CellMLPhysiome: 1 - B

1

1ac — v0.0.1

Linear 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 — v0.0.1

Cell 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 — v0.0.1

Synchronized 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 — v0.0.1

Basket Catheter Emulator

Details

An 64 electrode basket catheter emulator CTK-Plugin.

2d5 — v0.0.1

Moore, 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 — v0.0.1

Alexander 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 — v0.0.1

Benson 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 — v0.0.1

Vasalou 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 — v0.0.1

A 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 — v0.0.1

Tran 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 — v0.0.1

A 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 — v0.0.1

Atrial 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 — v0.0.1

SED-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 — v0.0.1

Hill, 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 — v0.0.1

O'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 — v0.0.1

HH 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 — v0.0.1

Steady 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 — v0.0.1

Ni 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 — v0.0.1

Fenton, 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 — v0.0.1

A 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 — v0.0.1

A 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 — v0.0.1

McIntyre, 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 — v0.0.1

Models 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 — v0.0.1

Faber, 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 — v0.0.1

Goldbeter 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 — v0.0.1

A 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 — v0.0.1

Aguda, 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 — v0.0.1

Gupta, 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 — v0.0.1

Testing 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 — v0.0.1

A 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 — v0.0.1

Varela - 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 — v0.0.1

Noble 1962 model for Physiome article

Details

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

5

58f — v0.0.1

Loewe-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 — v0.0.1

A 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 — v0.0.1

Generic 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 — v0.0.1

Generic 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 — v0.0.1

Generic human lung scaffold

Details

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

62f — v0.0.1

rat flatmap

Details

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

63a — v0.0.1

Rat 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 — v0.0.1

Combine 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 — v0.0.1

Tong, 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 — v0.0.1

Tong, 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 — v0.0.1

Gattoni 2016

Details

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

3

314 — v0.0.1

Novak, 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 — v0.0.1

Cui, 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 — v0.0.1

Arresting 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 — v0.0.1

Aslanidi 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 — v0.0.1

Bagci 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 — v0.0.1

Barberis, 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 — v0.0.1

Bental, 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 — v0.0.1

Chen, 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 — v0.0.1

Kholodenko, 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 — v0.0.1

Computational 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 — v0.0.1

BG 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 — v0.0.1

paci_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 — v0.0.1

Grandi 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 — v0.0.1

Generic 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 — v0.0.1

Generic 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 — v0.0.1

Generic 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 — v0.0.1

Generic 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 — v0.0.1

Generic 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 — v0.0.1

Generic 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 — v0.0.1

Generic 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 — v0.0.1

Generic 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 — v0.0.1

Koivumäki, 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 — v0.0.1

Voigt, 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 — v0.0.1

Two 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 — v0.0.1

Adrian, 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 — v0.0.1

Aguda, 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 — v0.0.1

Aguda, 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 — v0.0.1

Albrecht, 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 — v0.0.1

Albrecht, 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 — v0.0.1

Alexander 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 — v0.0.1

Aon, 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: Aorta_Brown_Shi_et_al_2012 — v0.0.1

Workflows 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 — v0.0.1

Aslanidi 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 — v0.0.1

Aslanidi_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 — v0.0.1

Aslanidi 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 — v0.0.1

Asthagiri, 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 — v0.0.1

Bagci 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 — v0.0.1

Bagci 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 — v0.0.1

Bakker, 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 — v0.0.1

Bakker, 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 — v0.0.1

Barberis, 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 — v0.0.1

Baylor, 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 — v0.0.1

Beard, 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 — v0.0.1

Covering 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 — v0.0.1

Beeler, 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 — v0.0.1

Beeler, Reuter, 1977 uncertainty example

Details

benson_2008 — v0.0.1

Benson 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 — v0.0.1

Bental, 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 — v0.0.1

Bernus, Wilders, Zemlin, Verschelde, Panfilov, 2002

Details

bertram_arnot_zamponi_2002 — v0.0.1

Bertram, 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 — v0.0.1

Bertram, 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 — v0.0.1

Bertram, 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 — v0.0.1

Bertram, 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 — v0.0.1

Bertram, 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 — v0.0.1

Bertram, 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 — v0.0.1

Bertram, 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 — v0.0.1

Bertram, 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`