1.21
FeLn_0 0.05
k14 10.0
k_m 50.0
k_02 0.5
k_17bNO 0.0002
k_19 10.0
P_oBcl_2 8.0e-5
k_05 0.0035
k_18 10.0
CO_2 1000.0
P_Cytc_mito 0.0003
k_9NO 0.025
p53 0.0066
k_2NO 0.1
k_10NO 0.0006
k_16 10.0
p53_thresh 0.004
k_4NO 6700.0
k_11NO 66.0
k_12 10.0
k_05b 0.0035
u_Bax 0.006
k_11 5.0
k12b 10.0
k_f0 0.1
P_Apaf_1 0.0003
k_06b 0.5
k_f6 0.001
u_Bcl_2 0.006
k_08 0.5
SOD 10.0
P_oBax 3.0e-5
k_7NO 2.0
k_00 0.5
k_21NO 66.0
k_01 0.5
k_19NO 10.0
k_05c 0.0035
k_12bNOp 1100.0
k12a 10.0
P_IAP 3.0e-5
k_12bNOm 81000.0
k_04b 0.5
k_14 5.0
P_Bid 3.0e-5
k_5NO 2400.0
PTPC_0 0.0
k_14NO 0.0002
k_11b 50000.0
v_m 320.0
k_17 5.0
p 4.0
k_1 1.0

States:

Name Description
IAP(time) 0.004
Casp3IAP(time) 0.0
Bcl_2(time) 0.004
FeLnNO(time) 0.0
NO_2(time) 0.0
Casp9IAP(time) 0.0
ApopCasp9_2Pro3(time) 0.0
NO(time) 0.0
ApopCasp9(time) 0.0
O_2m(time) 35.0
Casp9Pro3(time) 0.0
Apop(time) 0.0
Bax_2(time) 0.0
tBid(time) 0.0
Casp8(time) 0.0
FeLn(time) 0.05
Casp3(time) 0.0
GSH(time) 10000.0
PTPC(time) 0.0
ApopPro9_2(time) 0.0
ONOO_m(time) 0.0
ApopPro9(time) 0.0
tBid_mito(time) 0.0
tBidBax(time) 0.0
Cytc(time) 0.0
ApopCasp9IAP(time) 0.0
Casp8Bid(time) 0.0
CcOX(time) 0.1
Casp3Bcl_2(time) 0.0
CytcApaf_1(time) 0.0
Casp9(time) 0.0
ApopCasp9_2(time) 0.0
Pro9(time) 0.004
GSNO(time) 0.0
ApopCasp9_2IAP(time) 0.0
Casp3Bid(time) 0.0
Bid(time) 0.004
Pro3(time) 0.004
Cytc_mito(time) 0.004
N2O3(time) 0.0
Bax(time) 0.004
Apaf_1(time) 0.004

Observables: none

bakker_mensonides_teusink_vanhoek_michels_westerhoff_2000 @ v0.0.1

Bakker, Mensonides, Teusink, Vanhoek, Michels, Westerhoff, 2000

nothing

Parameters:

Name Description
K_Fru6P 0.12
Ki_GAP 0.098
vGDH_max_reverse 149.24
KM_ATP 0.026
vGlyK_max_forward 220.0
K_BPGA13 0.1
Ki_2 10.7
vGDH_max 1.0
K_Glc 2.0
KM_DHAP 0.015
sumc4 45.0
Keq_PGM 0.187
K_Glc6P 0.4
vPGK_max_reverse 18.56
vGlcTr_max 106.2
vPGK_max_forward 640.0
K_GAP 0.15
K_ADP 0.12
Keq_ENO 6.7
vGAPDH_max_reverse 984.9
K_pyruvate 1.96
vGlyK_max_reverse 334000.0
K_NADH 0.02
K_Gly3P 5.1
vPK_max 2600.0
vHK_max 625.0
K_NAD 0.45
K_GlcI 0.1
vPGK_max 1.0
Keq_AK 0.442
K_Gly 0.12
K_DHAP 1.2
vALD_max_reverse 219.555
Ki_1 15.8
vGlyK_max 1.0
vTPI_max 842.0
vPyrTr_max 200.0
alpha 0.75
KM_GAP 0.067
k 50.0
sumA 6.0
KM_Fru6P 0.82
sumc5 5.0
vGAPDH_max 1.0
K_ATP 0.19
vPGI_max 848.0
vALD_max_forward 184.5
KM_ADP 0.114
vPFK_max 780.0
vGPO_max 368.0
vGAPDH_max_forward 1470.0
vGDH_max_forward 533.0
K_PGA3 1.62
n 2.5

States:

Name Description
P(time) nothing
BPGA13(time) nothing
Gly(time) nothing
triose_P(time) nothing
Pyr(time) nothing
N(time) nothing
PGA3(time) nothing
GAP(time) nothing
Glc6P(time) nothing
NAD(time) nothing
GlcI(time) nothing
Gly3P(time) nothing
Fru16BP(time) nothing
NADH(time) nothing
hexose_P(time) nothing

Observables: none

bakker_michels_opperdoes_westerhoff_1997 @ v0.0.1

Bakker, Michels, Opperdoes, Westerhoff, 1997

nothing

Parameters:

Name Description
K_glycerol 0.12
K_Glc_i 0.1
V_GPO_max 200.0
V_GDH_max_plus 533.0
V_PYK_max 2600.0
Km_GA_3_P 0.067
K_Glc 2.0
V_PGK_max_ratio 0.029
V_pyruvate_transport_max 160.0
Km_ADP 0.114
V_HK_max 625.0
V_PFK_max 780.0
V_GAPDH_max_plus 1470.0
Keq_PGM 0.187
V_PGK_max_plus 640.0
Vc_Vg 22.3
C4 120.0
Keq_PGI 0.29
Keq_TIM 0.045
V_glucose_transport_max 106.2
K_ADP 0.12
K_3_PGA 1.62
Km_ATP 0.026
V_ALD_max_ratio 1.19
K_Gly_3_P 5.1
Keq_ENO 6.7
V_ALD_max_plus 780.0
K_pyruvate 1.96
C3 4.0
V_GDH_max_ratio 0.28
K_NADH 0.01
C1 3.9
C2 3.9
Km_Fru_6_P 0.82
K_NAD 0.4
K_1_3_BPGA 0.1
Keq_AK 0.442
K_DHAP 0.1
Ki_GA_3_P 0.098
Km_DHAP 0.015
V_GAPDH_max_ratio 0.67
alpha 0.75
k 50.0
V_GK_max_ratio 167.0
glycerol_g 0.0
Glc_o 5.0
K_ATP 0.19
V_GK_max_plus 0.0
K_GA_3_P 0.15
n 1.2

States:

Name Description
NADH_g(time) 0.01
hexose_P_g(time) 0.01
Fru_1_6_BP_g(time) 0.01
triose_P(time) 0.01
P_c(time) 0.01
Glc_i(time) 0.01
P_g(time) 0.01
one_three_BPGA_g(time) 0.01
PYR_c(time) 0.01
N(time) 0.01

Observables: none

barberis_klipp_vanoni_alberghina_2007 @ v0.0.1

Barberis, Klipp, Vanoni, Alberghina, 2007

nothing

Parameters:

Name Description
k_37 4363.6
k_25 0.55
k_1 0.03523
k_22 0.01
k_18 0.0008
k_29 0.55
k_19 0.01
k_5 4.2e-5
k_28 2.82
k_16 0.03
k_44 0.005
k_2 0.03523
k_39 1.0
k_30 42300.0
k_12 0.1
k_13 0.35
k_40 1.0
k_3 0.32
k_53 0.001
k_11 0.12
k_33 0.55
k_50 0.6
k_49 0.001
k_45 0.005
k_52 0.005
k_36 4363.6
k_21 0.0
k_4 0.32
k_15 0.01
k_32 84.6
k_46 0.1
k_43 0.005
k_23 0.01
k_41 1.0
k_24 2.82
k_27 0.55
k_20 0.01
k_42 0.005
k_8 4.0e-5
k_51 0.6
k_14 0.01
k_38 4363.6
k_7 0.01
k_10 0.12
k_47 1.0
k_growth 0.0051
k_48 0.012
k_31 0.55
k_6 1.0e-5
k_35 0.0005
k_9 5.0e-5
k_17 0.01
k_26 2.82
k_34 8.46

States:

Name Description
whi5p_c(time) 0.0
far1_c(time) 0.0037926
cdk1cln3far1_n(time) 0.0
sic1_c(time) 0.039234
sbfwhi5_n(time) 0.025544
cdk1cln2_c(time) 0.0
v_c(time) 0.5
cdk1clb5sic1_n(time) 0.0
cln3_c(time) 0.000485
cln3_n(time) 0.0
cdk1cln3far1p_n(time) 0.0
sbf_n(time) 0.0
cdk1cln3_n(time) 0.0
cdk1clb5_n(time) 0.0
cdk1clb5_c(time) 0.0
far1P_n(time) 0.0
far1_n(time) 0.0
cdk1cln2_n(time) 0.0
cdk1clb5sic1_c(time) 0.0
v_n(time) 0.5
sbfwhi5p_n(time) 0.0
mcln2_n(time) 0.0
mclb5_n(time) 0.0
cdk1_n(time) 0.0074127
whi5_c(time) 0.073564
cln2_c(time) 0.0
mclb5_c(time) 0.0
cdk1_c(time) 0.333333
whi5p_n(time) 0.0
clb5_c(time) 0.0
whi5_n(time) 0.0
mcln2_c(time) 0.0
sic1P_n(time) 0.0
cdk1clb5sic1p_n(time) 0.0

Observables: none

baylor_hollingworth_chandler_2002 @ v0.0.1

Baylor, Hollingworth, Chandler, 2002

nothing

Parameters:

Name Description
k1_ 2642.0
k4_ 0.0
k4 20.0
k3 1.0e14
k1 2.033e14
k3_ 10.0
k2 1.017e14
k2_ 13.21

States:

Name Description
Pr(time) 3000.0
Mg(time) 1000.0
PrFluo(time) 88.12
CaFluo(time) 0.01
CaATP(time) 1.0
CaPrFluo(time) 0.01
CaE_(time) 0.01
Ca2E_(time) 1.0
ATP(time) 8000.0
CaTrop(time) 0.01
Parv(time) 1500.0
Ca(time) 0.05
E(time) 240.0
MgParv(time) 0.01
Trop(time) 360.0
Ca2Trop(time) 0.01
CaParv(time) 0.01
CaE(time) 0.01
Fluo(time) 11.88

Observables: none

beard_2005 @ v0.0.1

Beard, 2005

nothing

Parameters:

Name Description
x_F1 150.93
mincond 1.0e-12
x_AK 0.0
r 4.5807
x_Pi2 327.0
dG_C4o -122.94
dG_F1o 36.03
n_A 3.0
K_e 0.15
x_ANT 0.0079204
ATP_e 0.0
k_mADP 3.5e-6
x_C3 0.091737
k_PiH 0.00045082
k_Pi1 0.00013413
x_C4 3.2562e-5
x_K 0.0
p_A 85.0
Mg_tot 0.005
k_Pi3 0.00019172
k_Pi2 0.00067668
RT 2.4734
C_im 6.756756756756757e-6
x_Hle 250.0
x_DH 0.09183
x_KH 2.9802e7
K_AK 0.4331
Pi_e 0.000125
ADP_e 0.0
k_O2 0.00012
pH_e 7.1
Ctot 0.0027
k_Pi4 0.02531
x_Pi1 339430.0
AMP_e 0.0
K_DT 2.4e-5
x_buff 100.0
Qtot 0.00135
x_C1 0.36923
dG_C3o -32.53
dG_C1o -69.37
NADtot 0.00297
K_DD 0.000347
gamma 5.99
W_m 0.72376
F 0.096484
x_MgA 1.0e6

States:

Name Description
O2(t) 2.6e-5
ATP_mi(t) 0.0
Pi_x(t) 0.001
ATP_x(t) 0.0
ATP_mx(t) 0.0
dPsi(t) 160.0
ADP_mx(t) 0.0
AMP_i(t) 0.0
ADP_i(t) 0.0
K_x(t) 0.14
ADP_mi(t) 0.0
Mg_x(t) 0.005
ADP_x(t) 0.01
NADH_x(t) 0.0015
ATP_i(t) 0.0
QH2(t) 0.0008
Pi_i(t) 0.001
Cred(t) 0.001
H_x(t) 6.30957344480193e-8

Observables: none

becker_2010 @ v0.0.1

Covering a Broad Dynamic Range: Information Processing at the Erythropoietin Receptor

Cell surface receptors convert extracellular cues into receptor activation, thereby triggering intracellular signaling networks and controlling cellular decisions. A major unresolved issue is the identification of receptor properties that critically determine processing of ligand-encoded information. We show by mathematical modeling of quantitative data and experimental validation that rapid ligand depletion and replenishment of the cell surface receptor are characteristic features of the erythropoietin (Epo) receptor (EpoR). The amount of Epo-EpoR complexes and EpoR activation integrated over time corresponds linearly to ligand input; this process is carried out over a broad range of ligand concentrations. This relation depends solely on EpoR turnover independent of ligand binding, which suggests an essential role of large intracellular receptor pools. These receptor properties enable the system to cope with basal and acute demand in the hematopoietic system.

Parameters:

Name Description
k_exSAv 0.011
k_offSAv 0.006799
k_di 0.003179
k_de 0.0164
B_max 129.0
k_mob 0.4178
k_off 0.01721
k_ex 0.00994
k_e 0.07483
B_maxSAv 129.0
k_t 0.03294
k_on 0.00010496
k_onSAv 2.294e-6

States:

Name Description
x_7(time) 76.0
x_2(time) 2010.19
x_12(time) 0.0
x_6(time) 0.0
x_8(time) 999.293
x_3(time) 0.0
x_4(time) 0.0
x_5(time) 0.0
x_1(time) 516.0
x_10(time) 0.0
x_9(time) 0.0
x_11(time) 0.0

Observables: none

beeler_reuter_1977 @ v0.0.1

Beeler, Reuter, 1977

nothing

Parameters:

Name Description
IstimPeriod 1000.0
IstimAmplitude 0.5
C 0.01
g_s 0.0009
g_Na 0.04
IstimPulseDuration 1.0
g_Nac 3.0e-5
E_Na 50.0
IstimStart 10.0
IstimEnd 50000.0

States:

Name Description
d(time) 0.003
j(time) 0.975
V(time) -84.624
h(time) 0.988
m(time) 0.011
Cai(time) 0.0001
f(time) 0.994
x1(time) 0.0001

Observables: none

beeler_reuter_1977_uncertexample @ v0.0.1

Beeler, Reuter, 1977 uncertainty example

nothing

Parameters: none

States: none

Observables: none

benson_2008 @ v0.0.1

Benson 2008

nothing

Parameters:

Name Description
prnak 0.01833
iupmax 0.004375
tissue 0.0
KmNao 87.5
Km 0.0015
KmBSR 0.00087
stim_offset 0.0
BSLmax 1.124
ibarpca 0.0575
GNaL 0.0065
kmko 1.5
KmCao 1.3
tbar 0.07
kmpca 0.0005
gitodv 0.1805
Kmto2 0.1502
KmNai 12.3
eta 0.35
l 0.01
FonRT 0.0374358835078
nsrmax 15.0
CTNaClmax 9.8443e-6
dtau_rel_max 10.0
ksat 0.27
kmc 0.00238
NCXmax 5.85
Na_o 140.0
CTKClmax 7.0756e-6
stim_duration 3.0
ibarnak 0.61875
csqnbar 10.0
Kmup 0.00092
Ca_o 1.8
cbar 0.05
a 0.0011
stim_period 1000.0
kmt 0.0005
KmCa 0.000125
KmCaMK 0.15
gacai 1.0
K_o 5.4
gacao 0.341
dKmPLBmax 0.00017
kmnai 10.0
kmcsqn 0.8
KmBSL 0.0087
dJupmax 0.75
pca 0.000243
stim_amplitude -20.0
Cl_o 100.0
PCl 4.0e-7
BSRmax 0.047
GClb 0.000225
KmCai 0.0036
F 96485.0
CaMK0 0.05

States:

Name Description
Cl_i(time) 15.59207157178
xr(time) 7.24074e-6
fca2(time) 0.893052931249
Ca_ss(time) 0.00012271265
fca(time) 0.97836624923
dp(time) 8.98230672628
f(time) 0.999961508634
J(time) 0.991924983076
xs1(time) 0.019883138161
Ca_nsr(time) 1.832822335168
mL(time) 0.001356538159
m(time) 0.001356538159
xs2(time) 0.019890650554
ro(time) 0.0
Ca_jsr(time) 1.737580994071
Na_i(time) 12.972433387269
zdv(time) 0.829206149767
d(time) 1.64013e-6
V(time) -85.781844107117
f2(time) 0.992234519148
ydv(time) 0.013970786703
CaMKtrap(time) 0.021123704774
K_i(time) 135.469546216758
AA(time) 0.000816605172
ydv2(time) 0.99996472752
H(time) 0.987317750543
Ca_i(time) 0.00012131666
ri(time) 0.862666650318
hL(time) 0.26130711759

Observables: none

bental_2006 @ v0.0.1

Bental, 2006

nothing

Parameters:

Name Description
P_w 47.0
V_T 0.41
V_D 0.151
sigma_c 3.3e-5
L 1.712e8
r_2 0.12
K_T 10000.0
P_m 760.0
E 2.5
sigma 1.4e-6
D_o 1.56e-5
omega 1.256637
T_h 0.002
f_om 0.21
K_R 3.6e6
V_c 0.071
l_2 164000.0
R 1.0
D_c 3.16e-5
f_cm 0.0

States:

Name Description
P_A(time) 760.0
f_o(time) 0.1368
f_c(time) 0.05263
p_o(time) 40.0
p_c(time) 46.0
z(time) 4.4219e-7
V_A(time) 1.0

Observables: none

bernus_wilders_zemlin_verschelde_panfilov_2002 @ v0.0.1

Bernus, Wilders, Zemlin, Verschelde, Panfilov, 2002

nothing

Parameters: none

States: none

Observables: none

bertram_arnot_zamponi_2002 @ v0.0.1

Bertram, Arnot, Zamponi, 2002

nothing

Parameters:

Name Description
R_gas_const 8314.41
kr_minus 2.5
P 0.006
r 10.0
ka_minus 0.0015
g_syn 0.2
Temp 310.0
kb_minus 1.0
g_Ca 1.2
Cm 1.0
Dc 220.0
kr_plus 0.15
kG3_minus 1.024
IstimAmplitude 40.0
kb_plus 2000.0
IstimPulseDuration 1.0
Ca_ex 2000.0
ka_plus 200.0
IstimEnd 50000.0
IstimPeriod 100.0
T_bar 4000.0
kG2_minus 0.016
kG_minus 0.00025
IstimStart 10.0
V_syn 0.0
F 96485.0

States:

Name Description
C_G1(time) 0.0
V_post(time) -65.0
V(time) -65.0
C2(time) 0.0
a(time) 0.0
C1(time) 1.0
C3(time) 0.0
n_post(time) 0.0
C_G3(time) 0.0
b(time) 0.0
n(time) 0.0
R(time) 0.0
C4(time) 0.0
C_G2(time) 0.0

Observables: none

bertram_pedersen_luciani_sherman @ v0.0.1

Bertram, Pedersen, Luciani and Sherman 2006

nothing

Parameters:

Name Description
p12 120.0
Ctoff3 270000.0
Fhold 1.0
Ctest 0.1
p13 10.0
p4 0.6
Cmito 1.8
Chold 0.1
khyd 5.0e-5
Cton1 120000.0
p6 177.0
p23 0.001
p20 2.0
Cton2 180000.0
p21 0.01
kgpdh 0.0005
Fton 90000.0
Ftoff 330000.0
p2 1.0
p8 7.0
p1 400.0
p11 5.0
p17 0.002
p3 0.01
fm 0.01
Ac_tot 2500.0
Ctoff2 210000.0
p24 0.016
p15 8.5
p22 1.1
Jhydbas 5.0e-5
p14 190.0
p16 35.0
Ctoff1 150000.0
p5 0.1
FRT 0.037
p10 177.0
p7 5.0
Cton3 240000.0
p18 -0.03
p9 0.1
Ftest 5.0
p19 0.35
Amtot 15.0
NADtot 10.0
gamma 0.001

States:

Name Description
ADPm(time) 7.4
PSIm(time) 93.0
Cam(time) 0.1
NADHm(time) 0.6
ADPc(time) 1850.0
FBP(time) 0.5
c(time) 0.1

Observables: none

bertram_previte_sherman_kinard_satin_2000 @ v0.0.1

Bertram, Previte, Sherman, Kinard, Satin, 2000

nothing

Parameters:

Name Description
gK 1300.0
Vs1 -40.0
VK -80.0
tnbar 9.09
Vs2 -42.0
ss1 0.5
taus2 120000.0
sn 10.0
gCa 280.0
ss2 0.4
Vn -9.0
gs2 32.0
taus1 1000.0
Vl -40.0
lambda 1.1
gs1 3.0
Vm -22.0
gl 25.0
sm 7.5
Cm 4524.0
VCa 100.0

States:

Name Description
V(time) -43.0
n(time) 0.03
s1(time) 0.1
s2(time) 0.434

Observables: none

bertram_rhoads_cimbora_2008 @ v0.0.1

Bertram, Rhoads and Cimbora 2008

nothing

Parameters:

Name Description
VK -80.0
vn -9.0
vs2 -40.0
autos1 1.0
p0 0.2
s2knot 0.47
s1knot 1.0
delNoise 3.0
tau_s2 30000.0
autos2 1.0
gs2 16.0
gs1 22.0
gl 41.0
tau_n_bar 8.25
sm 7.5
Cm 4525.0
noise 1.0
gK 1300.0
tau_p 100.0
w 1.0
ss1 5.0
sn 10.0
gCa 280.0
vs1 -50.0
ss2 15.0
Vl -40.0
vm -22.0
tau_s1 1000.0
alpha_p 1.0
VCa 100.0

States:

Name Description
p(time) 0.14
V(time) -40.0
n(time) 0.0
s1(time) 0.9
s2(time) 0.5

Observables: none

bertram_satin_pedersen_luciani_sherman_2007 @ v0.0.1

Bertram, Satin, Pedersen, Luciani, Sherman, 2007

nothing

Parameters:

Name Description
fer 0.01
VK -75.0
vn -16.0
pleak 0.0002
NADmtot 10.0
khydbas 5.0e-5
p13 10.0
kPMCA 0.1
Cbas 0.05
fcyt 0.01
kSERCA 0.4
f42 20.0
JGK 0.4
gkATP_ 16000.0
p4 0.6
f23 0.2
JGPDHbas 0.0005
tau_n 20.0
atot 2500.0
Cmito 1.8
Vc_Ver 31.0
khyd 5.0e-5
sn 5.0
p23 0.01
p6 177.0
p20 2.0
kd 0.5
p21 0.04
k3 50000.0
f41 20.0
p2 1.0
p8 7.0
p1 400.0
p11 5.0
VCa 25.0
p17 0.002
f13 0.02
p3 0.01
p24 0.016
AMP 500.0
p15 8.5
p22 1.1
p14 190.0
gkCa 300.0
bottom1 1.0
kappa 0.001
k4 1000.0
lambda 0.06
p16 35.0
sm 12.0
v -20.0
p5 0.1
gK 2700.0
FRT 0.037410133
p10 177.0
p7 5.0
alpha 4.5e-6
topa1 0.0
p18 -0.03
p9 0.1
k1 30.0
gCa 1000.0
kGPDH 0.0005
p19 0.35
Amtot 15.0
gamma 0.001
f43 20.0
fmito 0.01
VmaxPFK 5.0
k2 1.0
cm 5300.0

States:

Name Description
ADPm(time) 11.1
G6P(time) 301.0
Cam(time) 0.2
c(time) 0.17
adp(time) 1137.0
NADHm(time) 0.4
delta_psi(time) 164.0
n(time) 0.0
Vm(time) -60.0
FBP(time) 2.16
Caer(time) 345.0

Observables: none

bertram_satin_zhang_smolen_sherman_2004 @ v0.0.1

Bertram, Satin, Zhang, Smolen, Sherman, 2004

nothing

Parameters:

Name Description
kg 10.0
gkatpbar 25000.0
lambdaer 1.0
fer 0.01
VK -75.0
sigmaV 31.0
r 1.0
pleak 0.0002
taun 20.0
pfkbas 0.06
kdd 17.0
bottom1 1.0
k4 1000.0
fatp 20.0
fcyt 0.01
ktt 1.0
lambda 0.005
Cm 5300.0
vg 2.2
gK 2700.0
atot 3000.0
topa1 0.0
fbt 20.0
taua 300000.0
Rgk 0.2
alpha 4.5e-6
k1 30.0
fmt 20.0
ktd 26.0
kd 0.5
gCa 1000.0
Kserca 0.4
r1 0.35
famp 0.02
k3 50000.0
cat 2.0
ffbp 0.2
gKCa 600.0
epser 1.0
kpmca 0.2
k2 1.0
VCa 25.0

States:

Name Description
V(time) -60.0
n(time) 0.0
c(time) 0.25
adp(time) 780.0
g6p(time) 200.0
cer(time) 185.0
fbp(time) 40.0

Observables: none

bertram_sherman_2004 @ v0.0.1

Bertram, Sherman, 2004

nothing

Parameters:

Name Description
fer nothing
vn nothing
g_K_Ca nothing
r nothing
pleak nothing
d_inact nothing
V_K nothing
d_act nothing
IP3 nothing
d_IP3 nothing
kPMCA nothing
fcyt nothing
kSERCA nothing
g_Ca nothing
kD nothing
sm nothing
Cm nothing
tau_n nothing
alpha nothing
sn nothing
g_K nothing
g_K_ATP nothing
V_Ca nothing
vm nothing
sa nothing
tau_a nothing
Vcyt_Ver nothing

States:

Name Description
V(time) nothing
n(time) nothing
c(time) nothing
a(time) nothing
c_er(time) nothing

Observables: none

bertram_smolen_sherman_mears_atwater_martin_soria_1995 @ v0.0.1

Bertram, Smolen, Sherman, Mears, Atwater, Martin, Soria, 1995

nothing

Parameters:

Name Description
V_CRAC 0.0
f 0.01
kerp 0.1
k_Ca 0.07
dip3 0.2
sigma_er 5.0
g_K_Ca 1200.0
Vm_f -20.0
Vj -53.0
V_K -70.0
Sj 2.0
IP3 0.0
g_Ca_f 810.0
Vn -15.0
verp 0.24
Sm_s 10.0
lambda_n 1.85
lambda_er 250.0
Cm 6158.0
dinh 0.4
Vm_s -16.0
Sm_f 7.5
Ca_er_bar 3.0
Sn 6.0
g_K 3900.0
g_K_ATP 150.0
dact 0.1
perl 0.02
V_Ca 100.0
g_leak 0.0
gamma 3.607e-6
g_Ca_s 510.0
g_CRAC 75.0
kdkca 0.55

States:

Name Description
jm(time) 0.12
V(time) -61.0
n(time) 0.0005
Ca_i(time) 0.11
Ca_er(time) 9.0

Observables: none

bhalla_iyengar_1999 @ v0.0.1

Bhalla, Iyengar, 1999

nothing

Parameters: none

States: none

Observables: none

bindschadler_sneyd_2001 @ v0.0.1

Bindschadler, Sneyd, 2001

nothing

Parameters:

Name Description
R1 6.0
R5 1.6
Kp 0.18
D 0.01
k1 44.0
j_leak 0.2
r4 20.0
kf 28.0
r2 100.0
R3 50.0
k3 1.6
Vp 1.2
k2 26.5
p 0.2778

States:

Name Description
c2(time) 0.1
h2(time) 0.1
h1(time) 0.8
c1(time) 0.3

Observables: none

bingzheng_zhenye_liansong_1990 @ v0.0.1

Bingzheng, Zhenye, Liansong, 1990

nothing

Parameters:

Name Description
a3 1.38
a2 0.0164
a1 0.000517
b3 0.0138
b2 0.053
a4 0.6
a7 0.0081
a6 0.0084
a5 0.00498
a0 0.0014
b1 0.0598

States:

Name Description
X2(time) 0.0
X1(time) 10.0
X3(time) 0.0

Observables: none

bondarenko_szigeti_bett_kim_rasmusson_2004 @ v0.0.1

Bondarenko, Szigeti, Bett, Kim, Rasmusson, 2004

nothing

Parameters:

Name Description
Kpc_max 0.23324
R 8.314
T 298.0
stim_start 20.0
Km_CSQN 800.0
Kpcb 0.0005
k_minus_htrpn 3.2e-5
Km_Nai 21000.0
k_plus_a 0.006075
kf 0.023761
Km_Cl 10.0
Ko 5400.0
i_NaK_max 0.88
Cm 1.0
v3 0.45
Km_CMDN 0.238
E_Cl -40.0
g_Kto_f 0.0798
k_sat 0.1
K_mNa 87500.0
eta 0.35
LTRPN_tot 70.0
g_Ks 0.00575
Acap 0.0001534
i_CaL_max 7.0
tau_tr 20.0
g_Kr 0.078
Km_pCa 0.5
K_mCa 1380.0
k_minus_a 0.07125
stim_duration 0.5
k_minus_b 0.965
v1 4.5
i_pCa_max 1.0
Cao 1800.0
Vmyo 2.584e-5
Km_up 0.5
g_Nab 0.0026
tau_xfer 8.0
g_Kto_s 0.0629
Kpc_half 20.0
Km_Ko 1500.0
stim_period 71.43
stim_end 100000.0
k_minus_ltrpn 0.0196
kb 0.036778
k_plus_b 0.00405
CSQN_tot 15000.0
CMDN_tot 50.0
E_CaL 63.0
Nao 140000.0
HTRPN_tot 140.0
g_Na 13.0
VJSR 1.2e-7
k_plus_c 0.009
g_Cab 0.000367
stim_amplitude -80.0
g_ClCa 10.0
VNSR 2.098e-6
m 3.0
g_Kss 0.0324
v2 1.74e-5
k_minus_c 0.0008
Vss 1.485e-9
g_CaL 0.1729
k_plus_ltrpn 0.0327
g_Kur 0.0975
k_NaCa 292.8
k_plus_htrpn 0.00237
F 96.5
n 4.0

States:

Name Description
C_Na2(time) 0.020752
O_K(time) 0.000175298
O_Na(time) 7.13483e-7
ato_f(time) 0.00265563
P_C2(time) 0.00016774
C2(time) 0.000124216
I2_Na(time) 1.55787e-9
HTRPN_Ca(time) 125.29
C3(time) 5.78679e-9
C_K2(time) 0.000641229
O(time) 9.30308e-19
I2(time) 3.45847e-14
IC_Na2(time) 0.0113879
C_Na1(time) 0.000279132
P_RyR(time) 0.0
nKs(time) 0.000262753
C4(time) 1.19816e-13
ito_f(time) 0.999977
Nai(time) 14237.1
I1_Na(time) 6.73345e-7
Cass(time) 0.115001
IC_Na3(time) 0.34278
ato_s(time) 0.000417069
V(time) -82.4202
LTRPN_Ca(time) 11.2684
IF_Na(time) 0.000153176
CaJSR(time) 1299.5
C_K1(time) 0.000992513
aur(time) 0.000417069
iKss(time) 1.0
iur(time) 0.998543
P_O1(time) 1.49102e-5
Ki(time) 143720.0
ito_s(time) 0.998543
I_K(time) 3.19129e-5
CaNSR(time) 1299.5
I3(time) 1.85106e-14
Cai(time) 0.115001
P_O2(time) 9.51726e-11
aKss(time) 0.000417069
I1(time) 4.97923e-19

Observables: none

bonhoeffer_rembiszewski_ortiz_nixon_2000 @ v0.0.1

Bonhoeffer, Rembiszewski, Ortiz, Nixon, 2000

nothing

Parameters:

Name Description
p 0.05
c 0.3
b 0.001
dE 0.1
dT 0.01
K_ 5.0
qa 0.001
dI 0.3
al 0.01
ql 0.001
s 10.0
K 0.1
dE_ 0.25

States:

Name Description
E(time) 1.0
T(time) 1.0
I(time) 1.0
Il(time) 1.0

Observables: none

borghans_1997 @ v0.0.1

Borghans 1997

nothing

Parameters:

Name Description
K_y 0.2
K_p 1.0
K_z 0.3
a 10000.0
K_2s 0.0265
V_M2 6.5
K_d 0.4
V_M2i 3.1
K_f 0.5
K_2 0.1
K_3s 0.1
upsilon_p 2.5
d 100.0
V_M2s 1.5
V_M3s 0.169
K_3z 0.022
k_d 5000.0
K_a 0.2
upsilon_d 80.0
V_M3i 25.0
v_0 0.015
beta 1.0
K_2i 0.005
V_M3 19.5
epsilon 0.1
K_3y 0.065
K 1.0
k_r 5.0
v_1 0.012
n 4.0

States:

Name Description
Z(time) 0.0
rho(time) 0.2
A(time) 0.5
Y(time) 0.0
X(time) 0.5

Observables: none

bornheimer_maurya_farquhar_subramaniam_2004 @ v0.0.1

Bornheimer et al. 2004

nothing

Parameters:

Name Description
G_tot 1.0e-8
P_minus2 25.0
P_minus4 25.0
k1 529000.0
P_minus3 0.013
k2 8.38e-6
P_minus1 0.013

States:

Name Description
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) 1.0e-6
GA(time) 0.0
RGAT(time) 0.0
RGA(time) 0.0
D(time) 0.000149
GAT(time) 0.0
RGAD(time) 0.0

Observables: none

boyett_zhang_garny_holden_2001 @ v0.0.1

Boyett, Zhang, Garny, Holden, 2001

nothing

Parameters:

Name Description
alpha_r 333.5
f_u 0.06
CmCentre 2.0e-5
Na_i 8.0
T 310.0
alpha_ur 533.6
alpha_ds 3300.0
K_m_K 0.621
Ca_i 0.0001
d_NaCa 0.0001
B_s 0.2
dCell 0.0
g_K_r_Centre 0.000797
g_b_Ca_Periphery 4.3e-5
k_NaCa_Periphery 8.8e-6
g_to_Centre 0.00491
g_K_s_Periphery 0.0104
g_Ca_T_Centre 0.0043
beta_fR 2.0
f_r 0.3
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
alpha_fR 6670.0
g_b_K_Centre 2.52e-5
g_to_Periphery 0.03649
i_Ca_P_max 0.24
g_b_Ca_Centre 1.32e-5
Na_o 140.0
g_sus_Periphery 0.0114
K_i 140.0
K_m_u 0.005
Ca_o 2.0
g_b_Na_Periphery 0.000189
E_Ca_T 45.0
tau_P_i 0.002
g_st 0.00214
g_Ca_L_Periphery 0.0659
f_d 0.1
B_d 0.4
g_K_r_Periphery 0.016
K_o 5.4
K_m_Na 5.64
Vol_c 8.0e-12
K_m_b 0.002
CmPeriphery 6.5e-5
g_K_s_Centre 0.000518
alpha_1 0.172
g_f_Na_Centre 0.000548
J_Ca_u_max 9.6e-10
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
K_m_r 0.001
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
J_Ca_P_max 9.6e-10
F 96845.0

States:

Name Description
xs(time) 0.082293827208
y(time) 0.03889291759
f_T(time) 0.038968420558
P_af(time) 0.13034201158
d_L(time) 0.04804900895
m(time) 0.092361701692
d_s(time) 0.23
P_as(time) 0.46960956028
q(time) 0.29760539675
d_T(time) 0.42074047435
h2(time) 0.01445216109
V(time) -39.013558536
Ca_u(time) 6.983
Ca_d(time) 0.001544
f_s(time) 0.283
r(time) 0.064402950262
P_i(time) 0.87993375273
f_L(time) 0.48779845203
Ca_r(time) 4.909
h1(time) 0.015905380261
Ca_s(time) 0.05487
f_R(time) 0.188

Observables: none

brightman_fell_2000 @ v0.0.1

Brightman, Fell, 2000

nothing

Parameters:

Name Description
k14 0.005
f 0.2
V_22 920000.0
v_1 1.0
kn3 0.7
k25 8.3
K_21 9000.0
V_26 400000.0
k9 12.0
kn12 10.0
V_20 920000.0
k8 0.35
K_22 600000.0
DT 6.5
V_28 75.0
kn1 0.73
k12 0.0163
K_25 90000.0
K_20 600000.0
k16 0.0012
k_13 15.0
K_24 600000.0
k_11 0.0
kn14 60.0
k3 0.0484
k17 27.0
k2_4 1.0e-7
V_24 200000.0
kn7 0.000347
K_19 9000.0
k21 50.0
k15 720.0
K_23 90000.0
k19 50.0
k4 0.001383
k6 0.35
V_18 97000.0
kn11 3.81
K_26 600000.0
k11 0.002
kn16 3.0
K_10 6000.0
K_28 20000.0
k23 8.3
E 0.12
k1 3.8421e8
V_10 300000.0
K_27 600000.0
k27 1.6
k7 1.0
K_18 6000.0
K_9 6000.0
k2 0.7
k5 0.35

States:

Name Description
MEKPP(time) 0.0
X(time) 0.0
Ras_GAP(time) 0.0
GSP(time) 0.0
ShcP(time) 0.0
RL(time) 0.0
t(time) 0.0
ERK(time) 750000.0
RasGTP(time) 200.0
Li(time) 0.0
ERKPP(time) 0.0
Rs(time) 11100.0
Ri(time) 3900.0
ERKP(time) 0.0
Ras_ShcGS(time) 0.0
R2L2(time) 0.0
RasGDP(time) 19800.0
Rafa(time) 0.0
MEK(time) 360000.0
L(time) 1.0e-7
GAP(time) 15000.0
ShcGS(time) 0.0
R2i(time) 0.0
GS(time) 20000.0
Raf(time) 10000.0
Ras_Raf(time) 0.0
Shc(time) 30000.0
MEKP(time) 0.0
R2_CPP(time) 0.0

Observables: none

brown_choe_shanahan_czeisler_1997 @ v0.0.1

Brown, Choe, Shanahan, Czeisler, 1997

nothing

Parameters:

Name Description
tau_C 23.67
tau_lamda 24.04
A_max 6.51
tau_I 2.82
tau_alpha 25.92
t_off 1792.0
t_on 1316.0

States:

Name Description
H1(time) 0.05
H2(time) 1.0

Observables: none

bueno_2007 @ v0.0.1

Bueno, 2007

nothing

Parameters:

Name Description
mcell 0.0
tau_v_plus 1.45
endo 0.0
u_m 0.3
u_p 0.13
k_s 2.0994
V_0 -83.0
u_s 0.9087
V_fi 2.7
tau_s1 2.7342
epi 1.0

States:

Name Description
u(time) 0.0
v(time) 1.0
s(time) 0.0
w(time) 1.0

Observables: none

bugbuster @ v0.0.1

Bugbuster Standard Virtual Biological Machine

Please click on one of the exposures below for documentation and model file access.

Parameters: none

States: none

Observables: none

bugenhagen_cowley_beard_2010 @ v0.0.1

Bugenhagen 2010

A computational model of the overall baroreflex heart rate control system.

Parameters: none

States: none

Observables: none

butera_rinzel_smith_1999 @ v0.0.1

Butera, Rinzel, Smith, 1999

nothing

Parameters:

Name Description
C 21.0
theta_h -48.0
sigma_h 6.0
g_KS 5.6
E_K -85.0
tau_k_max 10000.0
sigma_m -5.0
sigma_n -4.0
g_NaP 2.8
i_app 0.0
sigma_k -6.0
E_L -50.0
g_Na 28.0
theta_n -29.0
g_L 2.8
theta_k -38.0
tau_h_max 10000.0
g_K 11.2
E_syn_e 0.0
g_tonic_e 0.0
tau_n_max 10.0
E_Na 50.0
theta_m -34.0

States:

Name Description
V(time) -55.0
h(time) 0.46
n(time) 0.01
k(time) 0.22

Observables: none

butera_rinzel_smith_II_1999 @ v0.0.1

Butera, Rinzel, Smith II 1999

nothing

Parameters: none

States: none

Observables: none

C


calzone_thieffry_tyson_novak_2007 @ v0.0.1

Calzone, Thieffry, Tyson, Novak, 2007

nothing

Parameters:

Name Description
k_iwee__ 1.0
j_m 0.05
k_sstg 0.02
k_astg__ 1.0
j_afz 0.01
k_awee 0.3
k_istg 0.3
k_in 0.15
k_wee__ 1.0
j_iie 0.01
k_ez 0.5
k_sc 0.01
Wee1_T 0.8
k_dstg 0.015
j_astg 0.05
k_stg_ 0.2
k_stg__ 2.0
k_outw 0.01
j_awee 0.05
k_dn_ 0.01
k_inw 0.04
k_astg_ 0.0
j_istg 0.05
k_dc_ 0.01
k_ins 0.08
k_out 0.0
j_aie 0.01
k_sxm 0.0005
j_iwee 0.05
k_wee_ 0.005
k_dm_ 0.002
k_dm__ 0.2
k_dn__ 1.5
k_iwee_ 0.01
k_aie 1.0
k_ifz 0.2
epsilon 7.0e-5
k_outs 0.02
k_sxp 0.001
k_iie 0.4
j_ifz 0.01
k_afz 1.0

States:

Name Description
Stg_n(time) 0.0
preMPF_n(time) 0.0
StgP_n(time) 0.0
Stg_m(time) 1.0
IE(time) 0.0
N(time) 1.0
preMPF_c(time) 0.0
FZY(time) 0.0
Wee1_c(time) 0.0
MPF_c(time) 1.0
StgP_c(time) 0.0
Xp(time) 0.0
Wee1P_n(time) 0.0
Wee1_n(time) 0.0
Xm(time) 0.0
Stg_c(time) 1.0
MPF_n(time) 0.0

Observables: none

campbell_chandra_2006 @ v0.0.1

Campbell, Chandra, 2006

nothing

Parameters:

Name Description
f 1.0
g 1.0
L_0 2.12
k_off 1.0
alpha 0.1
epsilon 1.0
x_0 1.0
k_a 0.0
k_on 1.0
beta 2.0

States:

Name Description
R_on(time) 1.0
A(time) 0.0
x(time) 1.0
L(time) 2.12

Observables: none

cardenas_1996 @ v0.0.1

The Glucose-induced Switch Between Glycogen Phosphorylase and Glycogen Synthase in the Liver: Outlines of a Theoretical Approach

The glucose-induced switch between glycogen phosphorylase and glycogen synthase in the liver is investigated by means of a theoretical approach based on a minimal, bicyclic cascade model involving the reversible phosphorylation of the two enzymes. The aim of the analysis is to evaluate the contribution of different factors to the sequential changes in the activity of glycogen phosphorylase and glycogen synthase observed following the addition of suprathreshold amounts of glucose.

Parameters:

Name Description
V_4 0.2
K_a4 0.5
alpha 9.0
K_a3 0.5
GLC 32.5
K_a2 10.0
V_M2 0.22
G6P 0.4
beta 9.0
K_3 0.4
K_1 0.1
V_M3 0.05
V_1 1.25
K_a1 10.0
K_4 0.4
K_2 0.2
k6 0.03
k5 2.75

States:

Name Description
G6P(time) 0.1
GLC(time) 5.0
GSa(time) 0.02
Pha(time) 0.845

Observables: none

cardiovascular_circulation_dvad @ v0.0.1

Cardiovascular Circulation DVad

nothing

Parameters: none

States: none

Observables: none

cardiovascular_circulation_ivad @ v0.0.1

Cardiovascular Circulation IVad

nothing

Parameters: none

States: none

Observables: none

cardiovascular_circulation_systemic @ v0.0.1

Cardiovascular Circulation Systemic

nothing

Parameters:

Name Description
T 1.0
C 20.5
Ts2 0.45
Vlv0 500.0
L 0.0017
P0 0.0
PlvIni 1.0
Emax 2.5
ElvMin 0.1
CVmi 400.0
Emin 0.1
P0sat 100.0
Q0sat 0.0
Rsat 0.05
V0 20.0
CV 400.0
ElaMin 0.15
ElvMax 2.5
Vini 4.0
VlvIni 5.0
Csvn 20.5
Csat 1.6
Pini 1.0
CVao 350.0
Ts1 0.3
Lsas 6.2e-5
Csas 0.08
Rscp 0.52
VlaIni 4.0
Rsas 0.003
Rsar 0.5
Tpww 0.09
Vla0 20.0
ElaMax 0.25
P0svn 0.0
Tpwb 0.92
Q0 0.0
Rsvn 0.075
P0sas 100.0
PlaIni 1.0
Q0sas 0.0
R 0.5
Lsat 0.0017

States:

Name Description
Pi(t) 0.0
Qo(t) 0.0
V(t) 20.0

Observables: none

cardiovascular_circulation_westkessel @ v0.0.1

Cardiovascular Circulation Westkessel

nothing

Parameters: none

States: none

Observables: none

cartwright_husain_1986 @ v0.0.1

Cartwright, Husain, 1986

nothing

Parameters:

Name Description
dR 0.1
dT 0.023
T_ 8.0
L_ 30.0
rL 5.0
dL 0.015
rR 0.1
rT 0.01

States:

Name Description
T(time) 12.0
R(time) 0.0
L(time) 10.0

Observables: none

chang_fujita_1999 @ v0.0.1

Chang, Fujita, 1999

nothing

Parameters:

Name Description
k14 1.065e6
k20 218.0
k21 100000.0
k10 418300.0
k9 100000.0
k13 100000.0
k18 100000.0
k25 100000.0
k15 100000.0
k26 31.92
k29 100000.0
k8 89400.0
k19 1000.0
k4 4.928e6
k22 418300.0
Na_ 10.0
k6 1.065e6
Cl 96.0
k11 100000.0
Na 50.0
k12 4.982e6
k23 100000.0
k16 89400.0
D_ 1.0e-6
D 1.0e-6
k31 100000.0
k32 0.1166
k1 100000.0
Cl_ 40.0
k27 100000.0
k28 138900.0
k3 100000.0
k7 100000.0
k17 458700.0
k30 0.3514
k5 100000.0
k2 418300.0
k24 31.92

States:

Name Description
ENaD(time) 0.08333
ENa(time) 0.08333
ED_(time) 0.08333
ENa_(time) 0.08333
E_(time) 0.08333
ENaD_(time) 0.08333
ENaCl(time) 0.08333
E(time) 0.08333
ENaCl_(time) 0.08333
ECl(time) 0.08333
ED(time) 0.08333
ECl_(time) 0.08333

Observables: none

chang_fujita_2001 @ v0.0.1

Chang, Fujita, 2001

nothing

Parameters:

Name Description
psi 1.0
k2 7.87e6
F 96500.0
k10 92600.0
k9 514000.0
T 310.0
KH 1.0
HCO3 1.0
k8 8.28e6
k4 8.28e6
Ki_Cl 0.528
k6 7.87e6
Na_ 9.5
H 1.0
k11 324000.0
H_ 1.0
psi_ -89.6
Na 1.0
Cl 1.0
k12 58300.0
k1 1.0e8
Cl_ 1.0
k3 1.0e8
ATP_ 1.0
HCO3_ 1.0
NH4_ 1.3
k7 1.0e8
Ki_HCO3 0.423
Pi_ 1.0
k5 1.0e8
R 8.314
ADP_ 1.0
NH4 1.0

States:

Name Description
ENH4(time) nothing
EHCO3_(time) nothing
ENa(time) nothing
EH_(time) nothing
ENa_(time) nothing
E_(time) nothing
EH(time) nothing
EH2(time) nothing
E(time) nothing
EH2_(time) nothing
EHCO3(time) nothing
ECl(time) nothing
ECl_(time) nothing
ENH4_(time) nothing

Observables: none

chang_fujita_b_1999 @ v0.0.1

Chang, Fujita, B, 1999

nothing

Parameters:

Name Description
RT 2.579
L_mc_v 5.22e-9
C_s_Imp 0.04525
J_mc_NaCl_max 3.21e-5
K_mc_K_KCl 0.053
K_Na_ATPase 0.012
K_mc_Cl_KCl 0.0213
P_ms_Na 4.8e-6
J_mc_KCl_max 6.31e-8
C_c_Imp 0.1124
P_ms_K 4.8e-6
C_m_Imp 0.1033
P_mc_Na 3.27e-6
P_ms_Cl 2.4e-6
P_mc_K 4.9e-7
J_a_max 2.69e-6
P_mc_Cl 1.43e-6
L_ms_v 0.0
P_sc_K 0.000474
K_mc_Na_NaCl 0.0511
psi_m -28.0
L_sc_v 5.22e-7
psi_c -86.4
psi_s 0.0
K_mc_Cl_NaCl 0.0192
F 96.48
P_sc_Cl 9.16e-5

States:

Name Description
C_m_Na(time) 0.05
C_c_K(time) 0.1637
C_c_Na(time) 0.0164
C_m_K(time) 0.002
C_s_Cl(time) 0.112
C_c_Cl(time) 0.0203
C_s_K(time) 0.00425
C_s_Na(time) 0.1438
C_m_Cl(time) 0.03

Observables: none

chassagnole_rais_quentin_fell_mazat_2001 @ v0.0.1

Chassagnole, Rais, Quentin, Fell, Mazat, 2001

nothing

Parameters:

Name Description
K_hsp 0.31
K_iLys 9.45
h_Thr 4.09
V_max_HK 483.0
V_max_TS 208.0
V_max_HDH 2585.0
K_eq 284000.0
K_Pi 10.2
V_max_AK_III 299.0
h 1.41
K_ihs 4.7
K_NADP 0.144
V_max_AK_I 463.0
K_iThr 1.09
alpha 2.47
K_aspp 0.022
K_asp 0.97
h_Lys 2.8
K_ASA 0.11
K_ATP 0.072
K_ADP 0.25
K_NADPH 0.029
K_iATP 4.35
V_max_ASD 598.0
K_hs 0.11

States:

Name Description
Pi(time) 0.0
hsp(time) 0.0
ATP(time) 30.0
Asp(time) 10.0
ASA(time) 0.0
NADPH(time) 0.0
NADP(time) 0.0
aspp(time) 0.0
Thr(time) 0.0
hs(time) 0.0
Lys(time) 0.0
ADP(time) 0.0

Observables: none

chay_1997 @ v0.0.1

Chay, 1997

nothing

Parameters:

Name Description
g_NS 5.0
lamda_h 12.5
k_Ca 7.0
T 310.0
K_NS 50.0
g_K_Ca 5.0
Sh -7.0
Sd 5.0
Ca_o 2500.0
V_K -75.0
Vn -18.0
lamda_n 12.5
K_Ca 1.0
omega 0.2
V_Na 80.0
Vm -25.0
V_fast 80.0
Cm 1.0
VNS -20.0
g_NaL 0.3
P_Ca 2.0
Vh -48.0
g_fast 600.0
k_rel 0.2
Vd -10.0
Sn 14.0
lamda_d 2.5
g_K_ATP 2.0
g_K_dr 600.0
Sm 9.0
R 8314.0
F 96485.0
k_pump 30.0

States:

Name Description
d(time) 0.0031711238
V(time) -38.34146
n(time) 0.1836403
h(time) 0.214723
Ca_i(time) 0.6959466
Ca_lum(time) 102.686

Observables: none

chay_lee_fan_1995 @ v0.0.1

Chay, Lee, Fan, 1995

nothing

Parameters:

Name Description
kg 0.005
ld 250.0
G_total 200.0
hd 100.0
rho_kc 90000.0
Ks 300.0
hg 0.0
rho_hc 1.0
kp_ 2.0e-7
KD 25.0
PLC_total 10.0
rho_lc 200.0
hp_ 0.5
kd_ 700.0

States:

Name Description
G_alpha_GDP(time) nothing
DAG(time) nothing
PLC_active(time) nothing
Ca_i(time) nothing
G_alpha_GTP(time) nothing

Observables: none

chen_calzone_csikasznagy_cross_novak_tyson_2004 @ v0.0.1

Chen, Calzone, Csikasznagy, Cross, Novak, Tyson, 2004

nothing

Parameters:

Name Description
ks_bud 0.2
Ji_tem 0.1
epsilon_sbf_n2 2.0
ks_n2__ 0.15
epsilon_sbf_n3 10.0
ka_apc 0.1
kd_b2__ 0.4
kd_swi 0.08
kas_esp 50.0
kas_rent 200.0
ki_mcm 0.15
Ja_apc 0.1
kdi_rentp 2.0
kd_net 0.03
epsilon_f6_k2 0.03
ks2_pds__ 0.055
kd3_c1 1.0
Jspn 0.14
kas_f5 0.01
Kez2 0.2
ks_b2__ 0.04
C0 0.4
kd1_pds_ 0.01
Ji_apc 0.1
epsilon_c1_n2 0.06
epsilon_cdh_n2 0.4
epsilon_f6_n2 0.06
ks_20__ 0.6
kd1_c1 0.01
Cdc15_T 1.0
kg 0.007702
ks_f6___ 0.004
ka_15_ 0.002
kd_b5__ 0.16
kpp_c1 4.0
epsilon_c1_n3 0.3
ka_cdh_ 0.01
J20_ppx 0.15
ks_f6_ 0.024
ks_c1_ 0.012
ks_ori 2.0
epsilon_ori_b5 0.9
Ja_tem 0.1
epsilon_sbf_b5 2.0
epsilon_f6_b5 0.1
epsilon_bud_n2 0.25
kpp_f6 4.0
ks_swi__ 0.08
ks_b2_ 0.001
ks_swi_ 0.005
ka_cdh__ 0.8
ks_20_ 0.006
kkp_net__ 0.6
epsilon_cdh_b2 1.2
Tem1_T 1.0
epsilon_bud_n3 0.05
kas_b2 50.0
kd_20 0.3
kd_n2 0.12
epsilon_c1_b2 0.45
ka_mcm 1.0
ks_b5_ 0.0008
ks1_pds__ 0.03
Ji_mcm 0.1
ka_20__ 0.2
ks_cdh 0.01
ks_net 0.084
ks_c1__ 0.12
epsilon_f6_n3 0.3
Ji_cdh 0.03
ki_15 0.5
epsilon_c1_b5 0.1
ks_pds_ 0.0
ka_swi 2.0
kd_14 0.1
Jd2_f6 0.05
ka_sbf 0.38
ki_cdh_ 0.001
Esp1_T 1.0
kas_b5 50.0
kas_rentp 1.0
ki_sbf_ 0.6
kd_ppx_ 0.17
kd2_f6 1.0
kpp_net_ 0.05
ki_sbf__ 8.0
kd2_pds__ 0.2
ki_apc 0.15
epsilon_bud_b5 1.0
ks_n2_ 0.0
Kez 0.3
kd_ppx__ 2.0
ks_spn 0.1
kkp_net_ 0.01
epsilon_cdh_b5 8.0
kdi_f2 0.5
kd3_pds__ 0.04
kd_b5_ 0.01
kdi_b5 0.06
kd1_f6 0.01
kd2_c1 1.0
kdi_f5 0.01
ka_15__ 1.0
Ja_cdh 0.03
Ji_sbf 0.01
Jpds 0.04
Jd2_c1 0.05
epsilon_c1_k2 0.03
epsilon_ori_b2 0.45
ki_cdh__ 0.08
kd_ori 0.06
Dn3 1.0
kpp_net__ 3.0
Ja_sbf 0.01
ki_swi 0.05
ks_14 0.2
kd_spn 0.06
kd_b2p 0.15
kdi_b2 0.05
kas_f2 15.0
epsilon_f6_b2 0.55
Jn3 6.0
kd3_f6 1.0
kd_b2_ 0.003
ka_20_ 0.05
kd_cdh 0.01
epsilon_cdh_n3 0.25
Ja_mcm 0.1
kd_bud 0.06
B0 0.054
ka_15___ 0.001
ks_f6__ 0.12
kdi_rent 1.0
kdi_esp 0.5
ks_b5__ 0.005
ks_ppx 0.1

States:

Name Description
Swi5(time) 0.9562
Clb5(time) 0.0518
Cdc14_T(time) 2.0
Cdh1_T(time) 1.0
Net1(time) 0.0186
Net1_T(time) 2.8
Sic1P(time) 0.0064
C2(time) 0.2384
Cdh1(time) 0.9305
Pds1(time) 0.0256
C2P(time) 0.024
Sic1(time) 0.0229
F2P(time) 0.0274
Swi5_T(time) 0.9765
Cdc15(time) 0.6565
F5(time) 7.2e-5
mass(time) 1.206
Cln2(time) 0.0652
BUD(time) 0.0085
C5P(time) 0.0069
C5(time) 0.0701
Cdc20_A(time) 0.4443
Cdc6(time) 0.1076
RENT(time) 1.0495
APC_P(time) 0.1015
SPN(time) 0.0305
ORI(time) 0.0009
PPX(time) 0.1232
Clb2(time) 0.1469
Esp1(time) 0.3013
F5P(time) 7.9e-6
Cdc6P(time) 0.0155
Tem1(time) 0.9039
F2(time) 0.2361
Cdc20_T(time) 1.9163
Cdc14(time) 0.4683

Observables: none

chen_csikasz_nagy_gyorffy_val_novak_tyson_2000 @ v0.0.1

Chen, Csikasz-Nagy, Gyorffy, Val, Novak, Tyson, 2000

nothing

Parameters: none

States: none

Observables: none

chen_popel_2006 @ v0.0.1

Chen, Popel, 2006

nothing

Parameters:

Name Description
k14 53.9
O2 172.0
k_1 0.1
k_8 0.1
k10 3.33
k13 0.033
k9 11.4
k12 0.91
k_5 98.0
k_4 11.4
k1 0.1
k8 0.1
k_10 89.9
k4 1.89
k3 0.91
k7 0.91
k6 12.6
k_9 1.89
k5 2.58
k2 0.91
k11 29.4

States:

Name Description
NOHA(time) 0.0
Fe3_O2_NOHA(time) 0.0
NO3(time) 0.0
Fe3_NO(time) 0.0
Fe3(time) 0.045
citrulline(time) 0.0
Fe3_Arg(time) 0.0
Fe2_NOHA(time) 0.0
NO(time) 0.0
Arg(time) 100.0
Fe2_Arg(time) 0.0
Fe3_O2_Arg(time) 0.0
Fe2_NO(time) 0.0
Fe3_NOHA(time) 0.0
Fe2(time) 0.0

Observables: none

chen_popel_2007 @ v0.0.1

Chen, Popel, 2007

nothing

Parameters: none

States: none

Observables: none

cheng_brown_loeb_2000 @ v0.0.1

Cheng, Brown, Loeb, 2000

nothing

Parameters:

Name Description
c1 23.0
nf0 2.1
cv1 9.18
L_r1 1.17
L_r2 1.17
as2 0.96
nf1 3.3
T_f4 200.0
T_f2 0.1
LT_r 0.964
as1 1.76
V_Y 0.1
omega 0.75
bv 0.69
f_env 1.0
nf 1.0
mass 0.005
T_f3 200.0
T_s 43.0
L_max 0.13
c_Y 0.35
c2 23.0
av2 0.0
LT 0.02
av0 -1.53
eta 0.001
k1 0.046
rho 2.12
beta 1.55
F_max 23.0
av1 0.0
T_L 0.088
T_f1 0.35
V_max -9.15
cv0 -5.7
af 0.56
cT 27.8
kT 0.0047
T_Y 200.0
k2 0.046

States:

Name Description
f_int(time) nothing
f_eff(time) nothing
V(time) nothing
L_eff(time) nothing
Y(time) nothing
T_f(time) nothing
S(time) nothing
L(time) nothing

Observables: none

ciliberto_novak_tyson_2003 @ v0.0.1

Ciliberto, Novak, Tyson, 2003

nothing

Parameters:

Name Description
ks_bud 0.1
ka_mcm 1.0
Js_cdc20 0.3
IE_total 1.0
Va_wee 0.3
ki_sbf_2 2.0
khsl1 1.0
ka_cdc20 1.0
Ji_mcm 0.1
kd_swe_1 0.007
Ja_wee 0.05
Mih1_total 1.0
kd_clb_1 0.015
ki_mcm 0.15
ka_sbf_1 1.0
kd_sic_1 1.0
ks_clb 0.015
Ja_ie 0.01
kmih_1 5.0
Ji_cdh 0.01
kswe_1 2.0
Mcm_total 1.0
kd_swe_2 0.05
ks_cdc20_2 0.3
kd_cdc20 0.1
ki_cdh_1 2.0
kd_clb_2 1.0
ks_cdc20_1 0.005
ks_sweC 0.0
Va_mih 1.0
ki_cdc20 0.25
kd_clb_3 0.1
Ji_wee 0.05
ka_ie 0.1
epsilon 0.5
ka_cdh_1 1.0
Ja_cdc20 0.001
Ji_ie 0.01
kmih_2 0.5
kd_sic 0.01
Vi_mih 0.3
khsl1r 0.01
Jm 10.0
Ja_mih 0.1
Ja_cdh 0.01
ks_swe 0.0025
kswe_3 0.2
mu 0.005
Ji_mih 0.1
Ji_sbf 0.01
kdiss 0.1
ka_sbf_2 0.0
Ja_sbf 0.01
ka_cdh_2 10.0
Vi_wee 1.0
Cdh1_total 1.0
ki_sbf_1 1.0
SBF_total 1.0
kd_cln 0.1
ki_cdh 35.0
Ji_cdc20 0.001
ki_ie 0.04
Ja_mcm 0.1
kd_bud 0.1
kass 300.0
kd_sic_2 3.0
kswe_2 0.01
ks_sic 0.1
ks_cln 0.1

States:

Name Description
Mih1_a(time) 0.808
PTrim(time) 0.0
M(time) 0.802
BE(time) 0.0
Mcm_a(time) 0.933
Swe1M(time) 0.018
Sic1(time) 0.003
Cln(time) 0.054
Cdc20(time) 1.172
Clb2(time) 0.184
PSwe1(time) 0.0
PClb2(time) 0.0
Trim(time) 0.084
Cdc20_a(time) 1.438
Cdh1_a(time) 0.993
Swe1(time) 0.0
SBF_a(time) 0.124
PSwe1M(time) 0.013
IE_a(time) 0.522

Observables: none

ciliberto_petrus_tyson_sible_2003 @ v0.0.1

Ciliberto, Petrus, Tyson, Sible, 2003

nothing

Parameters:

Name Description
koff 0.0001
L 0.4
kiinact 0.6
kdissoc 0.001
theta 0.3
Jwact 0.01
Jwinact 0.01
kassoc 0.1
Wee1_total 8.0
kiact 0.15
kwact 0.75
kedeg 0.017
k25A 0.1
Deg 0.0
kxdeg 0.01
kwee 1.5
Jiinact 0.01
kdact 0.023
kwinact 1.5
epsilon 0.001
kon 0.02
Jiact 0.01
n 4.0

States:

Name Description
Xic(time) 3.0
PCdk2_CycErem(time) 0.0
Xic_Cdk2_CycE(time) 0.0
Xic_PCdk2_CycE(time) 0.0
Cdk2_CycErem(time) 0.0
Wee1_a(time) 1.02
Kin_a(time) 0.6
Cdk2_CycE(time) 0.06
Xic_PCdk2_CycErem(time) 0.0
Deg_a(time) 0.0
Xic_Cdk2_CycErem(time) 0.0
PCdk2_CycE(time) 0.94
Xicrem(time) 0.0

Observables: none

ciliberto_tyson_2000 @ v0.0.1

Ciliberto, Tyson, 2000

nothing

Parameters:

Name Description
Vwee 0.025
Vwee_ 2.5
Kmie 0.01
k25 18.0
IEtot 1.0
V2_ 0.6
V25_ 0.4
Cdc25tot 1.0
Cdc2tot 1.0
V2 0.01
kie 4.5
kwr 0.8
q 1.0
s 0.021
k25r 0.8
Kmwr 1.0
Kmap 0.01
Kmw 0.1
kier 0.34
Kmier 0.01
Km25r 1.0
k1 0.024
kapr 0.3
Km25 0.1
Wee1tot 1.0
k3 1.15
kw 18.0
Kmapr 1.0
APCtot 1.0
V25 0.04
R 1.0
kap 0.3

States:

Name Description
Cdc25P(time) 0.4844362
IEP(time) 0.002287817
M(time) 0.0142077
Y(time) 0.01577552
APC_(time) 0.5051103
preMPF(time) 0.02541723
Wee1(time) 0.5155638

Observables: none

clancy_rudy_2001 @ v0.0.1

Clancy, Rudy, 2001

nothing

Parameters:

Name Description
nicholsarea 5.0e-5
preplength 0.001
gamma_Cai 1.0
gamma_Cao 0.341
hATP 2.0
stim_start 3.0
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
delta_Ca_ith 0.00018
Ko 4.5
gamma_Nao 0.75
Logicthresh 0.98
CMDN_max 0.05
Cm 0.001
c2 0.0001
mu_2 0.1
beta_in 1077.0
tau_tr 0.18
Ca_NSR_max 15.0
alpha_in 2172.0
kATP 0.00025
c1 0.00025
i_Kr_factor 1.0
stim_duration 0.002
Cao 1.8
g_Nab 0.004
K_mpCa 0.0005
gamma_Nai 0.75
mu_1 0.002
stim_period 1.0
stim_end 9.0
kdKNa 66.0
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_K_ATP_on 1.0
I_pCa 1.15
I_NaK 2.25
Nao 132.0
ATPi 3.0
K_mNai 10.0
P_Ca 0.00054
g_Na 18.5
I_up 8.75
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
nKNa 2.8
g_CaT 0.05
K_mTn 0.0005
nATP 0.24
K_mKo 1.5
CSQNthresh 0.7
gamma 0.15
F 96485.0
R 8314.0

States:

Name Description
OVRLDtrack3(time) 0.0
P_C1(time) 3.3836e-8
P_C3(time) 4.9493e-6
Ca_NSR(time) 1.558
OVRLDtrack2(time) 0.0
P_C2(time) 1.6778e-8
P_O(time) 1.089e-10
f(time) 0.99976
Cainfluxtrack(time) 0.0
P_UC3(time) 0.68280597
P_IF(time) 4.017e-5
xs1(time) 0.00445
APtrack2(time) 0.0
P_LC1(time) 7.0e-8
P_IS(time) 1.846e-5
P_LO_Na(time) 4.0e-8
P_O_Na(time) 4.753e-8
xs2(time) 0.00445
Nai(time) 10.904
P_I(time) 3.334e-11
APtrack(time) 0.0
APtrack3(time) 0.0
zdv(time) 0.011614
d(time) 3.2474e-6
g(time) 0.99425
P_LC3(time) 0.00187739
OVRLDtrack(time) 0.0
P_UO_Na(time) 3.17e-6
P_UC1(time) 0.0001437
V(time) -88.859
ydv(time) 0.99998
P_LC2(time) 1.946e-5
Ca_JSR(time) 1.556
Ki(time) 140.433
b(time) 0.0009757
P_UC2(time) 0.00721646
Cai(time) 0.0001073

Observables: none

clancy_rudy_2002 @ v0.0.1

Clancy, Rudy, 2002

nothing

Parameters:

Name Description
nicholsarea 5.0e-5
preplength 0.001
gamma_Cai 1.0
gamma_Cao 0.341
hATP 2.0
stim_start 3.0
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
delta_Ca_ith 0.00018
Ko 4.5
gamma_Nao 0.75
Logicthresh 0.98
CMDN_max 0.05
Cm 0.001
c2 0.0001
beta_in 1077.0
tau_tr 0.18
Ca_NSR_max 15.0
alpha_in 2172.0
kATP 0.00025
c1 0.00025
stim_duration 0.002
Cao 1.8
g_Nab 0.004
K_mpCa 0.0005
gamma_Nai 0.75
stim_period 1.0
stim_end 9.0
kdKNa 66.0
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_K_ATP_on 1.0
I_pCa 1.15
I_NaK 2.25
Nao 132.0
ATPi 3.0
K_mNai 10.0
P_Ca 0.00054
g_Na 23.5
I_up 8.75
g_Cab 0.003016
g_Kp 0.00552
stim_amplitude -50.0
G_rel_overload 4000.0
K_mrel 0.0008
CSQN_max 10.0
gamma_Ko 0.75
nKNa 2.8
g_CaT 0.05
K_mTn 0.0005
nATP 0.24
K_mKo 1.5
CSQNthresh 0.7
gamma 0.15
F 96485.0
R 8314.0

States:

Name Description
P_UIF(time) 2.25e-10
OVRLDtrack3(time) 0.0
Ca_NSR(time) 1.645
OVRLDtrack2(time) 0.0
P_O(time) 1.064e-10
P_LO(time) 4.37e-17
P_UC3(time) 9.06e-6
P_UO(time) 4.15e-13
P_O_Na(time) 3.491e-13
Nai(time) 11.544
APtrack(time) 0.0
g(time) 0.9944
V(time) -88.998
ydv(time) 0.99998
P_UIM2(time) 1.075e-12
b(time) 0.000963
P_IC2(time) 1.6e-8
P_UIM1(time) 6.49e-11
Cai(time) 0.000114
P_UIC3(time) 3.778e-6
P_C1(time) 3.341e-8
P_C3(time) 4.95e-6
P_IM1(time) 8.73e-12
P_C2(time) 1.657e-8
f(time) 0.9998
Cainfluxtrack(time) 0.0
P_LC1(time) 5.68e-14
P_IF(time) 7.571e-11
xs1(time) 0.00441
APtrack2(time) 0.0
P_IC3(time) 1.271e-6
xs2(time) 0.00441
P_I(time) 3.246e-11
APtrack3(time) 0.0
P_LC3(time) 9.535e-10
zdv(time) 0.01152
d(time) 3.176e-6
P_UIC2(time) 4.758e-8
OVRLDtrack(time) 0.0
P_UC1(time) 5.399e-10
P_LC2(time) 1.2e-11
Ca_JSR(time) 1.643
Ki(time) 140.275
P_UC2(time) 1.14e-7
P_IM2(time) 5.326e-14

Observables: none

cloutier_2009 @ v0.0.1

Cloutier 2009

nothing

Parameters:

Name Description
stim 1.0
Vmaxf_n_pgi 0.5
Sm_g 10500.0
PCrg_tot 5.0
Vmax_g_ATPase 0.035657
kn_pgk 0.4287
kfn_ck 0.0524681
Vmaxr_n_pgi 0.45
Vm_cg_GLC 0.0098394
Vmax_n_ATPase 0.04889
Vmax_g_hk 0.050461
dHb0 0.064
Km_ADP 0.00107
Vm -70.0
NAe 150.0
Vm_ec_LAC 0.0325
kpump 3.17e-7
Rcg 0.022
R_GLU_NA 0.075
Rce 0.0275
Km_ec_LAC 0.764818
Km_GLY 1.0
PCrn_tot 5.0
Ren 0.4444444444444444
k3 0.43
krn_ldh 0.1046
to 200.0
aATP_mito 5.0
Vg 0.25
Vmax_glyp 4.922e-5
tv 35.0
Vmax_n_hk 0.0513
Vmax_g_mito 0.008454
Vmax_glys 0.0001528
KO1 1.0
Vm_eg_GLC 0.038089
tend 300.0
PScapg 0.2457
sr 4.59186
Km_F6P_pfk 0.18
krg_ldh 0.54682
kn_pk 28.6
v2_n 2.55
Km_G6P_glys 0.5
krn_ck 0.015
gg_NA 0.00325
Km_O2 0.0029658
Km_eg_GLC 3.53
Vmax_ge_LAC 0.086124
kn_pfk 0.55783
Km_ne_LAC 0.09314
kfg_ck 0.0243
t1 2.0
Vmax_ne_LAC 0.1978
tend_GLY 440.0
CBF0 0.012
Rng 1.8
qak 0.92
Ki_ATP 0.7595
nh_O2 2.7
Km_G6P 0.5
GLCa 4.8
F 96500.0
HbOP 8.6
k2 0.46
deltaf 0.42
Vmax_g_gs 0.3
kfg_ldh 6.2613
v1_n 0.041
Km_cg_GLC 9.92
Km_pump 0.4243
sr_GLY 4.0
Km_F6P_pgi 0.06
Vn 0.45
Vmax_eg_GLU 0.0208
kg_pfk 0.403
t_n_stim 2.0
Vmax_gc_LAC 0.00021856
GLY_inh 4.2
Vmax_n_mito 0.05557
Km_gc_LAC 0.12862
nH 4.0
ATPtot 2.379
Vv0 0.0236
Vmaxf_g_pgi 0.5
to_GLY 83.0
Km_ATP 0.01532
Km_en_GLC 5.32
KO2 1.0
RT 2.57734e6
aGLY_inh 20.0
Vm_en_GLC 0.50417
kg_pgk 0.2514
Vm_ce_GLC 0.0489
PScapn 0.2202
Vmaxr_g_pgi 0.45
Km_PYR 0.0632
aG6P_inh_hk 20.0
Km_ge_LAC 0.22163
NADH_g_tot 0.22
Rcn 0.01222
KO3 1.0
G6P_inh_hk 0.6
Km_GLC 0.105
NADH_n_tot 0.22
NAero 3.0
krg_ck 0.02073
Reg 0.8
Vc 0.0055
CO2a 1.2
O2a 8.34
Sm_n 40500.0
gn_NA 0.0039
Ko2 0.089733
rATP_mito 20.0
LACa 0.313
k1 2.22
nOP 15.0
delta_GLY 62.0
kfn_ldh 5.3
Km_GLU 0.05
kg_pk 2.73
Km_ce_GLC 8.4568

States:

Name Description
CO2c(time) 2.12
PEPg(time) 0.0254
GLUe(time) 0.0
LACg(time) 0.4651
PYRn(time) 0.0388
O2g(time) 0.1589
ATPg(time) 2.24
GLUg(time) 0.0
G6Pn(time) 0.7275
ATPn(time) 2.2592
GLCg(time) 0.1656
F6Pn(time) 0.1091
GLUn(time) 3.0
GLCe(time) 0.3339
NAg(time) 13.36
G6Pg(time) 0.7326
PEPn(time) 0.0037
PYRg(time) 0.1711
GLYg(time) 2.5
GLCc(time) 4.6401
Vv(time) 0.0237
GAPn(time) 0.0418
O2n(time) 0.0975
LACe(time) 0.3986
GAPg(time) 0.0698
dHb(time) 0.0218
F6Pg(time) 0.1116
LACc(time) 0.3251
O2c(time) 7.4201
LACn(time) 0.3856
NADHn(time) 0.0319
NADHg(time) 0.0445
GLCn(time) 0.2633
NAn(time) 15.533
PCrn(time) 4.2529
PCrg(time) 4.6817

Observables: none

cloutier_wellstead_2009 @ v0.0.1

Cloutier Wellstead 2009

nothing

Parameters:

Name Description
Vlac_0 0.355
stim 1.0
Vmaxf_pfk2 0.0002
Km_ATP_hk 0.5
Km_ADP_op 0.005
nh_amp 2.0
Ka_AMP 0.05
Vmax_op 1.0
v1_n 0.5
tend 200.0
Km_ATP_pfk 0.05
kr_ck 1.26
ANP 2.51
Vmaxr_pfk2 0.0001036
kf_ck 3.0
Km_F6P_pfk 0.18
v2_n 0.0
Km_ATP_pfk2 0.05
Km_PYR_op 0.5
Q_adk 0.92
Vmax_ATPase 0.9355
t_n_stim 2.0
Kamp_pfk2 0.005
Km_F6P_pfk2 0.01
Vmax_hk 2.5
KI_F6P 0.068
K_LAC 0.641
Vmax_pfk 3.85
Km_F26P_pfk 0.01
Km_ADP_pk 0.005
nAMP 0.5
Km_F26P_pfk2 0.0001
Km_GAP_pk 0.4
Vmax_pk 5.0
kr_ldh 2.5355
K_LAC_eff 0.71
nATP 0.4
kf_ldh 12.5
to 50.0
KI_ATP 1.0
Km_ATP 0.5
PCrtot 20.0

States:

Name Description
GAP(time) 0.0405
F6P(time) 0.2
LAC(time) 0.5
PCr(time) 18.14
PYR(time) 0.1
F26P(time) 0.001
ATP(time) 2.402

Observables: none

colegrove_albrecht_friel_2000 @ v0.0.1

Colegrove, Albrecht, Friel, 2000

nothing

Parameters:

Name Description
EC50_extru 378.8
n_extru 1.8
k_leak 3.7e-7
Ca_o 0.002
k_inhib 500.0
kuni_max 75.9
Vmax_NaCa -35.0
gamma 2.0
EC50_uni 10.0
n_uni 2.0
Vmax_extru 28.3
n_inhib 6.0
EC50_NaCa 307.0

States:

Name Description
Ca_m(time) 5.0e-8
Ca_i(time) 0.002

Observables: none

conradie_bruggeman_ciliberto_csikasz_nagy_novak_westerhoff_snoep_2010 @ v0.0.1

Conradie, Bruggeman, Ciliberto, Csikasz-Nagy, Novak, Westerhoff and Snoep, 2010

nothing

Parameters: none

States: none

Observables: none

cooling_hunter_crampin_2007 @ v0.0.1

Cooling, Hunter, Crampin, 2007

nothing

Parameters:

Name Description
kf2 0.000275
kf16 1.25
kf13 6.0
PIP2 4000.0
kf4 0.3
kf9 0.0042
Ls 0.1
kf15 3.8
Km14 19.8
Kd2 27500.0
ts 10.0
kf3 1.0
kf14 0.444
kf1 0.0003
kf6 1.0
Kd1 3.0e-5
Vc 2550.0
Kd11 0.1
Kd4 3.0e-5
kf10 0.042
kf12 6.0
kf7 0.15
kf5 0.0004
Km15 5.0
kr10 1.0
Rpc 4.61
kr9 1.0
kr8 0.0167
kf11 0.0334
kr3 0.001
kf8 0.0167

States:

Name Description
Pc(t) 9.09
Gd(t) 10000.0
Rlgp(t) 0.0
Ca(t) 0.1
Rg(t) 5.06
R(t) 13.9
Pcg(t) 0.0
P(t) 90.9
Rlg(t) 0.0
Rl(t) 0.0
Pg(t) 0.0
IP3(t) 0.015
Gt(t) 0.0

Observables: none

cooling_hunter_crampin_CellML_2008 @ v0.0.1

Cooling, Hunter, Crampin, Cellml, 2008

nothing

Parameters:

Name Description
kf2 3.8
kr2 1.0
PIP2 4000.0
kf4 0.3
Kd4 3.0e-5
Ls 0.1
Kd2 27500.0
ts 10.0
kf3 1.0
kf5 0.0004
kf1 0.444
Km1 19.8
kf6 1.0
Rpc 4.61
kr1 0.0167
Vc 2550.0
Kd1 3.0e-5
Km2 5.0
kr3 0.001

States:

Name Description
Pc(t) 9.09
Gd(t) 10000.0
Rlgp(t) 0.0
Ca(t) 0.1
Rg(t) 5.06
R(t) 13.9
Pcg(t) 0.0
P(t) 90.9
Rlg(t) 0.0
Rl(t) 0.0
Pg(t) 0.0
IP3(t) 0.015
Gt(t) 0.0

Observables: none

corrias_buist_2007 @ v0.0.1

Corrias, Buist, 2007

nothing

Parameters:

Name Description
J_max_CaSR 0.31705
Na_o 137.0
K_i 164.0
T 310.0
Q10K 1.365
Cm_SM 77.0
G_max_ka_SM 9.0
Q10Na 2.45
G_max_Ltype 65.0
Ca_o 2.5
G_max_Na_SM 3.0
G_max_kr_SM 35.0
T_exp 297.0
G_max_bk 0.0144
Vol_SM 3500.0
E_NSCC -28.0
t_ICCpeak 98.0
period 20000.0
delta_VICC 59.0
K_o 5.9
Q10Ca 2.1
G_max_LVA 0.18
Ach 1.0e-5
V_decay 37.25
G_max_BK 45.7
Gcouple 1.3
t_ICCplateau 7582.0
t_ICC_stimulus 10000.0
Cl_o 134.0
R 8314.4
G_max_NSCC_SM 50.0
F 96486.0
Na_i 10.0

States:

Name Description
d_Ltype_SM(time) 0.0
h_Na_SM(time) 0.05787
f_ca_Ltype_SM(time) 1.0
m_Na_SM(time) 0.005
xa1_SM(time) 0.00414
f_LVA_SM(time) 0.99
Vm_SM(time) -69.75
xr2_SM(time) 0.82
m_NSCC_SM(time) 0.0
xa2_SM(time) 0.72
f_Ltype_SM(time) 0.95
Ca_i(time) 8.0e-5
d_LVA_SM(time) 0.02
xr1_SM(time) 0.0

Observables: none

corrias_buist_2008 @ v0.0.1

Corrias, Buist, 2008

nothing

Parameters: none

States: none

Observables: none

CorriasPurkinje @ v0.0.1

Model of a rabbit Purkinje cell

This workspace contains information regarding the model of a rabbit Purkinje cell published as:

Corrias A., Giles W., Rodriguez B "Ionic mechanisms of electrophysiological properties and repolarization abnormalities in rabbit Purkinje fibers" American Journal of Physiology (Heart and Circulatory Physiology).

Here you can find a CellML file that can be supplied to openCell for running the model in isolation as well as to Chaste (April, 2011 release) for incorporating the model into mono/bidomain simulations.

Parameters:

Name Description
T 310.0
stim_start 700.0
tau_x_to_fast 5.0
G_max_Ltype 5.4
G_max_k1 20.0
tau_x_Ttype 1.0
tau_x_na_late 15.0
SERCA_max 120.0
d_NaCa 0.001
Krel 0.001
G_max_kb 0.01
DIFF_max 5000.0
G_max_cab 0.0001
G_max_ks 3.0
g_nak 442.2
Cm 69.0
G_max_na_late 2.0
periphery_fraction 0.2
g_NaCa 0.001
G_max_kr 1.5
bulk_fraction 0.6
tau_x_Ltype 0.7
G_f_na 0.045290323
tau_y_na_fast 2.0
Na_o 140.0
stim_duration 0.5
Kpmca 0.0001
n_NaCa 3.0
Cao 2.0
G_max_Ttype 0.9
Ca_o 2.0
sr_fraction 0.06
G_f_k 0.188709677
tau_x_na_fast 0.005
stim_period 500.0
stim_end 9.0e6
G_max_to_fast 10.0
PMCA_max 5.0
REL_max 2500.0
K_o 5.4
tau_y_to_fast 350.0
G_max_to_sustained 3.0
H 1.6
Nao 140.0
LEAK_max 10.0
Kmr 1.7
stim_amplitude -4320.0
Kmf 0.000246
G_max_nab 0.01
G_max_na_fast 1140.0
gamma 0.5
cell_volume 13266.5
Hpmca 1.5
R 8314.472
F 96485.3415

States:

Name Description
y_ks(time) 0.0
y_Ttype(time) 0.01
y_Ltype(time) 0.1
y_gate_f_na(time) 0.011099
y_kr(time) 0.25
Ca_i_peripheral(time) 1.0e-5
x_Ttype(time) 0.001337
Ca_i_bulk(time) 3.2e-5
y_na_fast(time) 0.978861
Ca_sr(time) 0.17
Na_i(time) 6.7
x_na_fast(time) 7.0e-6
y_ca_Ltype(time) 0.7
K_i(time) 140.0
x_ks(time) 1.0
x_to_fast(time) 0.0
y_na_late(time) 0.864489
Vm(time) -88.34
y_to_fast(time) 0.7
x_Ltype(time) 3.0e-6
y_gate_f_k(time) 0.011099
x_na_late(time) 1.2e-5

Observables: none

cortassa_ECME_2006 @ v0.0.1

Cortassa et al (2006) ECME model

Parameters: none

States: none

Observables: none

cortassa_aon_marban_winslow_orourke_2003 @ v0.0.1

Cortassa, Aon, Marban, Winslow, Orourke, 2003

nothing

Parameters:

Name Description
Na_i 10.0
na 2.8
Km_MAL 1.493
Kcat_CS 3.2
kh1 1.13e-5
kh2 26.7
stim_start 0.0
Kh_2 5.98e-5
delta_psi_0 0.091
KNa 9.4
Kres 1.35e18
Kres_F 5.765e13
Kcat_SDH 1.0
delta_psi_B 0.05
Km_NAD 38.7
Ka_ADP 0.062
pc2 4.585e-14
ATP_i 6.5
Ki_FUM 1.3
Kd_Ca 1.27
Ki_NADH 0.19
Vmax_NaCa 0.005
r2 1.728e-9
pc1 9.651e-14
rho_F1 0.06
GLU 20.0
p1 1.346e-8
kh4 5.62e-6
Kd_Mg 0.0308
Kcat_IDH 1.94
p3 6.65e-15
ET_CS 0.4
b 0.5
KE_ACO 2.22
pulse_value 1.0
KCa 0.375
Kh_1 8.1e-5
kf_FH 0.83
K_trans 19.0
H 2.5e-5
r3 1.059e-26
CoA 0.02
Vmax_uni 0.000625
n_alpha_KG 1.2
ET_MDH 0.154
kf_AAT 0.644
K_act 0.38
r1 2.077e-18
ni 1.0
ET_IDH 0.109
rc1 2.656e-19
Ka_Ca 1.41
KF1 1.71e6
F 96480.0
n 3.0
Mg 0.4
f 0.0003
T 310.16
ET_SDH 0.5
gH 0.01
L 110.0
pb 3.373e-7
Kcat_MDH 27.75
AcCoA 0.0002
Km_AcCoA 0.0126
Cm 15.0
pa 1.656e-5
g 0.85
ET_KGDH 0.5
FADH2 1.24
Ke_SL 3.115
Ki_OAA 0.0031
rc2 8.632e-27
p2 7.739e-7
Km_ISOC 1.52
stim_duration 0.4
delta_pH -0.6
Km_OAA 0.00064
kh3 6.68e-9
k_offset 0.0399
Vmax_ANT 0.05
kf_SL 0.127
h 0.5
Ke_FH 1.0
rho_res_F 0.0045
stim_end 10000.0
Kcat_KGDH 0.15
Ke_AAT 6.6
C_Kint 1.0
Kf_ACO 12.5
ra 6.394e-10
rho_res 0.0006
Km_alpha_KG 1.94
Kisdh_OAA 0.15
Km_Suc 0.03
k_C_ASP 0.01
C_mito 1.812
FAD 0.01
Pi 20.0
R 8.315
rb 1.762e-13
C_PN 10.0

States:

Name Description
SCoA(time) 0.01
Suc(time) 0.01
Ca_m(time) 0.01
OAA(time) 0.01
alpha_KG(time) 0.01
ASP(time) 0.01
delta_psi_m(time) 0.01
MAL(time) 0.01
ISOC(time) 0.01
ADP_m(time) 0.1
FUM(time) 0.01
NADH(time) 0.01

Observables: none

cortassa_aon_winslow_orourke_2004 @ v0.0.1

Cortassa, Aon, Winslow, Orourke, 2004

nothing

Parameters:

Name Description
Na_i 10.0
na 2.8
Km_MAL 1.493
stim_start 0.0
kh1 1.13e-5
kh2 26.7
Kcat_CS 3.2
Kh_2 5.98e-5
Kcc 0.01
phi2_GPX 0.5
NADPH 1.0
delta_psi_0 0.091
delta_psi_bm 0.004
k1_CAT 17000.0
KNa 9.4
Kres 1.35e18
Kres_F 5.765e13
Kcat_SDH 1.0
ET_GR 0.00127
delta_psi_B 0.05
Km_NAD 38.7
fr 50.0
Ka_ADP 0.062
pc2 4.585e-14
ATP_i 6.5
Ki_FUM 1.3
GT 1.0
Kd_Ca 1.27
Ki_NADH 0.19
Ki_H2O2 0.5
Vmax_NaCa 0.005
r2 1.728e-9
pc1 9.651e-14
rho_F1 0.06
GLU 20.0
p1 1.346e-8
kh4 5.62e-6
Kd_Mg 0.0308
Kcat_IDH 1.94
p3 6.65e-15
ET_CS 0.4
b 0.5
KE_ACO 2.22
pulse_value 1.0
KCa 0.375
Kh_1 8.1e-5
kappa 70.0
K_trans 19.0
kf_FH 0.83
H 2.5e-5
r3 1.059e-26
CoA 0.02
Vmax_uni 0.000625
phi1_GPX 0.15
n_alpha_KG 1.2
ET_MDH 0.154
kf_AAT 0.644
k1_SOD 2.4e6
K_act 0.38
r1 2.077e-18
ni 1.0
ET_IDH 0.109
Ka_Ca 1.41
k5_SOD 0.5
rc1 2.656e-19
Mg 0.4
F 96480.0
n 3.0
KF1 1.71e6
f 0.0003
KM_NADPH 38.7
T 310.16
ET_SDH 0.5
gH 0.01
ET_SOD 0.0004
L 110.0
k1_GR 0.0308
ET_CAT 0.001
pb 3.373e-7
ET_GPX 0.00141
KM_GSSG 1.94
Kcat_MDH 27.75
AcCoA 0.0002
Km_AcCoA 0.0126
Cm 15.0
pa 1.656e-5
g 0.85
ET_KGDH 0.5
FADH2 1.24
Ke_SL 3.115
Ki_OAA 0.0031
shunt 0.05
GL 0.0782
rc2 8.632e-27
p2 7.739e-7
Km_ISOC 1.52
k3_SOD 48000.0
stim_duration 0.4
delta_pH -0.6
Km_OAA 0.00064
kh3 6.68e-9
k_offset 0.0399
Vmax_ANT 0.05
kf_SL 0.127
a 0.001
h 0.5
Ke_FH 1.0
Gmax 7.82
stim_end 10000.0
rho_res_F 0.0045
Kcat_KGDH 0.15
Kf_ACO 12.5
C_Kint 1.0
Ke_AAT 6.6
ra 6.394e-10
rho_res 0.0006
Km_alpha_KG 1.94
Kisdh_OAA 0.15
Km_Suc 0.03
j 0.12
k_C_ASP 0.01
Pi 20.0
FAD 0.01
C_mito 1.812
R 8.315
C_PN 10.0
rb 1.762e-13

States:

Name Description
SCoA(time) 0.01
Suc(time) 0.01
O2_i(time) 0.01
Ca_m(time) 0.01
OAA(time) 0.01
alpha_KG(time) 0.01
ASP(time) 0.01
delta_psi_m(time) 0.01
O2_m(time) 0.01
MAL(time) 0.01
GSH(time) 0.01
ISOC(time) 0.01
ADP_m(time) 0.1
H2O2(time) 0.01
FUM(time) 0.01
NADH(time) 0.01

Observables: none

costa_holmes_mcculloch_2001 @ v0.0.1

Costa, Holmes, Mcculloch, 2001

nothing

Parameters: none

States: none

Observables: none

courtemanche_ramirez_nattel_1998 @ v0.0.1

Courtemanche, Ramirez, Nattel, 1998

nothing

Parameters:

Name Description
Km_TRPN 0.0005
T 310.0
TRPN_max 0.07
stim_start 50.0
K_rel 30.0
Km_CSQN 0.8
Ca_up_max 15.0
K_sat 0.1
i_NaK_max 0.59933874
I_up_max 0.005
g_to 0.1652
CMDN_max 0.05
Cm 100.0
g_B_K 0.0
Km_K_o 1.5
Km_CMDN 0.00238
K_mNa 87.5
g_Ks 0.12941176
g_K1 0.09
g_Ca_L 0.12375
tau_tr 180.0
g_Kr 0.029411765
I_NaCa_max 1600.0
K_mCa 1.38
Na_o 140.0
stim_duration 2.0
K_up 0.00092
g_B_Na 0.0006744375
Ca_o 1.8
V_cell 20100.0
stim_period 1000.0
stim_end 50000.0
K_o 5.4
i_CaP_max 0.275
g_Na 7.8
g_B_Ca 0.001131
stim_amplitude -2000.0
K_Q10 3.0
CSQN_max 10.0
Km_Na_i 10.0
gamma 0.35
R 8.3143
F 96.4867

States:

Name Description
d(time) 0.0001367
oa(time) 0.03043
oi(time) 0.9992
Ca_rel(time) 1.488
xr(time) 3.296e-5
V(time) -81.18
h(time) 0.9649
v(time) 1.0
xs(time) 0.01869
ua(time) 0.004966
f(time) 0.9996
K_i(time) 139.0
ui(time) 0.9986
u(time) 2.35e-112
f_Ca(time) 0.7755
j(time) 0.9775
m(time) 0.002908
Ca_up(time) 1.488
Ca_i(time) 0.0001013
w(time) 0.9992
Na_i(time) 11.17

Observables: none

cronwright_rohwer_prior_2002 @ v0.0.1

Cronwright, Rohwer, Prior, 2002

nothing

Parameters:

Name Description
K_G3P 1.2
K_NADH 0.023
V 18.0
K_Pi 1.0
K_eq 10000.0
K_ATP 0.73
K_F16BP 4.8
K_NAD 0.93
K_ADP 2.0
K_DHAP 0.54
Vf 36.0

States:

Name Description
G3P(time) 24.0

Observables: none

csilkasz_nagy_2006 @ v0.0.1

Csilkasz-Nagy 2006

nothing

Parameters:

Name Description
k_s20pp 0.15
J_ih1 0.01
k_dbhpp 2.0
k_assb 0.0
k_itfp 0.25
k_depp 0.0
k_assa 25.0
k_dib 0.05
k_aweepp 0.0
k_iwee 1.0
k_itfppp 0.0
k_diepp 5.0
k_ih1app 0.2
k_dipp 0.1
k_diapp 5.0
k_atfp 0.0
J_itf 0.01
J_aie 0.01
J_iwee 0.05
k_afb 1.0
k_debpp 0.5
k_25pp 5.0
J_14di 12.0
k_iweepp 1.0
k_weepp 0.2
J_afi 88.0
k_asse 50.0
J_awee 0.05
k_dissa 1.0
k_itfapp 0.1
k_ih1pp 0.35
J_iie 0.01
k_sap 0.0
k_itfbpp 0.1
maxmass 10000.0
CycD_0 0.05
k_ifb 0.1
k_die 0.0
J_aAPC 0.1
k_asa 50.0
J_a20 0.005
k_s20p 0.0
k_ase 0.0
k_ifip 88.0
k_ih1bpp 1.0
k_a20 0.5
k_deapp 0.5
J_ifb 0.1
k_aweep 0.3
k_dbp 0.005
k_sipp 0.0
k_weep 0.02
k_afi 88.0
J_a25 0.1
k_dippp 0.8
k_a25 0.0
J_afb 0.1
k_itfpp 8.0
k_ifibpp 88.0
J_ifi 88.0
n 1.0
k_i25pp 0.0
k_dbpp 0.4
k_ifipp 0.05
Cdh1_T 1.0
k_atfpp 1.5
k_i25p 0.3
k_sep 0.01
k_depppp 0.0
k_atfepp 0.5
k_deppp 0.0
k_asb 60.0
k_ih1epp 0.1
J_iAPC 0.1
k_25p 0.01
k_dappp 0.0
k_atfdpp 3.0
k_sbpp 0.03
k_ih1p 0.0
k_iweep 0.0
k_dia 0.06
J_atf 0.01
k_ah1pp 3.5
k_ah1p 0.18
k_dep 0.01
k_atfppp 0.38
k_sbp 0.01
k_dapp 2.0
J_20 1.0
J_ah1 0.01
k_dibpp 5.0
k_aAPC 0.1
k_dipppp 0.12
k_a25pp 1.0
J_i20 0.005
J_i25 0.1
k_dip 0.8
k_ih1ppp 0.1
mu 0.004951
k_ih1pppp 0.06
k_d20 0.15
APC_T 1.0
k_disse 1.0
k_a25p 0.0
k_dbcpp 0.1
k_iAPC 0.15
k_sapp 0.025
k_dbppp 0.15
k_deepp 0.1
k_atfpppp 3.0
k_dap 0.02
k_ih1dpp 0.0
k_atfapp 0.2
k_14di 0.0
k_dippppp 0.1
k_aie 0.07
k_dissb 0.0
n20 1.0
k_iie 0.18
k_ih1ppppp 0.005
k_didpp 0.0
k_i20 0.25
k_sepp 0.18
k_sip 1.8

States:

Name Description
Cdc20_i(time) 0.01855352707207203
Cdc20_A(time) 0.6605867147445679
actCycB(time) 0.1903585940599442
actCycE(time) 0.2092024385929108
pB(time) 0.009814870543777943
Cdh1(time) 0.9992357492446899
preMPF(time) 0.01
Tri_A(time) 0.01715379953384399
CKI(time) 0.2954076826572418
actCycA(time) 0.09450308233499527
Tri_E(time) 0.3117263317108154
APCP(time) 0.6716265678405762
CycE(time) 0.07760512828826904
Tri_B(time) 0.01
CycB(time) 0.1668413728475571
CycA(time) 0.00994044542312622
mass(time) 1.174216866493225
pBCKI(time) 0.0
BCKI(time) 0.0
Cdc20_T(time) 0.7702387571334839

Observables: none

cui_kaandorp_2006 @ v0.0.1

Cui, Kaandorp, 2006

nothing

Parameters:

Name Description
Kx 500.0
f 0.1
kc 10.0
V3 10000.0
K2 0.1
kM_minus 100.0
alpha 0.006
Caex 1.0
kN_minus 5.0
K1 4.3
CaMtotal 25.0
Vx 1000.0
kN_plus 5.0
kM_plus 500.0
V1 30000.0
CaNtotal 25.0
V2 100.0
N 13.0
lamda 5.0
K3 100.0
d 0.4

States:

Name Description
h(time) 0.0
m(time) 0.0
x(time) 0.0
z(time) 1.0e-8

Observables: none

cui_kaandorp_2008 @ v0.0.1

Cui, Kaandorp, 2008

nothing

Parameters:

Name Description
k14 0.5
k34 0.0552
k38 0.1
k18 0.1
k9 0.5
k25 0.15
k40 0.1
k29 0.4
k8 0.1
k39 0.1
k37 0.2
k12 0.1
k16 0.1
k31 0.1
k43 0.03
k32 0.05
k41 0.02
k33 0.114
k3 2760.0
k28 0.1
k42 0.03
Ca 0.2
k17 0.1
k20 0.1
k21 0.15
k10 0.1
k13 0.5
k15 0.1
k35 0.15
k26 0.1
k19 0.5
k4 0.072
k22 0.15
k6 0.0567
t_half 15.0
k11 0.1
k23 0.15
k1 5.0
k36 0.1
k27 0.4
k7 5.0
k30 0.1
k24 0.1
k2 100.0
k5 50.0

States:

Name Description
CaMCa(time) 7.88e-7
CaNc(time) 0.91
MCIPp(time) 0.00776
MCIPpp(time) 0.0798
NFATpc_CaNc_star(time) 8.15e-5
NFATpc(time) 0.00494
MCIPp_GSK3betac(time) 0.0011
MCIPp_CaNc_star(time) 0.000107
NFATc(time) 2.0e-5
GSK3betan(time) 0.339
MCIP_BMK1(time) 2.14e-5
CaNc_star(time) 0.0275
CaNn(time) 0.0057
P1433(time) 0.708
NFATpn(time) 8.01e-5
Comp2(time) 0.283
NFATc_GSK3betac(time) 1.36e-6
BMK1(time) 0.012
CaNn_star(time) 0.0568
NFATn_GSK3betan(time) 8.46e-5
Comp1(time) 0.00521
MCIPpp_CaNc_star(time) 0.0011
GSK3betac(time) 0.17
NFATn(time) 0.000499
CaM(time) 25.2
Comp3(time) 0.014
MRNA(time) 0.000333
NFATpn_CaNn_star(time) 2.27e-6
MCIP(time) 0.000215

Observables: none

cui_kaandorp_lloyd_2008 @ v0.0.1

Cui, Kaandorp, Lloyd, 2008

nothing

Parameters:

Name Description
k_1 0.9
k2c 0.0037
r5 30000.0
td 2700.0
k1a 1.0
k1 0.025
k1b 0.01253
k2b 0.0002
r4 0.009
k2a 5.0e-5
r1 273.0
r2 0.0003437
Zn 1.0e-5
td0 1800.0
k_2 0.3
r6 0.01506
r3 4.41e10
k2 0.02

States:

Name Description
Qz5(time) 0.0
Rw(time) 50.0
Mw(time) 0.0
Px(time) 50.0
Tp(time) 10000.0
Zn(time) 10000.0
Py1(time) 0.0
Dw(time) 4.0
Dz(time) 2.0
Mz(time) 0.0
Tp1(time) 0.0
Qw2(time) 0.0
Qz4(time) 0.0
Px1(time) 0.0
Qz3(time) 0.0
Rz(time) 100.0
Qz1(time) 0.0
Qz2(time) 0.0
Py(time) 25.0
Qw1(time) 0.0

Observables: none

curien_ravanel_dumas_2003 @ v0.0.1

Curien, Ravanel, Dumas, 2003

nothing

Parameters: none

States: none

Observables: none

D


dash_bassingthwaighte_2004 @ v0.0.1

Dash, Bassingthwaighte, 2004

nothing

Parameters: none

States: none

Observables: none

david_cumin_phd_model @ v0.0.1

David Cumin PhD Model

nothing

Parameters: none

States: none

Observables: none

davies_2012 @ v0.0.1

Davies isAP 2012

A modified version of the Hund-Rudy 2004 dog model, as used by AstraZeneca for in-silico Action Potential (isAP) simulations. This model was described in Davies et al., Am J Physiol Heart Circ Physiol 302:H1466-H1480, (2012).

Parameters:

Name Description
prnak 0.01833
GNa 8.25
iupmax 0.004375
CaMK0 0.05
KmNao 87.5
GK1 0.5
Km 0.0015
KmBSR 0.00087
stim_offset 0.0
BSLmax 1.124
tau_pow_calcium 10.0
ibarpca 0.0575
GNaL 0.011
kmko 1.5
KmCao 1.3
tbar 0.07
kmpca 0.0005
gitodv 0.1805
Kmto2 0.1502
KmNai 12.3
eta 0.35
l 0.01
FonRT 0.0374358835078
Cto 300.0
nsrmax 15.0
CTNaClmax 9.8443e-6
dtau_rel_max 10.0
ksat 0.27
kmc 0.00238
GCab 7.980336e-7
NCXmax 5.85
Na_o 150.0
CTKClmax 7.0756e-6
stim_duration 1.0
ibarnak 0.61875
csqnbar 10.0
Kmup 0.00092
Ca_o 1.8
cbar 0.05
a 0.0011
stim_period 1000.0
kmt 0.0005
KmCa 0.000125
KmCaMK 0.15
gacai 1.0
K_o 4.0
gacao 0.341
dKmPLBmax 0.00017
kmnai 10.0
kmcsqn 0.8
KmBSL 0.0087
dJupmax 0.75
pca 0.000243
stim_amplitude -80.0
GKrMax 0.0138542
Cl_o 154.6
PCl 4.0e-7
BSRmax 0.047
GClb 0.000225
gks_max 0.00746925
F 96485.0
KmCai 0.0036

States:

Name Description
Cl_i(time) 20.1543792471096
xr(time) 0.255981702631947
fca2(time) 0.854261813196152
Ca_ss(time) 0.000225131045297696
fca(time) 0.961568137796573
dp(time) 8.99805432294836
f(time) 0.999986839648304
J(time) 0.998157020148849
xs1(time) 0.0147449166757808
Ca_nsr(time) 4.14835141174613
mL(time) 0.000382187369845771
m(time) 0.000382187369845771
xs2(time) 0.0147504787196957
ro(time) -1.07543858779373e-32
Ca_jsr(time) 4.1270622547589
Na_i(time) 17.9964119779802
zdv(time) 0.787996527242362
d(time) 5.38067794749339e-7
V(time) -93.2932771154856
f2(time) 0.989081601403786
ydv(time) 0.00894974857468432
CaMKtrap(time) 0.0971591072782679
K_i(time) 134.555737634453
AA(time) 0.0014969201082975
ydv2(time) 0.999992183094244
H(time) 0.99765453819431
Ca_i(time) 0.000223768331231758
ri(time) 0.716604593002322
hL(time) 0.488129650338831

Observables: none

dawson_lea_irvine_2003 @ v0.0.1

Dawson, Lea, Irvine, 2003

nothing

Parameters:

Name Description
k2 100.0
k4_ 1.0
k10 500.0
k9 5000.0
k7_ 1.0
k1 1.0
k8 500.0
k3_ 10.0
k2_ 12000.0
k4 1.0
k3 100.0
k6_ 2.4
k7 10.0
k6 2.0
k5 10.0
k1_ 10.0
k5_ 1.0

States:

Name Description
R_(time) nothing
Ca_cyt(time) nothing
O1(time) nothing
I(time) nothing
R(time) nothing
Ca_L(time) nothing
O2(time) nothing
C1(time) nothing
R__(time) nothing
Ca_ER(time) nothing

Observables: none

decker_2009 @ v0.0.1

Decker 2009

nothing

Parameters:

Name Description
prnak 0.01833
gamma_Cai 1.0
gamma_Cao 0.341
T 310.0
PCab 1.99508e-7
iupbar 0.004375
tau_hL 600.0
KmNao 87.5
Km 0.0015
CT_Na_Cl_max 2.46108e-5
delta_beta_0 1.0
cmdn_bar 0.05
KmpCa 0.0005
sigma 1.0
stim_offset 0.0
V_half -92.0
BSLmax 1.124
KmBSR 0.00087
theta 1.0
zCl -1.0
kmup 0.00092
Vmax 4.5
tautr 25.0
gto1 0.497458
h_beta 10.0
KmCao 1.3
alpha_CaMK 0.05
kmko 1.5
KmNai 12.3
theta_I 1.0e-6
Krel_tau 0.0123
km_trpn 0.0005
eta 0.27
l 0.01
delta_kmPLB_bar 0.00017
kCa_ito2 0.4
Krel_infinity 1.0
tau_i2f 8.0
km_cmdn 0.00238
gKr_max 0.0138542
ksat 0.32
g_K1_max 0.5
gamma_Ca_i 1.0
gNaL 0.0065
K_beta 0.28
tau_diff_ss 2.0
nsrbar 15.0
Na_o 140.0
stim_duration 0.5
PCa 0.00015552
gClb 0.000225
delta_iupCaMK_bar 0.75
ibarnak 1.4
gpCa 0.0575
csqnbar 10.0
Ca_o 1.8
CT_K_Cl_max 1.77e-5
a 0.0011
stim_period 1000.0
kappa 0.1125
PNab 3.2e-9
gKp 0.00276
K_o 5.4
beta_0 4.75
trpn_bar 0.07
tau_diff 0.2
kmnai 2.6
kmcsqn 0.8
Ito2_max_scaling_factor 1.0
g_Na 9.075
KmCa_act 0.000125
KmBSL 0.0087
gamma_Ca_o 0.341
CaMK_0 0.05
stim_amplitude -80.0
PCl 9.0e-7
Cl_o 100.0
h_rel 8.0
gKs_max 0.0826
beta_CaMK 0.00068
BSRmax 0.047
R 8314.0
KmCai 0.0036
F 96485.0
kmCaMK 0.15

States:

Name Description
Ca_NSR(time) 1.01475649943057
C(time) 0.99996982093287
C13(time) 0.000644426171899078
C3(time) 0.0512272866698557
O(time) 2.26882961412491e-5
mL(time) 0.00101841101248412
Irel(time) 0.000714227102027745
Ca_ss_sr(time) 0.00011296707102434
C5(time) 0.000152923243503507
C11(time) 0.00371438476499172
Cl_ss(time) 20.6683605553303
C_star(time) 7.49117189549873e-6
a(time) 1.76776038804228e-5
C1(time) 0.476679784307081
C14(time) 8.62495047666861e-5
Na_ss_sr(time) 8.01033434859049
i1s(time) 0.947581184798815
i1f(time) 0.997976503910799
C7(time) 0.053324572164618
C10(time) 0.0138769647384953
OI(time) 8.01952813127322e-17
i2f(time) 0.996044894628276
hL(time) 0.319611809402137
CI_star(time) 1.9237001017021e-9
Cl_i(time) 20.6683603724432
xr(time) 4.06959064407486e-6
C6(time) 0.132814156809568
C2(time) 0.255181042718489
C9(time) 0.000318368292970148
j(time) 0.99709036251243
O1(time) 1.05292905767805e-5
m(time) 0.00101841101248412
C4(time) 0.0045705849736195
C12(time) 0.000248553788631871
C15(time) 1.12344645485893e-5
CI(time) 5.89853003114132e-11
Na_i(time) 8.01031392415197
O_star(time) 1.23556404128518e-10
h(time) 0.991354143386887
K_i(time) 144.907134343314
Ca_ss_CaL(time) 0.000119239795531548
Ca_JSR(time) 0.993914988616979
Vm(time) -87.4947322902196
CaMK_trap(time) 0.0114911034744777
Ca_i(time) 8.38749860095482e-5
C8(time) 0.00713656414955778

Observables: none

deformingheart @ v0.0.1

Deforming Heart

nothing

Parameters: none

States: none

Observables: none

DeltaNotch @ v0.0.1

Delta-Notch Intercellular Signalling

nothing

Parameters: none

States: none

Observables: none

demir_clark_giles_1999 @ v0.0.1

Demir, Clark, Giles, 1999

nothing

Parameters:

Name Description
g_Ca_L_cont 0.02115
T 310.0
K_m_K 0.621
P_Na 0.00344
g_K_ACh_base 0.007833
Km_Iso 0.00014
K_ADC 0.008
Mg_i 2.5
f_Vagal 200.0
d_NaCa 0.0001
alpha_up 0.08
V_PDE 20.0
i_NaK_max 0.2192
alpha_rel 0.5
g_f_K 0.0128821
K_PDE 6.0
Cm 5.5e-5
Ca_b 2.0
g_B_K 6.94e-5
beta_up 0.072
tau_p 0.01
k_rel 0.004
Na_b 140.0
k_xcs 0.9
i_Ca_P_max 0.02869
ACh 0.0
Vol 3.497e-6
cGMP 0.002
g_B_Na 0.00016
E_Ca_T 45.0
P_M2_ADC 0.02
k_SRCa 22.0
K_m_Na 5.46
g_B_Ca 3.64e-5
Iso 0.0
Km_ACh 0.00014
g_f_Na 0.0067478
k_cyca 5.0e-5
E_Ca_L 46.4
g_Ca_T 0.02521
gamma 0.5
K_NaCa 1.248e-5
R 8314.472
K_b 5.4
F 96485.3415

States:

Name Description
P_a(time) 0.02302278
F3(time) 0.8859153
Ca_Mg_Trop(time) 0.7618549
y(time) 0.09227776
Mg_Mg_Trop(time) 0.2097049
f_T(time) 0.1945111
d_L(time) 0.002572773
cAMP(time) 0.003
m(time) 0.250113
Ca_Calmod(time) 0.1411678
Na_i(time) 9.701621
Ca_Trop(time) 0.07331396
d_T(time) 0.02012114
Ca_rel(time) 16.85024
h2(time) 0.002065463
V(time) -49.54105
K_c(time) 5.389014
Ca_Calse(time) 0.9528726
a(time) 0.0
K_i(time) 140.7347
Ca_c(time) 2.00474
P_i(time) 0.3777728
F1(time) 0.1133251
f_L(time) 0.98651
h1(time) 0.001386897
Na_c(time) 139.9988
Ca_up(time) 16.95311
Ca_i(time) 0.0003787018
F2(time) 0.0007594214

Observables: none

demir_clark_giles_murphey_1994 @ v0.0.1

Demir, Clark, Giles, Murphey, 1994

nothing

Parameters:

Name Description
Vol 3.497e-6
T 310.0
K_m_K 0.621
P_Na 0.00344
g_B_Na 0.00016
E_Ca_T 45.0
Mg_i 2.5
d_NaCa 0.0001
alpha_up 0.08
i_NaK_max 0.2192
alpha_rel 0.5
g_f_K 0.0128821
k_SRCa 22.0
Cm 5.5e-5
K_m_Na 5.46
Ca_b 2.0
beta_up 0.072
g_B_K 6.94e-5
tau_p 0.01
g_B_Ca 3.64e-5
k_rel 0.004
Na_b 140.0
g_f_Na 0.0067478
k_cyca 5.0e-5
E_Ca_L 46.4
k_xcs 0.9
g_Ca_T 0.02521
g_Ca_L 0.02115
gamma 0.5
K_NaCa 1.248e-5
R 8314.472
i_Ca_P_max 0.02869
F 96485.3415
K_b 5.4

States:

Name Description
P_a(time) 0.02302278
F3(time) 0.8859153
Ca_Mg_Trop(time) 0.7618549
y(time) 0.09227776
Mg_Mg_Trop(time) 0.2097049
f_T(time) 0.1945111
d_L(time) 0.002572773
m(time) 0.250113
Ca_Calmod(time) 0.1411678
Na_i(time) 9.701621
Ca_Trop(time) 0.07331396
d_T(time) 0.02012114
Ca_rel(time) 16.85024
h2(time) 0.002065463
V(time) -49.54105
K_c(time) 5.389014
Ca_Calse(time) 0.9528726
Ca_c(time) 2.00474
K_i(time) 140.7347
P_i(time) 0.3777728
F1(time) 0.1133251
f_L(time) 0.98651
h1(time) 0.001386897
Na_c(time) 139.9988
Ca_up(time) 16.95311
Ca_i(time) 0.0003787018
F2(time) 0.0007594214

Observables: none

demiray_1981 @ v0.0.1

Demiray, 1981

nothing

Parameters: none

States: none

Observables: none

dempsher_gann_phair_1984 @ v0.0.1

Dempsher, Gann, Phair, 1984

nothing

Parameters:

Name Description
Ka 10.0
Q 0.042
Vmsm 6.0
Kbac 10.0
C 6.25
P 0.052
Kcb 0.01
T 8.0
Km 270.0
Kdsm 10.0
HY 16.4
Ko 0.013
Kmptr 150.0
AH 16.4
Vm 1890.0
Kb 1.0e6
Kd 2.11
HA 0.5
Vmptr 500.0
D 125.0
Vdsm 10.0
S 76.0
Kcf 0.00033
U 0.0015
Crpt 3.0
LH 0.724
R 3.0
K 80.0
Lmtr 1.65
n 4.0

States:

Name Description
CHOM(time) 139.0
V(time) 11.3
CHON(time) 3.03
HYPR(time) 0.64
W(time) 10.0
Kfor(time) 0.37
CORT(time) 5.2
Kmtr(time) 0.446
cAMP(time) 0.95
CHOC(time) 532.0
PREG(time) 6.56
CHOL(time) 3000.0
PRO(time) 0.64

Observables: none

depaor_timmons_1986 @ v0.0.1

Depaor, Timmons, 1986

nothing

Parameters:

Name Description
p 1.05
alpha 1.0
t2 0.5
k 10.5
a 1.0
t1 0.1
beta 1.0
r1 1.2
r0 0.5
t4 20.0
d 5.0

States:

Name Description
x3(time) 0.0
r(time) 0.5
h(time) 0.0
x2(time) 0.0
x1(time) 0.0

Observables: none

devries_sherman_2000 @ v0.0.1

Devries, Sherman, 2000

nothing

Parameters:

Name Description
V_m -20.0
g_s 4.0
theta_n 5.6
tau 20.0
V_K -75.0
V_s -22.0
g_K 10.0
g_K_ATP 1.2
tau_s 20000.0
V_Ca 25.0
V_n -17.0
lambda 0.9
g_Ca 3.6
theta_m 12.0
p 0.5
theta_s 8.0

States:

Name Description
V(time) -64.0
n(time) 0.01
s(time) 0.01

Observables: none

devries_sherman_2001 @ v0.0.1

Devries, Sherman, 2001

nothing

Parameters:

Name Description
V_m -20.0
g_s 4.0
theta_n 5.6
tau 20.0
V_K -75.0
beta 0.0
V_s -38.0
g_K 10.0
tau_s 35000.0
V_Ca 25.0
V_n -16.0
g_Ca 3.6
lamda 0.8
theta_m 12.0
theta_s 10.0

States:

Name Description
V(time) nothing
n(time) nothing
s(time) nothing

Observables: none

deyoung_keizer_1992 @ v0.0.1

Deyoung, Keizer, 1992

nothing

Parameters:

Name Description
c1 nothing
a3 nothing
v4 nothing
a2 nothing
a1 nothing
v1 nothing
b2 nothing
alpha nothing
K_d1 nothing
IP3_cold nothing
Ir nothing
b5 nothing
a4 nothing
k4 nothing
v2 nothing
k3 nothing
a5 nothing
c0 nothing
K_d2 nothing
v3 nothing

States:

Name Description
Ca_i(time) nothing
IP3(time) nothing
x_001(time) nothing
x_010(time) nothing
x_000(time) nothing

Observables: none

difrancesco_noble_1985 @ v0.0.1

Difrancesco, Noble, 1985

nothing

Parameters:

Name Description
T 310.0
C 0.075
Km_to 10.0
Km_Ca 0.0005
Ca_up_max 5.0
length 2.0
d_NaCa 0.001
Ve 0.00157
g_f_K 3.0
Kb 4.0
delta_f 0.0001
g_to 0.28
Km_K1 210.0
tau_rep 2.0
tau_up 0.025
K_mNa 40.0
g_K1 920.0
delta_m 1.0e-5
delta_y 1.0e-5
K_mCa 0.001
V_e_ratio 0.1
tau_rel 0.05
I_p 125.0
Cao 2.0
n_NaCa 3.0
g_Nab 0.18
K_mf2 0.001
Km_f 45.0
radius 0.05
delta_d 0.0001
Nao 140.0
alpha_f2 5.0
K_mK 1.0
rCa 2.0
P_si 15.0
g_Na 750.0
g_Cab 0.02
g_f_Na 3.0
i_pulse 0.0
i_K_max 180.0
gamma 0.5
K_NaCa 0.02
R 8314.472
pf 0.7
F 96485.3415

States:

Name Description
d(time) 0.005
Ca_rel(time) 1.0
V(time) -87.0
h(time) 0.8
f2(time) 1.0
x(time) 0.01
y(time) 0.2
f(time) 1.0
Kc(time) 4.0
Ki(time) 140.0
p(time) 1.0
m(time) 0.01
Ca_up(time) 2.0
Cai(time) 5.0e-5
Nai(time) 8.0
s(time) 1.0

Observables: none

dijkstra_neal_beever_france_1992 @ v0.0.1

Dijkstra, Neal, Beever and France, 1992

nothing

Parameters:

Name Description
v_AmMa_star 0.0528
D_Vl 1.0
J_Am_HaVa 0.00861
D_Sr 1.0
f_Hf_AmMc 0.526
Y_Ps_InPs 0.0091
Y_Vl_StVl 1.0
Y_Ps_PdPs 1.0
J_Hc_PsAm 0.0165
D_Ac 1.0
f_Ce_Fd 1.0
Y_Bu_PsBu 1.0
v_PsMc_star 0.0576
Y_As_HaAs 112.5
M_Hc_AmMc 0.0159
phi_pH_AmAb 7.85
pH 7.0
M_Sd_SdHa_star 0.416
v_HaVa_star 0.1646
Y_Li_InLi 0.0015
Y_Pr_CePr 1.0
D_Fu 1.0
M_Fd_FdHc_star 0.332
D_Pd 1.0
Y_Am_McAm 0.0084
Y_Ps_MaMd 0.0067
Y_Ps_SaPs 0.001
phi_pH_AcAb 6.48
R_Ha_PsMa 1.291
M_Pr_PrAb 0.338
Y_Pr_HePr 1.0
M_pH_AmAb 7.5
Y_Ac_CeAc 1.0
Y_Am_PsAm 1.257
Y_Ha_SrHa 0.0062
T_Pd_star 0.66
f_Hf_AmMa 0.526
Y_Pr_PsPr 1.0
v_FdHc_star 0.1646
Y_Sd_InSd 0.0062
V_Ru 1.0
Y_Ac_PsAc 1.0
M_Vl_VlAb 0.338
R_Ha_McMa 0.0086
T_Pd 1.0
R_Hc_PsMc 1.291
Y_Ac_WrAc 1.0
Y_Pu_InPu 0.0091
Y_Hc_FdHc 1.0
phi_pH_PrAb 6.48
v_SdHa_star 0.2179
J_Ps_HcVa 0.01465
D_Pu 1.0
Y_Bu_WrBu 1.0
Y_Bu_HeBu 1.0
M_Ps_PsMc 0.0224
J_Am_HcVa 0.00861
M_pH_FdHc 5.97
D_Ps 1.0
Y_Li_MaMd 0.00021
v_HaAs_star 0.053
Y_Ha_SdHa 1.0
f_Hf_HaAs 0.306
phi_pH_FdHc 22.9
D_Li 1.0
v_AcAb_star 7.86
v_UeAm_star 0.00165
M_Ps_PsMa 0.0224
M_Am_AmAb 0.0132
Y_Ha_WrHa 0.0062
Y_Vl_PsVl 1.0
J_pH_VlAb 6.45
M_Bu_BuAb 0.338
Y_Ac_InAc 0.0167
M_Mc_McEg 34.694
Y_Ma_AmMa 118.91
D_Fd 1.0
J_pH_BuAb 6.45
J_Ha_McAm 0.0165
M_Am_AmMc 0.00135
f 1.0
Y_Ac_StAc 1.0
Y_Fd_InFd 0.0062
J_pH_AcAb 6.45
D_Sd 1.0
Y_Vl_WrVl 1.0
T_Sd 1.0
M_Ac_AcAb 0.338
R_Hc_AmMc 1.793
Y_Ps_McPs 0.0067
Y_Fu_InFu 0.0062
v_BuAb_star 7.86
v_AmMc_star 0.0528
Y_Pr_WrPr 1.0
f_Lc_Le 2.25
T_Sd_star 1.04
Y_Am_InAm 0.0588
Y_Ma_McMa 149.48
v_PrAb_star 7.86
pm 1.0
k_SoEx 1.0
J_Ha_PsAm 0.0165
M_Pd_PdPs_star 0.264
Y_Bu_CeBu 1.0
Y_Am_UeAm 2.0
v_AmAb_star 1.1
Y_Vl_HeVl 1.0
k_FlEx 1.0
M_Ha_PsMa 0.0248
v_PsAm_star 0.0144
f_Hf_PsMc 0.711
f_Po_Ma 0.35
D_Pr 1.0
M_Ha_McMa 0.0248
J_pH_PrAb 6.45
v_PdPs_star 0.0576
M_Ha_HaAs 0.0268
T_Fd 1.0
Y_Ma_PsMa 149.48
D_La 1.0
v_PsMa_star 0.0576
J_Am_UeAm 0.00621
Y_Pr_StPr 1.0
v_VlAb_star 7.86
D_Bu 1.0
T_Fd_star 0.83
M_Ha_HaVa 0.055
R_Ha_AmMa 1.793
Y_Vl_InVl 0.0098
M_Hc_HcVa 0.055
Y_Bu_StBu 1.0
M_Am_AmMa 0.00135
phi_pH_VlAb 6.48
M_Ha_AmMa 0.0159
Y_Ha_MaMd 0.0062
Y_Mc_PsMc 149.48
Y_Pr_InPr 0.0135
Y_Ac_HeAc 1.0
v_McEg_star 15.439
Y_Ha_LaHa 0.0025
f_Hf_McMa 0.711
Y_Pd_InPd 0.0091
Y_Mc_AmMc 118.91
phi_pH_BuAb 6.48
M_Ps_PsAm 0.0289
f_Hf_PsMa 0.711
Y_Bu_InBu 0.0114
D_Wr 1.0
J_Ps_HaVa 0.01465
Y_Vl_CeVl 1.0
M_Hc_PsMc 0.0248
D_Am 1.0
f_Ni_Fe 1.0
v_HcVa_star 0.1646

States:

Name Description
Q_Pu(time) 1.0
Q_Ac(time) 1.0
Q_Bu(time) 1.0
Q_Li(time) 1.0
Q_Ma(time) 1.0
Q_As(time) 1.0
Q_Am(time) 1.0
Q_Pr(time) 1.0
Q_Mc(time) 1.0
Q_Hc(time) 1.0
Q_Vl(time) 1.0
Q_Fd(time) 1.0
Q_Fu(time) 1.0
Q_Sd(time) 1.0
Q_Ps(time) 1.0
Q_Pd(time) 1.0
Q_Ha(time) 1.0

Observables: none

dixit_perelson_2004 @ v0.0.1

Dixit, Perelson, 2004

nothing

Parameters:

Name Description
F 1.0
ka 14.64
c 23.0
k 2.4e-8
IC50 9.0e-7
ke 6.86
D 600.0
tau 1.5
kecell 1.1
delta 0.01
Vd 28000.0
m 0.01
N 2500.0
kacell 24000.0
lamda 10000.0
fb 0.99
H 0.052
d 0.01

States:

Name Description
VNI(time) 2.0
VI(time) 1.0
T(time) 1.0e6
Cc(time) 0.0
T_(time) 1.0

Observables: none

dokos_celler_lovell_1996 @ v0.0.1

Dokos, Celler, Lovell, 1996

nothing

Parameters:

Name Description
K3ni 26.44
T 310.0
C 3.2e-5
P_KNa 0.035
tau_dL 0.002
K1ni 395.3
Cab 2.0
Kb 5.4
Kcni 26.44
KmK 1.0
Qco 0.0
Kco 3.663
g_fNa 0.0081
KmCaup 0.0005
KmCarel 0.001
tau_tr 0.4
tau_b 0.1
Kk 0.00026
tau_rel 0.005
K1no 1628.0
g_Nab 0.00024
K2no 561.4
Qn 0.4315
Nab 140.0
K3no 4.663
alpha_fL2 3.0
KbK 7.0e-5
K2ni 2.289
V_i 2.5e-6
beta_fL2 40000.0
KmNa 40.0
Qci 0.1369
Kci 0.0207
g_fK 0.0135
g_Na 0.25
i_up_max 0.0212
i_pmax 0.226
Kmf 10.3
kNaCa 4.0
g_CaT 0.085
g_CaL 0.4
R 8314.472
F 96485.3415

States:

Name Description
Caup(time) 0.5832
fL(time) 0.1505
dT(time) 0.001
h(time) 0.0087
x(time) 0.5682
y(time) 0.0287
Cao(time) 2.0004
fT(time) 0.1328
Ko(time) 5.4243
E(time) -64.9
Ki(time) 140.0073
fL2(time) 0.219
m(time) 0.0139
dL(time) 0.0001
Cai(time) 3.4e-5
Nai(time) 7.4994
Carel(time) 0.1101
Nao(time) 139.9929

Observables: none

dougherty_wright_yew_2005 @ v0.0.1

Dougherty, Wright, Yew, 2005

nothing

Parameters:

Name Description
ninh 1.5
pd 20.0
k_1 0.06
n_1 2.0
kI 0.7
clmax 1.0
r_2 5.0
kinhcng 1.0
R_tot 1.0
n_2 2.0
ef 2.0
V_Cl -50.0
G_tot 1.0
smax 71.0
cc1lin 0.88
k_2 20.0
hmc_1 2.0
gl 6.0
t_1 1.5
cc_2 26.0
cap 0.004
ck1lin 13.0
inf 1.9
V_l -70.0
cx2 13.0
inhmax 5.0
r_1 10.0
nI 2.0
kinh 2.0
V_cng 0.0
cnmax 1.0
cx1lin 1.0
ck_2 0.9
C_vol 1.0e-13
hmc_2 3.0
ninhcng 1.3
od 20.0
F 96490.0
t_0 0.5

States:

Name Description
aCaMK(time) 6.60756525051462e-8
V(time) -70.0
cAMP(time) 1.35648992164649e-88
CaCaM(time) 1.86113118246926e-13
bLR(time) 0.0
aG(time) 0.0
Ca(time) 5.09073088043779e-12

Observables: none

drouhard_roberge_1987 @ v0.0.1

Drouhard, Roberge, 1987

nothing

Parameters:

Name Description
C nothing
g_s nothing
beta_x1 nothing
Istim nothing
g_Na nothing
alpha_x1 nothing
E_Na nothing

States:

Name Description
d(time) nothing
V(time) nothing
h(time) nothing
m(time) nothing
Cai(time) nothing
f(time) nothing
x1(time) nothing

Observables: none

dumaine_towbin_brugada_vatta_nesterenko_nesterenko_brugada_brugada_antzelevitch_1999 @ v0.0.1

Dumaine, Towbin, Brugada, Vatta, Nesterenko, Nesterenko, Brugada, Brugada, Antzelevitch, 1999

nothing

Parameters:

Name Description
gamma_Cai nothing
gamma_Cao nothing
T nothing
Tn_max nothing
calcium_overload nothing
P_Na nothing
Km_Ca nothing
delta_Ca_i2 nothing
K_mup nothing
delta_Ca_ith nothing
K_sat nothing
gamma_Nao nothing
tau_on nothing
g_to nothing
CMDN_max nothing
Cm nothing
P_ns_Ca nothing
V_NSR nothing
R_A_V nothing
PR_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
V_JSR 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_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
gamma_Ko nothing
K_mTn nothing
K_NaCa nothing
K_mKo nothing
R nothing
P_K nothing
F nothing

States:

Name Description
d(time) nothing
V(time) nothing
X(time) nothing
Ca_NSR(time) nothing
h(time) nothing
z(time) nothing
y(time) nothing
f(time) nothing
Ko(time) nothing
Ca_JSR(time) nothing
Ki(time) nothing
j(time) nothing
m(time) nothing
Cai(time) nothing
Nai(time) nothing
Ca_foot(time) nothing

Observables: none

dupont_berridge_goldbeter_1990 @ v0.0.1

Latency correlates with period in a model for signal-induced Ca2+ oscillations based on Ca2+induced Ca2+ release

Oscillations in cytosolic Ca2+ develop in a variety of cells after an induction phase, called latency, the duration of which depends on the magnitude of external stimulation. Experiments in hepatocytes indicate that the period and latency of Ca2+ oscillations both decrease as the level of the stimulus increases. We analyze the correlation between period and latency in a model recently proposed for signal-induced Ca2+ oscillations. We show that the linear relationship between period and latency observed in the experiments arises naturally in this model as a result of the mechanism of Ca2(+)-induced Ca2+ release on which it is based.

Parameters:

Name Description
v0 2.7
K_A 0.9
k 10.0
v1 4.0
t_c 0.8
k_f 1.0
V_M2 65.0
m 2.0
V_M3 500.0
K_R 2.0
K_2 1.0
Beta_f 0.15
p 4.0
n 2.0

States:

Name Description
Z(time) 0.2
Y(time) 0.2

Observables: none

dupont_berridge_goldbeter_1991 @ v0.0.1

Dupont Berridge Goldbeter 1991

nothing

Parameters:

Name Description
n 2.0
KA 0.9
K2 1.0
k 10.0
v1 7.3
VM2 65.0
KR 2.0
beta 0.6
betaf 0.96
kf 1.0
m 2.0
tp 4.0
VM3 500.0
p 4.0
v0 1.0

States:

Name Description
Z(time) 0.1
Y(time) 0.64

Observables: none

dupont_erneux_1997 @ v0.0.1

Simulations of the effects of inositol 1,4,5=trisphosphate 3-kinase and S-phosphatase activities on Ca+ oscillations

Summary lnositol 1,4,5-trisphosphate (Ins-l ,4,5-P,) is responsible for Ca2+ mobilization in response to external stimulation in many cell types. The latter phenomenon often occurs as repetitive Ca2+ spikes. In this study, the effect of the two Ins-l ,4,5-P, metabolizing enzymes (Ins-l ,4,5-P, 3-kinase and 5-phosphatase) on the temporal pattern of Ca+ oscillations has been investigated. On the basis of the well-documented Ins-1,4,5-P, 3-kinase stimulation by the Ca+/calmodulin complex and of the experimentally-determined kinetic characteristics of these enzymes, we predict that 5-phosphatase primarily controls the levels of Ins-1,4,5-P,and, thereby, the occurrence and frequency of Ca+ oscillations. Consequently, the model reproduces the experimental observation performed in Chinese hamster ovary cells that 5-phosphatase overexpression has a much more pronounced effect on the pattern of Ca+ oscillations than 3- kinase overexpression. We also investigated, in more detail, under which conditions a similar effect could be observed in other cell types expressing various Ins-l ,4,5-P, 3-kinase activities. 

Parameters:

Name Description
n_i 4.0
V_p2 0.2
Ca_tot 80.0
b 0.0007
K_d 0.3
n_a 3.0
K_p 0.35
n_d 2.0
n_p 2.0
V_plc 1.3
K_p1 10.0
V_p1 5.0
K_inh 0.15
V_k 0.5
k 0.01
alpha 0.1
V_MP 4.0
K_p2 2.0
K_minus 0.5
K_k 1.0
K_act 0.56
K_1 2.57
gamma 0.2
K_IP 1.0

States:

Name Description
R_des(time) 0.1
IP4(time) 0.1
IP3(time) 0.1
C_cyto(time) 0.1

Observables: none

dupont_goldbeter_1992 @ v0.0.1

Dupont Goldbeter 1992

nothing

Parameters:

Name Description
Ka 1.0
n 2.0
KA 0.9
v0 1.0
K2 0.01
v1beta 2.4
VM2 65.0
k 10.0
KP 1.0
WT 10.0
vP 2.5
KR 2.0
vMK 100.0
kf 1.0
m 2.0
VM3 500.0
q 4.0
p 4.0
K1 0.01

States:

Name Description
Z(time) 0.2281
Y(time) 1.454
Wstar(time) 0.8916

Observables: none

E


earm_noble_1990 @ v0.0.1

Earm, Noble, 1990

nothing

Parameters:

Name Description
C_m 4.0e-5
T 310.0
stim_start 0.1
alpha_Calmod 100000.0
alpha_Trop 100000.0
length 0.08
d_NaCa 0.0001
K_leak_rate 0.0
alpha_up 3.0
i_NaK_max 0.14
g_to 0.01
Trop 0.15
beta_up 0.23
K_cyca 0.0003
beta_Trop 200.0
K_mNa 40.0
g_b_K 0.0017
g_K1 0.017
delta_m 1.0e-5
P_Ca_L 0.05
K_srca 0.5
V_e_ratio 0.4
g_b_Ca 5.0e-5
Na_o 140.0
stim_duration 0.002
K_c 4.0
K_m_rel 250.0
n_NaCa 3.0
Ca_o 2.0
ProdFracRate 1.0
V_up_ratio 0.01
stim_period 1.0
stim_end 100000.0
alpha_tr 50.0
Calmod 0.02
radius 0.01
beta_Calmod 50.0
g_b_Na 0.00012
K_xcs 0.4
V_rel_ratio 0.1
K_mK 1.0
g_Na 0.5
stim_amplitude -1.3
gamma 0.5
g_to_s 0.0
K_m_K1 10.0
k_NaCa 0.0001
R 8314.472
F 96485.3415

States:

Name Description
d(time) 0.0011
Ca_Trop(time) 0.0015
Ca_rel(time) 0.3
V(time) -91.6
h(time) 0.015
K_i(time) 140.0
ProdFrac(time) 0.0
ActFrac(time) 0.0
f_Ca(time) 0.785
r(time) 0.0
m(time) 0.076
Ca_up(time) 0.3
Ca_i(time) 1.0e-5
s(time) 1.0
Na_i(time) 6.48
Ca_Calmod(time) 0.0005

Observables: none

ebihara_johnson_1980 @ v0.0.1

Ebihara, Johnson, 1980

nothing

Parameters:

Name Description
C nothing
g_s nothing
beta_x1 nothing
Istim nothing
g_Na nothing
alpha_x1 nothing
E_Na nothing

States:

Name Description
d(time) nothing
V(time) nothing
h(time) nothing
m(time) nothing
Cai(time) nothing
f(time) nothing
x1(time) nothing

Observables: none

Edwards_et_al @ v0.0.1

Edwards, 2010

Cellular mechanisms underlying nitric oxide-induced vasodilation of descending vasa recta

Parameters: none

States: none

Observables: none

egli_bertram_sellix_freeman_2004 @ v0.0.1

Egli, Bertram, Sellix, Freeman, 2004

nothing

Parameters:

Name Description
rO 1100.0
DA_infinity 20000.0
vObar 500.0
qD 0.2
kO 9.0
qO 1.0
qP 0.5
vDbar 10000.0
kx 50.0
kD 300.0
rP 300000.0

States:

Name Description
DA(time) 20000.0
OT(time) 25.0
PRL(time) 20.0

Observables: none

electrecoblu @ v0.0.1

ElectrEcoBlu Standard Virtual Biological Machine

Please click on one of the exposures below for documentation and model file access.

Parameters: none

States: none

Observables: none

elowitz_leibler_2000 @ v0.0.1

Elowitz, Leibler, 2000

nothing

Parameters:

Name Description
n 2.0
tps_repr 0.0005
efficiency 20.0
mRNA_halflife 2.0
K_m 40.0
prot_halflife 10.0
tps_active 0.5

States:

Name Description
M_lacl(time) 0.0
P_tetR(time) 0.0
P_cl(time) 0.0
M_tetR(time) 20.0
M_cl(time) 0.0
P_lacl(time) 0.0

Observables: none

embc13_n62 @ v0.0.1

EMBC 2013 Tutorial - Noble 1962 reproducibility

This workspace is used in the EMBC 2013 VPH tutorial to demonstrate reproducibility of published data using CellML models and OpenCOR. Complete details available at: http://abibook.readthedocs.org/en/EMBC-2013-tutorial/tutorials/embc13/scenario2/opencor.html

Parameters: none

States: none

Observables: none

enciso_sontag_2004 @ v0.0.1

Enciso, Sontag, 2004

nothing

Parameters:

Name Description
b3 1.0
g2 10.0
b2 1.0
g1 10.0
b1 1.0

States:

Name Description
T(time) 0.0
R(time) 0.1
L(time) 0.0

Observables: none

endresen_1996 @ v0.0.1

Endresen, 1996

nothing

Parameters:

Name Description
V_B -50.0
V_3 -27.9375
g_j 0.0
V_4 6.321
lambda_w 20.7796
g_s 382.9118
V_2 7.8589
V_K -259.0783
V_s 214.1429
g_K 536.1093
V_1 -35.9358
Cm 60.0
ACh 1.0e-6

States:

Name Description
u(time) 0.2344555
V(time) -52.07606
w(time) 0.0008971

Observables: none

eskandari_wright_loo_2005 @ v0.0.1

Eskandari, Wright, Loo 2005

Kinetics of the Reverse Mode of the Na+/Glucose Cotransporter

Parameters:

Name Description
k0_54 12190.0
k0_56 10.0
Na_o 0.01
k0_21 500.0
k0_61_f 5.0
T 310.0
k0_34 50.0
Na_i 0.5
k0_65_r 4500.0
delta 0.7
z_c -2.0
k0_65_f 50.0
k0_25 0.3
z_Na 1.0
k0_12 80000.0
alpha_pp 0.0
k0_45 800.0
k0_61_r 3.0
k0_43 50.0
k0_16_f 35.0
k0_32 20.0
glucose_o 0.0
glucose_i 0.1
area 1.0e6
N_Avo 6.022e23
k0_23 100000.0
k0_52 0.00091
k0_16_r 350.0
N_C 3.0e6
R 8.314
F 96485.34
n 2.0

States:

Name Description
C_1(time) 0.0
C_3(time) 0.0
V(time) -0.15
C_2(time) 0.0
C_5(time) 0.0
C_6_temp(time) 0.0
C_4(time) 0.0

Observables: none

espinosa_1998 @ v0.0.1

Espinosa, 1998

nothing

Parameters:

Name Description
pf 0.7
T 310.0
stim_start 0.02
alpha_Calmod 100000.0
g_bca 0.00025
alpha_Trop 100000.0
length 74.0
d_NaCa 0.005
K_leak_rate 0.05
alpha_up 0.4
i_NaK_max 0.7
Km_f2ds 0.001
g_to 0.08
delta_f 0.0001
Trop 0.05
delta_x 0.0001
Cm 9.5e-5
beta_up 0.03
FRiNaCa 0.001
FrICa 1.0
K_cyca 0.0003
beta_Trop 200.0
K_mNa 40.0
g_bna 0.0001
g_K1 0.12
delta_m 1.0e-5
P_Ca_L 0.06
K_srca 0.5
V_e_ratio 0.4
Na_o 148.5
V_ds_ratio 0.1
stim_duration 0.002
speed_d 10.0
Kdecay 10.0
K_m_rel 250.0
g_tos 0.15
n_NaCa 3.0
Ca_o 2.5
shift_h 0.0
R_decay 20.0
V_up_ratio 0.01
stim_period 0.5
stim_end 9.0
K_mk1 10.0
K_m_Ca_ds 0.01
Calmod 0.02
radius 12.0
beta_Calmod 50.0
g_bk 0.004
K_m_Ca_cyt 0.0005
K_xcs 0.4
V_rel_ratio 0.1
P_CaK 0.003
K_mK 1.0
g_Na 0.6
speed_f 2.0
stim_amplitude -1.8
Km_f2 100000.0
i_K_max 1.5
P_CaNa 0.01
gamma 0.5
k_NaCa 0.0002
R 8314.472
F 96485.3415
K_b 5.4

States:

Name Description
d(time) 3.06884e-12
Ca_Trop(time) 0.0017012
Ca_rel(time) 0.43984
V(time) -86.27784
f2(time) 0.994096
h(time) 0.9759885
x(time) 2.3455e-6
f(time) 0.9999977
K_i(time) 140.1333
ActFrac(time) 0.0113161
ProdFrac(time) 0.9402563
Ca_ds(time) 0.0008364
r(time) 2.4223e-5
K_o(time) 5.3201028
m(time) 0.003956
Ca_up(time) 0.479749
Ca_i(time) 7.07933e-5
s(time) 0.954689
f2ds(time) 0.4387865
Na_i(time) 6.835
Ca_Calmod(time) 0.0024448

Observables: none

evans_errington_shelly_feeney_chapman_godfrey_smith_chappell_2004 @ v0.0.1

Evans, Errington, Shelly, Feeney, Chapman, Godfrey, Smith, Chappell, 2004

nothing

Parameters:

Name Description
kc_m nothing
BT nothing
ke nothing
ko_m nothing
kd nothing
Vn nothing
ki nothing
kb nothing
kc_c nothing
ko_c nothing
Vm nothing
Vc nothing

States:

Name Description
Lc(time) 0.0
Ln(time) 0.0
Lm(time) 10.0
Hc(time) 0.0
Hm(time) 0.0

Observables: none

F


faber_rudy_2000 @ v0.0.1

Faber, Rudy, 2000

nothing

Parameters:

Name Description
preplength 0.1
stim_start 10.0
Tn_max 0.07
CMDN_max 0.05
c2 0.0001
tau_tr 120.0
Ca_NSR_max 15.0
kATP 0.00025
Cao 1.8
gamma_Nai 0.75
K_relss 1.0
radius 0.011
i_K_ATP_on 1.0
I_pCa 1.15
I_NaK 2.25
Nao 140.0
ATPi 3.0
g_Kp 0.00552
stim_amplitude -80.0
K_mrel 0.0008
CSQN_max 10.0
nKNa 2.8
K_mKo 1.5
CSQNthresh 0.7
F 96485.0
nicholsarea 5.0e-5
gamma_Cao 0.341
qn 9.0
T 310.0
P_Na 6.75e-7
Km_Ca 0.0006
tau 4.75
K_mup 0.00092
G_Ks 0.433
stim_period 300.0
stim_end 9.0e6
kdKNa 66.0
K_mCSQN 0.8
K_mTRPN 0.0005
P_Ca 0.00054
I_up 0.00875
G_rel_overload 4.0
K_mTn 0.0005
R 8314.0
TRPN_max 0.07
G_rel_max 60.0
Ko 5.4
gamma_Nao 0.75
Logicthresh 0.98
c1 0.00025
g_Nab 0.004
G_Kr 0.02614
kappa 0.125
K_m_ns_Ca 0.0012
K_mNai 10.0
G_K1 0.75
gamma_Cai 1.0
hATP 2.0
PNaK 0.01833
delta_Ca_ith 0.00018
delta_m 1.0e-5
stim_duration 0.5
g_K_Na 0.12848
K_mpCa 0.0005
K_mCMDN 0.00238
gamma_Ki 0.75
A_cap 0.0001534
g_Na 16.0
g_Cab 0.003016
gamma_Ko 0.75
g_CaT 0.05
nATP 0.24
gamma 0.15
P_K 1.93e-7

States:

Name Description
OVRLDtrack3(time) 0.0
NSR(time) 1.516756041281
xr(time) 0.000207067204
Ca_NSR(time) 1.76731003671612
OVRLDtrack2(time) 0.0
f(time) 0.999390880784
Cainfluxtrack(time) 2.69380318286645e-196
APtrack2(time) 5.33944967562997e-195
xs1(time) 0.007136102382
j(time) 0.990731711845
m(time) 0.001513296212
xs2(time) 0.039518996812
Nai(time) 10.0
APtrack3(time) 0.000129515197402902
APtrack(time) 9.65910542308504e-196
zdv(time) 0.014537782303
d(time) 5.906564e-6
g(time) 0.988597502434
OVRLDtrack(time) 0.0
V(time) -85.126196430406
h(time) 0.985318710339
ydv(time) 0.99993940527
Ca_JSR(time) 1.12791401197882
Ki(time) 144.473230653346
b(time) 0.001378275288
JSR(time) 8.290468
CaT(time) 0.01544711
Cai(time) 0.000117482029668194
i_rel(time) -4.74565e-19

Observables: none

fall_keizer_2001 @ v0.0.1

Fall, Keizer, 2001

nothing

Parameters: none

States: none

Observables: none

fallon_lauffenburger_2000 @ v0.0.1

Fallon, Lauffenburger, 2000

nothing

Parameters:

Name Description
kr 0.0138
IL2 1.0
kh 0.035
Ve 1.0e-14
kt 0.007
Vs 11.0
ksyn 0.0011
ke 0.04
kx 0.15
NA 6.022e11

States:

Name Description
Cs(time) 1.0
Li(time) 0.01
Y(time) 2.5e8
Ld(time) 1.0
Ci(time) 1.0
Rs(time) 1500.0
Ri(time) 300.0
L(time) 10.0

Observables: none

farhy_bowers_veldhuis_2007 @ v0.0.1

Farhy, Bowers, Veldhuis, 2007

nothing

Parameters:

Name Description
t3 400.0
kr2 2200.0
C 10000.0
GHS 20.0
ng2 2.0
n1 5.0
S_basal 900.0
duration 0.2
g0 1.0
t5 10.0
k4 25.0
n5 2.0
g2 100.0
kr1 600.0
n3 2.0
g1 45000.0
t4 28.0
kr4 20400.0
ng0 2.9
t2 10.0
tg2 10000.0
ng1 3.0
k1 3.0
t1 400.0
n2 2.0
tg0 200.0
tg1 390.0
kghr 15.0
k3 40.0
onset 2.0
n4 5.0
kr3 63000.0
k2 25.0

States:

Name Description
GHRH(time) 0.0
SRIF_PeV(time) 0.0
ghr_GHRH(time) 0.0
SRIF_ArC(time) 0.0
GH(time) 0.0

Observables: none

faville_pullan_sanders_koh_lloyd_smith_2009 @ v0.0.1

Faville, Pullan, Sanders, Koh, Lloyd, Smith, 2009

A Biophysically-Based Mathematical Representation of Interstitial Cells of Cajal Pacemaker Potentials produced from a Unitary Potential Basis

Parameters: none

States: none

Observables: none

faville_pullan_sanders_smith_2008 @ v0.0.1

Faville, Pullan, Sanders, Smith, 2008

nothing

Parameters:

Name Description
k_1 6.4
T 310.16
P 1.0
KNCX 0.3
Km 0.01
A4 3.57
A5 2.7e-5
kIPR 2000.0
ENSCC 0.0
mu_S1S2 0.04
KNa 10000.0
gPM 420.0
h_beta 2.0
A6 2.31e-5
Cm 20.0
VNCX 0.5
KMCU 10.0
gamma_S2 1.0
R1 36.0
gamma_MT 200.0
VSERCA 100000.0
r2 200.0
hNa 4.0
K_beta 2.0
gNSCC_Ca_ 0.12
Bm 100.0
r_2 0.0
KINH 10.0
hNSCC 3.0
KNSCC 0.12
r4 750.0
gamma_ER 20.0
gNa 15000.0
gamma_S1 100.0
A2 0.0006
gNSCC_Na_ 220.0
VMCU 800.0
CO 1800.0
hINH 4.0
delta_s 26.0
g_beta 300.0
KPM 1.0
k1 0.0
gCa 0.01
R3 300.0
g_alpha 0.02
R 0.008314
F 0.09649
k2 4.0

States:

Name Description
phi3(time) 0.306
H(time) 0.787
CMT(time) 0.22
CS2(time) 0.023
Vm(time) -70.1
NS1(time) 10100.0
CS1(time) 0.12
CER(time) 203.0

Observa