- Author:
- WeiweiAi <wai484@aucklanduni.ac.nz>
- Date:
- 2022-10-19 10:24:37+13:00
- Desc:
- Add readme to link the documentation on overleaf.
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/701/rawfile/6741283829975cd4f084159e7734dcbece29f7b1/Experiments/Single_stim_experiment_5.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="Single_stim_experiment" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:xlink="http://www.w3.org/1999/xlink">
<import xlink:href="../cellLib/Components/units.cellml">
<units name="ms" units_ref="ms"/>
<units name="mV" units_ref="mV"/>
<units name="mM" units_ref="mM"/>
<units name="pA" units_ref="pA"/>
<units name="nA" units_ref="nA"/>
<units name="pF" units_ref="pF"/>
<units name="cmsq" units_ref="cmsq"/>
<units name="per_ms" units_ref="per_ms"/>
<units name="nS_per_pF" units_ref="nS_per_pF"/>
<units name="uJ_per_K_mmol" units_ref="uJ_per_K_mmol"/>
<units name="C_per_mol" units_ref="C_per_mol"/>
<units name="cm3" units_ref="cm3"/>
<units name="per_cmsq" units_ref="per_cmsq"/>
<units name="cm3_per_s" units_ref="cm3_per_s"/>
<units name="mM_per_ms" units_ref="mM_per_ms"/>
<units name="per_mMsq_ms" units_ref="per_mMsq_ms"/>
<units name="per_mM_ms" units_ref="per_mM_ms"/>
<units name="uN_per_um" units_ref="uN_per_um"/>
<units name="uN_ms_per_um" units_ref="uN_ms_per_um"/>
<units name="uN" units_ref="uN"/>
<units name="um" units_ref="um"/>
<units name="pA_per_pF" units_ref="pA_per_pF"/>
<units name="um_per_ms" units_ref="um_per_ms"/>
<units name="mF_per_cmsq" units_ref="mF_per_cmsq"/>
</import>
<units name="mol2_per_J_s_cmsq">
<unit exponent="2" units="mole"/>
<unit exponent="-1" units="joule"/>
<unit exponent="-1" units="second"/>
<unit exponent="-1" units="cmsq"/>
</units>
<units name="nmol2_per_J_s_cmsq">
<unit prefix="nano" units="mol2_per_J_s_cmsq"/>
</units>
<import xlink:href="../cellLib/Protocols/periodic-IStim-protocol.cellml">
<component component_ref="sPulse_protocol_ms" name="sPulse_protocol_ms"/>
</import>
<import xlink:href="../cellLib/Components/time.cellml">
<component component_ref="time_ms" name="time"/>
</import>
<import xlink:href="../Components/default_values_1.cellml">
<component component_ref="constants" name="constants"/>
<component component_ref="model_parameters" name="model_parameters"/>
<component component_ref="initial_conditions" name="initial_conditions"/>
</import>
<import xlink:href="../Components/wholeCell_2.cellml">
<component component_ref="wholeCell" name="wholeCell"/>
</import>
<!-- Connect the parameters to the protocol definition -->
<component name="Istim_para">
<variable initial_value="1000" name="t_ss" public_interface="out" units="ms"/>
<variable initial_value="0" name="I_holding" public_interface="out" units="pA_per_pF"/>
<variable initial_value="5000" name="t_act" public_interface="out" units="ms"/>
<variable initial_value="-0.4" name="I_actTest" public_interface="out" units="pA_per_pF"/>
<variable initial_value="-52.541" name="V_init" public_interface="out" units="mV"/>
<!--var V_init: mV {init: -52.1358, pub: out};//commented out in cpp-->
</component>
<connection>
<map_components component_1="Istim_para" component_2="sPulse_protocol_ms"/>
<map_variables variable_1="t_ss" variable_2="t_ss"/>
<map_variables variable_1="I_holding" variable_2="I_holding"/>
<map_variables variable_1="t_act" variable_2="t_act"/>
<map_variables variable_1="I_actTest" variable_2="I_actTest"/>
</connection>
<!-- Connect the time source variable to the model and stimulus protocol -->
<connection>
<map_components component_1="time" component_2="sPulse_protocol_ms"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="time" component_2="wholeCell"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="time" component_2="outputs"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="sPulse_protocol_ms" component_2="wholeCell"/>
<map_variables variable_1="I_stim" variable_2="I_stim"/>
</connection>
<connection>
<map_components component_1="sPulse_protocol_ms" component_2="outputs"/>
<map_variables variable_1="I_stim" variable_2="I_stim"/>
</connection>
<connection>
<map_components component_1="Istim_para" component_2="wholeCell"/>
<map_variables variable_1="V_init" variable_2="V_init"/>
</connection>
<!-- SED-ML (and CSim simulation description above) is only able to address variables at the top level of the model hierarchy, so we need to define the variables we want SED-ML to be able to address here. -->
<component name="outputs">
<variable name="time" public_interface="in" units="ms"/>
<variable name="V" public_interface="in" units="mV"/>
<variable name="I_stim" public_interface="in" units="pA_per_pF"/>
<variable name="ICa_tot" public_interface="in" units="pA_per_pF"/>
<variable name="INa_tot" public_interface="in" units="pA_per_pF"/>
<variable name="IK_tot" public_interface="in" units="pA_per_pF"/>
<variable name="ICl_tot" public_interface="in" units="pA_per_pF"/>
<variable name="I_tot" public_interface="in" units="pA_per_pF"/>
<variable name="I_CaL" public_interface="in" units="pA_per_pF"/>
<variable name="Cai" public_interface="in" units="mM"/>
<variable name="stress" public_interface="in" units="dimensionless"/>
<variable name="phosphorylation" public_interface="in" units="dimensionless"/>
<variable name="P_CaL" public_interface="in" units="dimensionless"/>
<variable name="I_CaT" public_interface="in" units="pA_per_pF"/>
<variable name="P_CaT" public_interface="in" units="dimensionless"/>
<variable name="I_Na" public_interface="in" units="pA_per_pF"/>
<variable name="P_Nai" public_interface="in" units="dimensionless"/>
<variable name="I_K1" public_interface="in" units="pA_per_pF"/>
<variable name="P_K1" public_interface="in" units="dimensionless"/>
<variable name="I_K2" public_interface="in" units="pA_per_pF"/>
<variable name="P_K2" public_interface="in" units="dimensionless"/>
<variable name="I_KA" public_interface="in" units="pA_per_pF"/>
<variable name="P_KA" public_interface="in" units="dimensionless"/>
<variable name="I_KCa" public_interface="in" units="pA_per_pF"/>
<variable name="I_Kleak" public_interface="in" units="pA_per_pF"/>
<variable name="P_Kleak" public_interface="in" units="dimensionless"/>
<variable name="I_h" public_interface="in" units="pA_per_pF"/>
<variable name="P_h" public_interface="in" units="dimensionless"/>
<variable name="I_Cl" public_interface="in" units="pA_per_pF"/>
<variable name="P_Cl" public_interface="in" units="dimensionless"/>
<variable name="I_Capump" public_interface="in" units="pA_per_pF"/>
<variable name="I_NaK" public_interface="in" units="pA_per_pF"/>
<variable name="I_NaCa" public_interface="in" units="pA_per_pF"/>
<variable name="I_NaKCl" public_interface="in" units="pA"/>
<variable name="I_NaKCl_Na" public_interface="in" units="pA"/>
<variable name="I_NaKCl_K" public_interface="in" units="pA"/>
<variable name="I_SOCNa" public_interface="in" units="pA_per_pF"/>
<variable name="I_SOCCa" public_interface="in" units="pA_per_pF"/>
<variable name="I_NSCa" public_interface="in" units="pA_per_pF"/>
<variable name="P_NSCa" public_interface="in" units="dimensionless"/>
<variable name="I_NSNa" public_interface="in" units="pA_per_pF"/>
<variable name="P_NSNa" public_interface="in" units="dimensionless"/>
<variable name="I_NSK" public_interface="in" units="pA_per_pF"/>
<variable name="P_NSK" public_interface="in" units="dimensionless"/>
<variable name="I_NSleak" public_interface="in" units="pA_per_pF"/>
<variable name="P_NSleak" public_interface="in" units="dimensionless"/>
<variable name="I_up" public_interface="in" units="pA"/>
<variable name="I_tr" public_interface="in" units="nA"/>
<variable name="I_rel" public_interface="in" units="nA"/>
<variable name="F_t" public_interface="in" units="uN"/>
</component>
<connection>
<map_components component_1="wholeCell" component_2="outputs"/>
<map_variables variable_1="V" variable_2="V"/>
<map_variables variable_1="ICa_tot" variable_2="ICa_tot"/>
<map_variables variable_1="INa_tot" variable_2="INa_tot"/>
<map_variables variable_1="IK_tot" variable_2="IK_tot"/>
<map_variables variable_1="ICl_tot" variable_2="ICl_tot"/>
<map_variables variable_1="I_tot" variable_2="I_tot"/>
<map_variables variable_1="I_CaL" variable_2="I_CaL"/>
<map_variables variable_1="Cai" variable_2="Cai"/>
<map_variables variable_1="stress" variable_2="stress"/>
<map_variables variable_1="phosphorylation" variable_2="phosphorylation"/>
<map_variables variable_1="P_CaL" variable_2="P_CaL"/>
<map_variables variable_1="I_CaT" variable_2="I_CaT"/>
<map_variables variable_1="P_CaT" variable_2="P_CaT"/>
<map_variables variable_1="I_Na" variable_2="I_Na"/>
<map_variables variable_1="P_Nai" variable_2="P_Nai"/>
<map_variables variable_1="I_K1" variable_2="I_K1"/>
<map_variables variable_1="P_K1" variable_2="P_K1"/>
<map_variables variable_1="I_K2" variable_2="I_K2"/>
<map_variables variable_1="P_K2" variable_2="P_K2"/>
<map_variables variable_1="I_KA" variable_2="I_KA"/>
<map_variables variable_1="P_KA" variable_2="P_KA"/>
<map_variables variable_1="I_KCa" variable_2="I_KCa"/>
<map_variables variable_1="I_Kleak" variable_2="I_Kleak"/>
<map_variables variable_1="P_Kleak" variable_2="P_Kleak"/>
<map_variables variable_1="I_h" variable_2="I_h"/>
<map_variables variable_1="P_h" variable_2="P_h"/>
<map_variables variable_1="I_Cl" variable_2="I_Cl"/>
<map_variables variable_1="P_Cl" variable_2="P_Cl"/>
<map_variables variable_1="I_Capump" variable_2="I_Capump"/>
<map_variables variable_1="I_NaK" variable_2="I_NaK"/>
<map_variables variable_1="I_NaCa" variable_2="I_NaCa"/>
<map_variables variable_1="I_NaKCl" variable_2="I_NaKCl"/>
<map_variables variable_1="I_NaKCl_Na" variable_2="I_NaKCl_Na"/>
<map_variables variable_1="I_NaKCl_K" variable_2="I_NaKCl_K"/>
<map_variables variable_1="I_SOCNa" variable_2="I_SOCNa"/>
<map_variables variable_1="I_SOCCa" variable_2="I_SOCCa"/>
<map_variables variable_1="I_NSCa" variable_2="I_NSCa"/>
<map_variables variable_1="P_NSCa" variable_2="P_NSCa"/>
<map_variables variable_1="I_NSNa" variable_2="I_NSNa"/>
<map_variables variable_1="P_NSNa" variable_2="P_NSNa"/>
<map_variables variable_1="I_NSK" variable_2="I_NSK"/>
<map_variables variable_1="P_NSK" variable_2="P_NSK"/>
<map_variables variable_1="I_NSleak" variable_2="I_NSleak"/>
<map_variables variable_1="P_NSleak" variable_2="P_NSleak"/>
<map_variables variable_1="I_up" variable_2="I_up"/>
<map_variables variable_1="I_tr" variable_2="I_tr"/>
<map_variables variable_1="I_rel" variable_2="I_rel"/>
<map_variables variable_1="F_t" variable_2="F_t"/>
</connection>
<!-- We connect the default parameters through to the model-->
<connection>
<map_components component_1="model_parameters" component_2="wholeCell"/>
<map_variables variable_1="nif" variable_2="nif"/>
<map_variables variable_1="IC50_nif" variable_2="IC50_nif"/>
<map_variables variable_1="E_Ca" variable_2="E_Ca"/>
<map_variables variable_1="T" variable_2="T"/>
<map_variables variable_1="Cm" variable_2="Cm"/>
<map_variables variable_1="Ac" variable_2="Ac"/>
<map_variables variable_1="Vc" variable_2="Vc"/>
<map_variables variable_1="Cao" variable_2="Cao"/>
<map_variables variable_1="Ko" variable_2="Ko"/>
<map_variables variable_1="Nao" variable_2="Nao"/>
<map_variables variable_1="Mgo" variable_2="Mgo"/>
<map_variables variable_1="Clo" variable_2="Clo"/>
<map_variables variable_1="Q10Ca" variable_2="Q10Ca"/>
<map_variables variable_1="Q10K" variable_2="Q10K"/>
<map_variables variable_1="Q10Na" variable_2="Q10Na"/>
<map_variables variable_1="Q10h" variable_2="Q10h"/>
<map_variables variable_1="Q10Cl" variable_2="Q10Cl"/>
<map_variables variable_1="Q10KCa" variable_2="Q10KCa"/>
<map_variables variable_1="T0CaL" variable_2="T0CaL"/>
<map_variables variable_1="T0CaT" variable_2="T0CaT"/>
<map_variables variable_1="T0K" variable_2="T0K"/>
<map_variables variable_1="T0Na" variable_2="T0Na"/>
<map_variables variable_1="T0h" variable_2="T0h"/>
<map_variables variable_1="T0Cl" variable_2="T0Cl"/>
<map_variables variable_1="T0KCa" variable_2="T0KCa"/>
<map_variables variable_1="g_CaL" variable_2="g_CaL"/>
<map_variables variable_1="E_CaL" variable_2="E_CaL"/>
<map_variables variable_1="K_mCaL" variable_2="K_mCaL"/>
<map_variables variable_1="tau_f1" variable_2="tau_f1"/>
<map_variables variable_1="g_CaT" variable_2="g_CaT"/>
<map_variables variable_1="E_CaT" variable_2="E_CaT"/>
<map_variables variable_1="g_Na" variable_2="g_Na"/>
<map_variables variable_1="g_K1" variable_2="g_K1"/>
<map_variables variable_1="g_K2" variable_2="g_K2"/>
<map_variables variable_1="g_KA" variable_2="g_KA"/>
<map_variables variable_1="N_BKCa" variable_2="N_BKCa"/>
<map_variables variable_1="C_est" variable_2="C_est"/>
<map_variables variable_1="tau_pf" variable_2="tau_pf"/>
<map_variables variable_1="tau_ps" variable_2="tau_ps"/>
<map_variables variable_1="P_BKCa" variable_2="P_BKCa"/>
<map_variables variable_1="g_Kleak" variable_2="g_Kleak"/>
<map_variables variable_1="g_h" variable_2="g_h"/>
<map_variables variable_1="P_NaK" variable_2="P_NaK"/>
<map_variables variable_1="g_Cl" variable_2="g_Cl"/>
<map_variables variable_1="K_dCl" variable_2="K_dCl"/>
<map_variables variable_1="tau_n" variable_2="tau_n"/>
<map_variables variable_1="J_pCa" variable_2="J_pCa"/>
<map_variables variable_1="K_mpCa" variable_2="K_mpCa"/>
<map_variables variable_1="hpCa" variable_2="hpCa"/>
<map_variables variable_1="g_NaK" variable_2="g_NaK"/>
<map_variables variable_1="K_dK" variable_2="K_dK"/>
<map_variables variable_1="n_K" variable_2="n_K"/>
<map_variables variable_1="K_dNa" variable_2="K_dNa"/>
<map_variables variable_1="n_Na" variable_2="n_Na"/>
<map_variables variable_1="J_NaCamax" variable_2="J_NaCamax"/>
<map_variables variable_1="K_mAllo" variable_2="K_mAllo"/>
<map_variables variable_1="n_Allo" variable_2="n_Allo"/>
<map_variables variable_1="k_sat" variable_2="k_sat"/>
<map_variables variable_1="gamma" variable_2="gamma"/>
<map_variables variable_1="K_mNai" variable_2="K_mNai"/>
<map_variables variable_1="K_mCai" variable_2="K_mCai"/>
<map_variables variable_1="K_mNao" variable_2="K_mNao"/>
<map_variables variable_1="K_mCao" variable_2="K_mCao"/>
<map_variables variable_1="L_NaKCl" variable_2="L_NaKCl"/>
<map_variables variable_1="R_NaKCl" variable_2="R_NaKCl"/>
<map_variables variable_1="g_SOCNa" variable_2="g_SOCNa"/>
<map_variables variable_1="g_SOCCa" variable_2="g_SOCCa"/>
<map_variables variable_1="K_mSOC" variable_2="K_mSOC"/>
<map_variables variable_1="g_NS" variable_2="g_NS"/>
<map_variables variable_1="g_leak" variable_2="g_leak"/>
<map_variables variable_1="K_dMg" variable_2="K_dMg"/>
<map_variables variable_1="PNa_PCs" variable_2="PNa_PCs"/>
<map_variables variable_1="PK_PCs" variable_2="PK_PCs"/>
<map_variables variable_1="PCa_PCs" variable_2="PCa_PCs"/>
<map_variables variable_1="P_Ca" variable_2="P_Ca"/>
<map_variables variable_1="P_Na" variable_2="P_Na"/>
<map_variables variable_1="I_sus" variable_2="I_sus"/>
<map_variables variable_1="F_BCa" variable_2="F_BCa"/>
<map_variables variable_1="S_CM" variable_2="S_CM"/>
<map_variables variable_1="B_F" variable_2="B_F"/>
<map_variables variable_1="K_d" variable_2="K_d"/>
<map_variables variable_1="K_dB" variable_2="K_dB"/>
<map_variables variable_1="I_up0" variable_2="I_up0"/>
<map_variables variable_1="K_mup" variable_2="K_mup"/>
<map_variables variable_1="Vol_u" variable_2="Vol_u"/>
<map_variables variable_1="Vol_r" variable_2="Vol_r"/>
<map_variables variable_1="tau_tr" variable_2="tau_tr"/>
<map_variables variable_1="tau_rel" variable_2="tau_rel"/>
<map_variables variable_1="F_rel" variable_2="F_rel"/>
<map_variables variable_1="CSQN" variable_2="CSQN"/>
<map_variables variable_1="K_CSQN" variable_2="K_CSQN"/>
<map_variables variable_1="R_leak" variable_2="R_leak"/>
<map_variables variable_1="K_r1" variable_2="K_r1"/>
<map_variables variable_1="K_r1minus" variable_2="K_r1minus"/>
<map_variables variable_1="K_r2" variable_2="K_r2"/>
<map_variables variable_1="K_r2minus" variable_2="K_r2minus"/>
<map_variables variable_1="MLCK_max" variable_2="MLCK_max"/>
<map_variables variable_1="K_MLCK" variable_2="K_MLCK"/>
<map_variables variable_1="K_CaMLCK" variable_2="K_CaMLCK"/>
<map_variables variable_1="C_ms" variable_2="C_ms"/>
<map_variables variable_1="p_M" variable_2="p_M"/>
<map_variables variable_1="n_M" variable_2="n_M"/>
<map_variables variable_1="K_2" variable_2="K_2"/>
<map_variables variable_1="K_3" variable_2="K_3"/>
<map_variables variable_1="K_4" variable_2="K_4"/>
<map_variables variable_1="K_5" variable_2="K_5"/>
<map_variables variable_1="K_7" variable_2="K_7"/>
<map_variables variable_1="l_c" variable_2="l_c"/>
<map_variables variable_1="l_c0" variable_2="l_c0"/>
<map_variables variable_1="l_s0" variable_2="l_s0"/>
<map_variables variable_1="l_opt" variable_2="l_opt"/>
<map_variables variable_1="k_x1" variable_2="k_x1"/>
<map_variables variable_1="k_x2" variable_2="k_x2"/>
<map_variables variable_1="k_s" variable_2="k_s"/>
<map_variables variable_1="k_p" variable_2="k_p"/>
<map_variables variable_1="v_x" variable_2="v_x"/>
<map_variables variable_1="f_AMp" variable_2="f_AMp"/>
<map_variables variable_1="f_AM" variable_2="f_AM"/>
<map_variables variable_1="mu_s" variable_2="mu_s"/>
<map_variables variable_1="alpha_s" variable_2="alpha_s"/>
<map_variables variable_1="alpha_p" variable_2="alpha_p"/>
<map_variables variable_1="beta" variable_2="beta"/>
</connection>
<connection>
<map_components component_1="constants" component_2="wholeCell"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="F" variable_2="F"/>
<map_variables variable_1="z_Na" variable_2="z_Na"/>
<map_variables variable_1="z_Ca" variable_2="z_Ca"/>
<map_variables variable_1="z_K" variable_2="z_K"/>
<map_variables variable_1="z_Cl" variable_2="z_Cl"/>
</connection>
<!-- We connect the initial conditions through to the model-->
<connection>
<map_components component_1="initial_conditions" component_2="wholeCell"/>
<map_variables variable_1="Cai_init" variable_2="Cai_init"/>
<map_variables variable_1="Nai_init" variable_2="Nai_init"/>
<map_variables variable_1="Ki_init" variable_2="Ki_init"/>
<map_variables variable_1="Cli_init" variable_2="Cli_init"/>
<map_variables variable_1="Cau_init" variable_2="Cau_init"/>
<map_variables variable_1="Car_init" variable_2="Car_init"/>
<map_variables variable_1="d_init" variable_2="d_init"/>
<map_variables variable_1="f1_init" variable_2="f1_init"/>
<map_variables variable_1="f2_init" variable_2="f2_init"/>
<map_variables variable_1="b_init" variable_2="b_init"/>
<map_variables variable_1="g_init" variable_2="g_init"/>
<map_variables variable_1="m_init" variable_2="m_init"/>
<map_variables variable_1="h_init" variable_2="h_init"/>
<map_variables variable_1="q_init" variable_2="q_init"/>
<map_variables variable_1="r1_init" variable_2="r1_init"/>
<map_variables variable_1="r2_init" variable_2="r2_init"/>
<map_variables variable_1="p_init" variable_2="p_init"/>
<map_variables variable_1="ps_init" variable_2="ps_init"/>
<map_variables variable_1="pf_init" variable_2="pf_init"/>
<map_variables variable_1="k1_init" variable_2="k1_init"/>
<map_variables variable_1="k2_init" variable_2="k2_init"/>
<map_variables variable_1="s_init" variable_2="s_init"/>
<map_variables variable_1="x_init" variable_2="x_init"/>
<map_variables variable_1="y_init" variable_2="y_init"/>
<map_variables variable_1="c1_init" variable_2="c1_init"/>
<map_variables variable_1="c2_init" variable_2="c2_init"/>
<map_variables variable_1="n_init" variable_2="n_init"/>
<map_variables variable_1="ls_init" variable_2="ls_init"/>
<map_variables variable_1="la_init" variable_2="la_init"/>
<map_variables variable_1="lx_init" variable_2="lx_init"/>
<map_variables variable_1="M_init" variable_2="M_init"/>
<map_variables variable_1="Mp_init" variable_2="Mp_init"/>
<map_variables variable_1="AM_init" variable_2="AM_init"/>
<map_variables variable_1="AMp_init" variable_2="AMp_init"/>
<map_variables variable_1="R00_init" variable_2="R00_init"/>
<map_variables variable_1="R10_init" variable_2="R10_init"/>
<map_variables variable_1="R01_init" variable_2="R01_init"/>
<map_variables variable_1="R11_init" variable_2="R11_init"/>
</connection>
</model>
