CellMLPhysiome: 1 - B
1
1ac
— v0.0.1Linear 2nd order nonhomogeneous ODE with constant coefficients
Details
Classical example: a linear second order nonhomogeneous ODE IVP with constant coefficients and constant right hand side.
See Wikipedia
States:
Name | Description |
---|---|
v(t) | 1.0 |
u(t) | 1.0 |
1b5
— v0.0.1Cell viability models for tissue exposed to thermal ablation temperatures.
Details
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 |
2
2bb
— v0.0.1Synchronized Scene Viewer
Details
A CTK-OpenCMISS ZINC Plugin that can render graphical elements across multiple opengl contexts and synchronize mouse events initiated by the user.
2bc
— v0.0.1Basket Catheter Emulator
Details
An 64 electrode basket catheter emulator CTK-Plugin.
2d5
— v0.0.1Moore, Li, 2004
Details
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 |
2d8
— v0.0.1Alexander and Wahl 2010
Details
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 |
2e3
— v0.0.1Benson 2008
Details
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 |
2f1
— v0.0.1Vasalou and Henson 2010
Details
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 |
3
3e0
— v0.0.1A model for pacemaking in substantia nigra neurons (A simple model based on a spherical geometry)
Details
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 |
4
4a2
— v0.0.1Tran 2017 - Cross-bridge model of shortening heat
Details
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.
4a3
— v0.0.1A model of intracellular pH control
Details
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 |
4be
— v0.0.1Atrial fibroblast model
Details
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 |
4c6
— v0.0.1SED-ML example
Details
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 |
4cd
— v0.0.1Hill, 1972 - a model of feto-maternal oxygen exchange
Details
This model is developed based on mathematical model of placental oxygen transfer by Ester Hill and Gordon Power (1972).
4e4
— v0.0.1O'Hara-Rudy-CiPA-v1.0 (2017)
Details
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 |
4e9
— v0.0.1HH Sodium Current model for estimation task
Details
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 |
4f0
— v0.0.1Steady state HMT
Details
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 |
5
5b0
— v0.0.1Ni et al. 2017 Human atrial model
Details
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 |
5bb
— v0.0.1Fenton, Karma, 1998
Details
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 |
5d7
— v0.0.1A computational human cardiac Purkinje electrophysiological model
Details
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 |
5e1
— v0.0.1A computational human ventricular electrophysiological model
Details
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 |
5f5
— v0.0.1McIntyre, Richardson, Grill, 2001
Details
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 |
2
25d
— v0.0.1Models for the OpenCOR and PMR tutorial by Peter Hunter
Details
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 |
25e
— v0.0.1Faber, Rudy, 2000 and Tong, Ghouri, Taggart, 2014
Details
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 |
3
35a
— v0.0.1Goldbeter Dupont Berridge 1990
Details
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 |
35c
— v0.0.1A single compartment model of pacemaking in dissasociated Substantia nigra neurons with hyperbolic tetrahedral geometry
Details
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 |
35e
— v0.0.1Aguda, B, 1999
Details
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 |
35f
— v0.0.1Gupta, Maurya, Stephens, Dennis and Subramaniam, 2009
Details
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 |
4
43c
— v0.0.1Testing RDF linking across CellML, SED-ML, and SVG
Details
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.
44c
— v0.0.1A 0D model of the Heart
Details
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 |
47c
— v0.0.1Varela - Canine Atrial Cell Models
Details
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 |
49e
— v0.0.1Noble 1962 model for Physiome article
Details
This is a workspace for testing out a Physiome article based on the Noble 1962 model.
5
58f
— v0.0.1Loewe-Lutz-Fabbri-Severi human sinus node cellular electrophysiology model
Details
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"
59a
— v0.0.1A Model of Cardiac Electrical Activity Incorporating Ionic Pumps and Concentration Changes, DiFrancesco, Noble, 1985
Details
This model reproduces the results as shown in the original paper, and also contains semantically relevant annotations.
6
61a
— v0.0.1Generic human heart scaffold
Details
Annotated heart scaffold for human available for registration of segmented neural anatomical-functional mapping of cardiac neural circuits. See SPARC portal for more details
61d
— v0.0.1Generic mouse lung scaffold
Details
Annotated lung scaffold for mouse available for registration of segmented neural anatomical-functional mapping of pulmonary neural circuits. See SPARC portal for more details.
62b
— v0.0.1Generic human lung scaffold
Details
Annotated lung scaffold for human available for registration of segmented neural anatomical-functional mapping of pulmonary neural circuits.
62f
— v0.0.1rat flatmap
Details
Files for the rat flatmap. Uses mapmaker
to generate map datasets for a flatmap server and viewer.
63a
— v0.0.1Rat whole body scaffold
Details
In this workspace we have the Scaffold Maker workflow and configuration files needed to produce the rat whole body scaffold for the SPARC project.
2
239
— v0.0.1Combine Archive Example
Details
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 |
261
— v0.0.1Tong, Choi, Kharche, Holden, Zhang, Taggart, 2011
Details
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 |
262
— v0.0.1Tong, Tribe, Smith, Taggart, 2014
Details
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 |
285
— v0.0.1Gattoni 2016
Details
Models from Sara Gattoni at Kings College London. Rat ventricular myocyte electrophysiology and calcium dynamics.
3
314
— v0.0.1Novak, Tyson, 1993
Details
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 |
354
— v0.0.1Cui, Kaandorp, 2006
Details
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 |
361
— v0.0.1Arresting the mitotic oscillator and the control of cell proliferation: insights from a cascade model for cdc2 kinase activation
Details
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 |
362
— v0.0.1Aslanidi 2009
Details
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 |
363
— v0.0.1Bagci 2008
Details
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 |
364
— v0.0.1Barberis, Klipp, Vanoni, Alberghina, 2007
Details
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 |
366
— v0.0.1Bental, 2006
Details
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 |
369
— v0.0.1Chen, Calzone, Csikasznagy, Cross, Novak, Tyson, 2004
Details
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 |
394
— v0.0.1Kholodenko, Demin, Moehren, Hoek, 1999
Details
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 |
4
486
— v0.0.1Computational analysis of the human sinus node action potential: model development and effects of mutations
Details
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 |
496
— v0.0.1BG Mica models
Details
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 |
5
593
— v0.0.1paci_hyttinen_aaltosetala_severi_2013
Details
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 |
595
— v0.0.1Grandi et al. 2011 Atrial Action Potential and Ca2+ Model
Details
Atrial AP model by Eleonora Grandi, Sandeep V. Pandit, Niels Voigt, Antony J. Workman, Dobromir Dobrev, José Jalife, and Donald M. Bers
6
612
— v0.0.1Generic mouse colon scaffold
Details
Annotated colon scaffold for mouse available for registration of segmented neural anatomical-functional mapping of enteric neural circuits. See SPARC portal for more details
613
— v0.0.1Generic pig colon scaffold
Details
Annotated colon scaffold for pig available for registration of segmented neural anatomical-functional mapping of enteric neural circuits. See SPARC portal for more details
614
— v0.0.1Generic human colon scaffold
Details
Annotated colon scaffold for human available for registration of segmented neural anatomical-functional mapping of enteric neural circuits. See SPARC portal for more details
615
— v0.0.1Generic rat stomach scaffold
Details
Annotated stomach scaffold for rat available for registration of segmented neural anatomical-functional mapping of enteric neural circuits. See SPARC portal for more details
616
— v0.0.1Generic rat heart scaffold
Details
Annotated heart scaffold for rat available for registration of segmented neural anatomical-functional mapping of cardiac neural circuits. See SPARC portal for more details
617
— v0.0.1Generic rat bladder scaffold
Details
Annotated bladder scaffold for rat available for registration of segmented neural anatomical-functional mapping of LUT neural circuits. See SPARC portal for more details
618
— v0.0.1Generic cat bladder scaffold
Details
Annotated bladder scaffold for cat available for registration of segmented neural anatomical-functional mapping of LUT neural circuits. See SPARC portal for more details
619
— v0.0.1Generic pig heart scaffold
Details
Annotated heart scaffold for pig available for registration of segmented neural anatomical-functional mapping of cardiac neural circuits. See SPARC portal for more details
630
— v0.0.1Koivumäki, Korhonen, Tavi 2011 Atrial AP model
Details
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 |
633
— v0.0.1Voigt, Heijman et al. 2013 human atrial AP model
Details
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 |
A
acikgoz_2009
— v0.0.1Two compartment model of diazepam biotransformation in an organotypical culture of primary human hepatocytes
Details
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 |
adrian_chandler_hodgkin_1970
— v0.0.1Adrian, Chandler, Hodgkin, 1970
Details
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 |
aguda_b_1999
— v0.0.1Aguda, B, 1999
Details
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 |
aguda_tang_1999
— v0.0.1Aguda, Tang, 1999
Details
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 |
albrecht_colegrove_friel_2002
— v0.0.1Albrecht, Colegrove, Friel, 2002
Details
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 |
albrecht_colegrove_hongpaisan_pivovarova_andrews_friel_2001
— v0.0.1Albrecht, Colegrove, Hongpaisan, Pivovarova, Andrews, Friel, 2001
Details
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 |
alexander_wahl_2010
— v0.0.1Alexander and Wahl 2010
Details
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 |
aon_cortassa_2002
— v0.0.1Aon, Cortassa, 2002
Details
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 |
Aorta_Brown_Shi_et_al_2012
— v0.0.1Workflows for analysis of valvular and aortic disease
Details
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.
aslanidi_atrial_model_2009
— v0.0.1Aslanidi Atrial Model 2009
Details
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 |
Aslanidi_etal_2010
— v0.0.1Aslanidi_etal_2010
Details
Aslanidi, Sleiman, Boyett, Hancox, Zhang, 2010
Ionic mechanisms for electrical heterogeneity between rabbit Purkinje fiber and ventricular cells
aslanidi_purkinje_model_2009
— v0.0.1Aslanidi 2009
Details
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 |
asthagiri_lauffenburger_2001
— v0.0.1Asthagiri, Lauffenburger, 2001
Details
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 |
B
bagci_2006
— v0.0.1Bagci 2006
Details
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 |
bagci_2008
— v0.0.1Bagci 2008
Details
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 |
bakker_mensonides_teusink_vanhoek_michels_westerhoff_2000
— v0.0.1Bakker, Mensonides, Teusink, Vanhoek, Michels, Westerhoff, 2000
Details
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 |
bakker_michels_opperdoes_westerhoff_1997
— v0.0.1Bakker, Michels, Opperdoes, Westerhoff, 1997
Details
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 |
barberis_klipp_vanoni_alberghina_2007
— v0.0.1Barberis, Klipp, Vanoni, Alberghina, 2007
Details
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 |
baylor_hollingworth_chandler_2002
— v0.0.1Baylor, Hollingworth, Chandler, 2002
Details
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 |
beard_2005
— v0.0.1Beard, 2005
Details
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 |
becker_2010
— v0.0.1Covering a Broad Dynamic Range: Information Processing at the Erythropoietin Receptor
Details
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 |
beeler_reuter_1977
— v0.0.1Beeler, Reuter, 1977
Details
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 |
beeler_reuter_1977_uncertexample
— v0.0.1Beeler, Reuter, 1977 uncertainty example
Details
benson_2008
— v0.0.1Benson 2008
Details
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 |
bental_2006
— v0.0.1Bental, 2006
Details
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 |
bernus_wilders_zemlin_verschelde_panfilov_2002
— v0.0.1Bernus, Wilders, Zemlin, Verschelde, Panfilov, 2002
Details
bertram_arnot_zamponi_2002
— v0.0.1Bertram, Arnot, Zamponi, 2002
Details
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 |
bertram_pedersen_luciani_sherman
— v0.0.1Bertram, Pedersen, Luciani and Sherman 2006
Details
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 |
bertram_previte_sherman_kinard_satin_2000
— v0.0.1Bertram, Previte, Sherman, Kinard, Satin, 2000
Details
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 |
bertram_rhoads_cimbora_2008
— v0.0.1Bertram, Rhoads and Cimbora 2008
Details
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 |
bertram_satin_pedersen_luciani_sherman_2007
— v0.0.1Bertram, Satin, Pedersen, Luciani, Sherman, 2007
Details
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 |
bertram_satin_zhang_smolen_sherman_2004
— v0.0.1Bertram, Satin, Zhang, Smolen, Sherman, 2004
Details
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 |
bertram_sherman_2004
— v0.0.1Bertram, Sherman, 2004
Details
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 |
bertram_smolen_sherman_mears_atwater_martin_soria_1995
— v0.0.1Bertram, Smolen, Sherman, Mears, Atwater, Martin, Soria, 1995
Details
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 |