//Created by libAntimony v2.4
model snyder_2000__environment(time_)

  // Variable initializations:
  time_ = ;
end

model snyder_2000__Ca_influx_across_the_SR(Rate_Ca_influx_across_the_SR, Ca_e, Ca_f)

  // Assignment Rules:
  Rate_Ca_influx_across_the_SR := k1 * (Ca_e - Ca_f);

  // Variable initializations:
  Ca_e = ;
  Ca_f = ;
  k1 = 0.2;
end

model snyder_2000__Ca_movement_through_the_SRRC(Ca_2_S1, Ca_S2, S1, S2, Ca_f, Ca_s, dCa2_S1_dt, dCa_S2_dt, dcas1_dt, dcas2_dt, Rate_Ca_movement_through_the_SRRC, time_)

  // Assignment Rules:
  dCa2_S1_dt := k_on1 * Ca_f * S1 - (power(k_off1, 2) / (k_on1 * Ca_f)) * Ca_2_S1;
  dCa_S2_dt := k_on2 * Ca_f * S2 - k_off2 * Ca_S2;
  dcas1_dt := k_on1 * Ca_f * (1 - cas1) - (power(k_off1, 2) / (k_on1 * Ca_f)) * cas1;
  dcas2_dt := k_on2 * Ca_f * (1 - cas2) - k_off2 * cas2;
  r_o := cas1 * (1 - cas2);
  Rate_Ca_movement_through_the_SRRC := k_s * r_o * (Ca_s - Ca_f);

  // Rate Rules:
  cas1' = dcas1_dt;
  cas2' = dcas2_dt;

  // Variable initializations:
  Ca_2_S1 = ;
  Ca_S2 = ;
  S1 = ;
  S2 = ;
  Ca_f = ;
  Ca_s = ;
  k_on1 = 2000000000;
  k_off1 = 1400;
  k_on2 = 13000000;
  k_off2 = 3.9;
  k_s = 9;
  cas1 = 0;
  cas2 = 0;
  time_ = ;
end

model snyder_2000__Ca_efflux_across_the_SR_by_NaCa_exchange(Ca_f, Rate_Ca_efflux_across_the_SR_by_NaCa_exchange)

  // Assignment Rules:
  Rate_Ca_efflux_across_the_SR_by_NaCa_exchange := (Vmax_NaCaX * Ca_f) / (Km_NaCaX + Ca_f);

  // Variable initializations:
  Ca_f = ;
  Km_NaCaX = 0.000036;
  Vmax_NaCaX = 0.0012;
end

model snyder_2000__Ca_movement_between_the_fuzzy_space_and_cytosol(Ca_c, Ca_f, Rate_Ca_movement_between_the_fuzzy_space_and_cytosol)

  // Assignment Rules:
  Rate_Ca_movement_between_the_fuzzy_space_and_cytosol := kf * (Ca_f - Ca_c);

  // Variable initializations:
  Ca_c = ;
  Ca_f = ;
  kf = 2500;
end

model snyder_2000__Ca_uptake_by_SR_Ca_ATPase(Ca_c, Ca_s, Rate_Ca_uptake_by_SR_Ca_ATPase)

  // Assignment Rules:
  Rate_Ca_uptake_by_SR_Ca_ATPase := (Vmax_s * (power(Ca_c, 2) - power(Ca_s, 2) / power(7000, 2))) / (power(Km_s, 2) + power(Ca_c, 2) + power(Ca_s, 2) / power(7000, 2));

  // Variable initializations:
  Ca_c = ;
  Ca_s = ;
  Km_s = 0.00000025;
  Vmax_s = 0.000525;
end

model snyder_2000__Ca_buffering_in_the_SR(Ca_CSQ, Ca_s, Rate_Ca_buffering_in_the_SR)

  // Assignment Rules:
  Rate_Ca_buffering_in_the_SR := K_ons * Ca_s * (Bmax_s - Ca_CSQ) - K_offs * Ca_CSQ;

  // Variable initializations:
  Ca_CSQ = ;
  Ca_s = ;
  K_ons = 8772;
  K_offs = 5.596536;
  Bmax_s = 0.008;
end

model snyder_2000__fuzzy_space_calcium(Ca_f, Rate_Ca_influx_across_the_SR, Rate_Ca_movement_through_the_SRRC, Rate_Ca_efflux_across_the_SR_by_NaCa_exchange, Rate_Ca_movement_between_the_fuzzy_space_and_cytosol, dcas1_dt, dcas2_dt, time_)

  // Rate Rules:
  Ca_f' = ((Rate_Ca_movement_through_the_SRRC - (Rt * (dcas1_dt + dcas2_dt) + Rate_Ca_movement_between_the_fuzzy_space_and_cytosol + Rate_Ca_efflux_across_the_SR_by_NaCa_exchange)) + Rate_Ca_influx_across_the_SR) / ((Bmax_f1 * Kb_f1) / power(Ca_f + Kb_f1, 2) + (Bmax_f2 * Kb_f2) / power(Ca_f + Kb_f2, 2) + V_f);

  // Variable initializations:
  Ca_f = 0.12e-6;
  Rt = 0.00000015;
  Bmax_f1 = 0.0002;
  Bmax_f2 = 0.0011;
  Kb_f1 = 0.000017;
  Kb_f2 = 0.000013;
  V_f = 0.0013;
  Rate_Ca_influx_across_the_SR = ;
  Rate_Ca_movement_through_the_SRRC = ;
  Rate_Ca_efflux_across_the_SR_by_NaCa_exchange = ;
  Rate_Ca_movement_between_the_fuzzy_space_and_cytosol = ;
  dcas1_dt = ;
  dcas2_dt = ;
  time_ = ;
end

model snyder_2000__cytosolic_calcium(Ca_c, Rate_Ca_movement_between_the_fuzzy_space_and_cytosol, Rate_Ca_uptake_by_SR_Ca_ATPase, time_)

  // Rate Rules:
  Ca_c' = (Rate_Ca_movement_between_the_fuzzy_space_and_cytosol - Rate_Ca_uptake_by_SR_Ca_ATPase) / ((Bmax_c * Kb_c) / power(Ca_c + Kb_c, 2) + (dye_c * Kb_dye) / power(Ca_c + Kb_dye, 2) + V_c);

  // Variable initializations:
  Ca_c = 1e-7;
  Bmax_c = 0.00012;
  dye_c = 0;
  Kb_c = 0.00000096;
  Kb_dye = 2e-7;
  V_c = 0.9287;
  Rate_Ca_movement_between_the_fuzzy_space_and_cytosol = ;
  Rate_Ca_uptake_by_SR_Ca_ATPase = ;
  time_ = ;
end

model snyder_2000__SR_calcium(Ca_s, Rate_Ca_movement_through_the_SRRC, Rate_Ca_uptake_by_SR_Ca_ATPase, Rate_Ca_buffering_in_the_SR, time_)

  // Rate Rules:
  Ca_s' = (Rate_Ca_uptake_by_SR_Ca_ATPase - Rate_Ca_movement_through_the_SRRC) / V_s - Rate_Ca_buffering_in_the_SR;

  // Variable initializations:
  Ca_s = 201e-6;
  V_s = 0.07;
  Rate_Ca_movement_through_the_SRRC = ;
  Rate_Ca_uptake_by_SR_Ca_ATPase = ;
  Rate_Ca_buffering_in_the_SR = ;
  time_ = ;
end

model snyder_2000__extracellular_calcium(Ca_e)

  // Variable initializations:
  Ca_e = 0.002;
end

model snyder_2000__calsequestrin_bound_calcium(Ca_CSQ, time_, Rate_Ca_buffering_in_the_SR)

  // Rate Rules:
  Ca_CSQ' = Rate_Ca_buffering_in_the_SR;

  // Variable initializations:
  Ca_CSQ = 0;
  time_ = ;
  Rate_Ca_buffering_in_the_SR = ;
end

model snyder_2000__SRRC_fast_activating_binding_site(S1, dCa2_S1_dt, time_)

  // Rate Rules:
  S1' = - dCa2_S1_dt;

  // Variable initializations:
  S1 = 0;
  dCa2_S1_dt = ;
  time_ = ;
end

model snyder_2000__SRRC_slow_inactivating_binding_site(S2, dCa_S2_dt, time_)

  // Rate Rules:
  S2' = - dCa_S2_dt;

  // Variable initializations:
  S2 = 0;
  dCa_S2_dt = ;
  time_ = ;
end

model snyder_2000__Ca_bound_to_the_SRRC_fast_activating_binding_site(Ca_2_S1, dCa2_S1_dt, time_)

  // Rate Rules:
  Ca_2_S1' = dCa2_S1_dt;

  // Variable initializations:
  Ca_2_S1 = 0;
  dCa2_S1_dt = ;
  time_ = ;
end

model snyder_2000__Ca_bound_to_the_SRRC_slow_inactivating_binding_site(Ca_S2, dCa_S2_dt, time_)

  // Rate Rules:
  Ca_S2' = dCa_S2_dt;

  // Variable initializations:
  Ca_S2 = 0;
  dCa_S2_dt = ;
  time_ = ;
end

model *snyder_2000____main()

  // Sub-modules, and any changes to those submodules:
  environment: snyder_2000__environment(time_);
  Ca_influx_across_the_SR: snyder_2000__Ca_influx_across_the_SR(Rate_Ca_influx_across_the_SR, Ca_e, Ca_f);
  Ca_movement_through_the_SRRC: snyder_2000__Ca_movement_through_the_SRRC(Ca_2_S1, Ca_S2, S1, S2, Ca_f, Ca_s, dCa2_S1_dt, dCa_S2_dt, dcas1_dt, dcas2_dt, Rate_Ca_movement_through_the_SRRC, time_);
  Ca_efflux_across_the_SR_by_NaCa_exchange: snyder_2000__Ca_efflux_across_the_SR_by_NaCa_exchange(Ca_f, Rate_Ca_efflux_across_the_SR_by_NaCa_exchange);
  Ca_movement_between_the_fuzzy_space_and_cytosol: snyder_2000__Ca_movement_between_the_fuzzy_space_and_cytosol(Ca_c, Ca_f, Rate_Ca_movement_between_the_fuzzy_space_and_cytosol);
  Ca_uptake_by_SR_Ca_ATPase: snyder_2000__Ca_uptake_by_SR_Ca_ATPase(Ca_c, Ca_s, Rate_Ca_uptake_by_SR_Ca_ATPase);
  Ca_buffering_in_the_SR: snyder_2000__Ca_buffering_in_the_SR(Ca_CSQ, Ca_s, Rate_Ca_buffering_in_the_SR);
  fuzzy_space_calcium: snyder_2000__fuzzy_space_calcium(Ca_f, Rate_Ca_influx_across_the_SR, Rate_Ca_movement_through_the_SRRC, Rate_Ca_efflux_across_the_SR_by_NaCa_exchange, Rate_Ca_movement_between_the_fuzzy_space_and_cytosol, dcas1_dt, dcas2_dt, time_);
  cytosolic_calcium: snyder_2000__cytosolic_calcium(Ca_c, Rate_Ca_movement_between_the_fuzzy_space_and_cytosol, Rate_Ca_uptake_by_SR_Ca_ATPase, time_);
  SR_calcium: snyder_2000__SR_calcium(Ca_s, Rate_Ca_movement_through_the_SRRC, Rate_Ca_uptake_by_SR_Ca_ATPase, Rate_Ca_buffering_in_the_SR, time_);
  extracellular_calcium: snyder_2000__extracellular_calcium(Ca_e);
  calsequestrin_bound_calcium: snyder_2000__calsequestrin_bound_calcium(Ca_CSQ, time_, Rate_Ca_buffering_in_the_SR);
  SRRC_fast_activating_binding_site: snyder_2000__SRRC_fast_activating_binding_site(S1, dCa2_S1_dt, time_);
  SRRC_slow_inactivating_binding_site: snyder_2000__SRRC_slow_inactivating_binding_site(S2, dCa_S2_dt, time_);
  Ca_bound_to_the_SRRC_fast_activating_binding_site: snyder_2000__Ca_bound_to_the_SRRC_fast_activating_binding_site(Ca_2_S1, dCa2_S1_dt, time_);
  Ca_bound_to_the_SRRC_slow_inactivating_binding_site: snyder_2000__Ca_bound_to_the_SRRC_slow_inactivating_binding_site(Ca_S2, dCa_S2_dt, time_);
end