diff --git a/tutorials/Rdesigneur/NN_mapk15.xml b/tutorials/Rdesigneur/NN_mapk15.xml new file mode 100644 index 00000000..013b7a50 --- /dev/null +++ b/tutorials/Rdesigneur/NN_mapk15.xml @@ -0,0 +1,2372 @@ + + + + + + Compartment + + + + + 50.0 + ee + 0.0005 + 0.2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CubeMesh + False + /kinetics + Compartment + + + + + + + CubeMesh + False + /kinetics + Compartment + + + + + + + CubeMesh + False + /kinetics + Compartment + + + + + + + + + 540.5405405405405 + 678.2608695652174 + 53 + 0 + 1e-10 + 0.0 + + + + + + + 702.7027027027027 + 608.6956521739131 + 55 + black + 0.0 + 0.0 + + + + + + + There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al) Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying it is comparable to CaMK levels. + + + + + 324.3243243243243 + 800.0 + pink + blue + 5e-13 + 0.0 + + + + + + + 648.6486486486486 + 800.0 + hotpink + blue + 1e-12 + 0.0 + + + + + + + This is the intermediate where the TR2 end (the high-affinity end) has bound the Ca but the TR1 end has not. + + + + + 540.5405405405405 + 800.0 + pink + blue + 1e-12 + 0.0 + + + + + + + This is the intermediate where the TR2 end (the high-affinity end) has bound the Ca but the TR1 end has not. + + + + + 432.43243243243245 + 800.0 + pink + blue + 1e-12 + 0.0 + + + + + + + 783.7837837837837 + 800.0 + blue + blue + 1e-12 + 0.0 + + + + + + + 891.8918918918919 + 52.17391304347826 + 25 + 40 + 1e-12 + 0.0 + + + + + + + 891.8918918918919 + 79.0 + white + black + 0.0 + 0.0 + + + + + + + 864.8648648648649 + 104.34782608695652 + red + 40 + 5e-12 + 0.0 + + + + + + + 837.8378378378378 + 131.0 + white + black + 0.0 + 0.0 + + + + + + + 891.8918918918919 + 27.0 + white + black + 0.0 + 0.0 + + + + + + + 783.7837837837837 + 79.0 + white + black + 0.0 + 0.0 + + + + + + + 972.972972972973 + 104.34782608695652 + red + 40 + 5e-12 + 0.0 + + + + + + + 756.7567567567568 + 104.34782608695652 + red + 40 + 1e-12 + 0.0 + + + + + + + 918.918918918919 + 173.91304347826087 + blue + 40 + 0.0 + 0.0 + + + + + + + 918.918918918919 + 166.0 + white + black + 0.0 + 0.0 + + + + + + + 756.7567567567568 + 173.91304347826087 + blue + 40 + 1e-12 + 0.0 + + + + + + + 810.8108108108108 + 104.34782608695652 + red + 40 + 1e-12 + 0.0 + + + + + + + 756.7567567567568 + 191.30434782608697 + blue + 40 + 0.0 + 0.0 + + + + + + + 972.972972972973 + 173.91304347826087 + blue + 40 + 0.0 + 0.0 + + + + + + + 972.972972972973 + 166.0 + white + black + 0.0 + 0.0 + + + + + + + 756.7567567567568 + 226.08695652173913 + 54 + 40 + 1e-10 + 0.0 + + + + + + + 918.918918918919 + 226.08695652173913 + 55 + 40 + 0.0 + 0.0 + + + + + + + 945.9459459459459 + 0.0 + blue + black + 2e-12 + 0.0 + + + + + + + 945.9459459459459 + 52.17391304347826 + blue + black + 2e-12 + 0.0 + + + + + + + 945.9459459459459 + 79.0 + white + black + 0.0 + 0.0 + + + + + + + There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al) Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying it is comparable to CaMK levels. + + + + + 513.5135135135134 + 347.82608695652175 + pink + blue + 5e-13 + 0.0 + + + + + + + 837.8378378378378 + 347.82608695652175 + hotpink + blue + 1e-12 + 0.0 + + + + + + + This is the intermediate where the TR2 end (the high-affinity end) has bound the Ca but the TR1 end has not. + + + + + 729.7297297297297 + 347.82608695652175 + pink + blue + 1e-12 + 0.0 + + + + + + + This is the intermediate where the TR2 end (the high-affinity end) has bound the Ca but the TR1 end has not. + + + + + 621.6216216216216 + 347.82608695652175 + pink + blue + 1e-12 + 0.0 + + + + + + + 972.972972972973 + 347.82608695652175 + blue + blue + 1e-12 + 0.0 + + + + + + + 0.0 + 313.04347826086956 + blue + blue + 2e-11 + 0.0 + + + + + + + This is the unphosphorylated K_A channel, which has the full channel conductance. + + + + + 729.7297297297297 + 34.78260869565217 + 25 + 40 + 0.0 + 0.0 + + + + + + + 837.8378378378378 + 34.78260869565217 + 52 + 40 + 0.0 + 0.0 + + + + + + + 648.6486486486486 + 382.60869565217394 + 50 + yellow + 1e-10 + 0.0 + + + + + + + There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al) Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying it is comparable to CaMK levels. + + + + + 432.43243243243245 + 486.9565217391305 + pink + blue + 5e-13 + 0.0 + + + + + + + 756.7567567567568 + 486.9565217391305 + hotpink + blue + 1e-12 + 0.0 + + + + + + + This is the intermediate where the TR2 end (the high-affinity end) has bound the Ca but the TR1 end has not. + + + + + 648.6486486486486 + 486.9565217391305 + pink + blue + 1e-12 + 0.0 + + + + + + + This is the intermediate where the TR2 end (the high-affinity end) has bound the Ca but the TR1 end has not. + + + + + 540.5405405405405 + 486.9565217391305 + pink + blue + 1e-12 + 0.0 + + + + + + + 891.8918918918919 + 486.9565217391305 + blue + blue + 1e-12 + 0.0 + + + + + + + 216.21621621621622 + 539.1304347826087 + blue + black + 2e-11 + 0.0 + + + + + + + + + 621.6216216216216 + 643.4782608695652 + white + black + + + + + + + + + + + + PSD_625_0_ * Ca_stim_477_0__Kf * Ca_input_475_0_-PSD_625_0_ * Ca_stim_477_0__Kb * Ca_473_0_ + + + + + + + + PSD_625_0_ + Ca_stim_477_0__Kf + Ca_input_475_0_ + + + + PSD_625_0_ + Ca_stim_477_0__Kb + Ca_473_0_ + + + + + + + + + + + + + Use K3 = 21.5 uM here from Stemmer and Klee table 3. kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10 24 Sep 2015 This is a bit too low affinity. Changing to match K2 at Kd = 2.8. + + + + + 702.7027027027027 + 747.8260869565217 + white + blue + + + + + + + + + + + + + PSD_625_0_ * CaM_Ca3_bind_Ca_483_0__Kf * Ca_473_0_*CaM_Ca3_485_0_-PSD_625_0_ * CaM_Ca3_bind_Ca_483_0__Kb * CaM_Ca4_497_0_ + + + + + + + + PSD_625_0_ + CaM_Ca3_bind_Ca_483_0__Kf + Ca_473_0_ + CaM_Ca3_485_0_ + + + + PSD_625_0_ + CaM_Ca3_bind_Ca_483_0__Kb + CaM_Ca4_497_0_ + + + + + + + + + + + + + Lets use the fast rate consts here. Since the rates are so different, I am not sure whether the order is relevant. These correspond to the TR2C fragment. We use the Martin et al rates here, plus the Drabicowski binding consts. All are scaled by 3X to cell temp. kf = 2e-10 kb = 72 Stemmer _and Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11. If kb=72, kf = 2e-10 (Exactly the same !) 19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into two steps, each binding 1 Ca. This improves numerical stability and is conceptually better too. Overall rates are the same, so each kf and kb is the square root of the earlier ones. So kf = 1.125e-4, kb = 8.4853 + + + + + 378.3783783783784 + 747.8260869565217 + white + blue + + + + + + + + + + + + + PSD_625_0_ * CaM_bind_Ca_487_0__Kf * Ca_473_0_*CaM_481_0_-PSD_625_0_ * CaM_bind_Ca_487_0__Kb * CaM_Ca_495_0_ + + + + + + + + PSD_625_0_ + CaM_bind_Ca_487_0__Kf + Ca_473_0_ + CaM_481_0_ + + + + PSD_625_0_ + CaM_bind_Ca_487_0__Kb + CaM_Ca_495_0_ + + + + + + + + + + + + + K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10 + + + + + 594.5945945945946 + 747.8260869565217 + white + blue + + + + + + + + + + + + + PSD_625_0_ * CaM_Ca2_bind_Ca_491_0__Kf * Ca_473_0_*CaM_Ca2_489_0_-PSD_625_0_ * CaM_Ca2_bind_Ca_491_0__Kb * CaM_Ca3_485_0_ + + + + + + + + PSD_625_0_ + CaM_Ca2_bind_Ca_491_0__Kf + Ca_473_0_ + CaM_Ca2_489_0_ + + + + PSD_625_0_ + CaM_Ca2_bind_Ca_491_0__Kb + CaM_Ca3_485_0_ + + + + + + + + + + + + + Lets use the fast rate consts here. Since the rates are so different, I am not sure whether the order is relevant. These correspond to the TR2C fragment. We use the Martin et al rates here, plus the Drabicowski binding consts. All are scaled by 3X to cell temp. kf = 2e-10 kb = 72 Stemmer _and Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11. If kb=72, kf = 2e-10 (Exactly the same !) 19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into two steps, each binding 1 Ca. This improves numerical stability and is conceptually better too. Overall rates are the same, so each kf and kb is the square root of the earlier ones. So kf = 1.125e-4, kb = 8.4853 + + + + + 486.4864864864865 + 747.8260869565217 + white + blue + + + + + + + + + + + + + PSD_625_0_ * CaM_Ca_bind_Ca_493_0__Kf * Ca_473_0_*CaM_Ca_495_0_-PSD_625_0_ * CaM_Ca_bind_Ca_493_0__Kb * CaM_Ca2_489_0_ + + + + + + + + PSD_625_0_ + CaM_Ca_bind_Ca_493_0__Kf + Ca_473_0_ + CaM_Ca_495_0_ + + + + PSD_625_0_ + CaM_Ca_bind_Ca_493_0__Kb + CaM_Ca2_489_0_ + + + + + + + + + + + + + 783.7837837837837 + 86.95652173913044 + white + 40 + + + + + + + + + + + + DEND_627_0_ * degrade_Y_501_0__Kf * AA_523_0_-DEND_627_0_ * degrade_Y_501_0__Kb * APC_532_0_ + + + + + + + + DEND_627_0_ + degrade_Y_501_0__Kf + AA_523_0_ + + + + DEND_627_0_ + degrade_Y_501_0__Kb + APC_532_0_ + + + + + + + + + + + + + 837.8378378378378 + 208.69565217391303 + white + 40 + + + + + + + + + + + + + DEND_627_0_ * Ca_activate_Raf_521_0__Kf * Raf_536_0_*Ca_545_0_^2-DEND_627_0_ * Ca_activate_Raf_521_0__Kb * act_Raf_538_0_ + + + + + + + + DEND_627_0_ + Ca_activate_Raf_521_0__Kf + Raf_536_0_ + + + Ca_545_0_ + 2 + + + + + DEND_627_0_ + Ca_activate_Raf_521_0__Kb + act_Raf_538_0_ + + + + + + + + + + + + + 783.7837837837837 + 0.0 + white + 40 + + + + + + + + + + + + DEND_627_0_ * dephosph_534_0__Kf * channel_p_586_0_ + + + + + + DEND_627_0_ + dephosph_534_0__Kf + channel_p_586_0_ + + + + + + + + + + + 837.8378378378378 + 156.52173913043478 + white + 40 + + + + + + + + + + + + + DEND_627_0_ * activate_PKC_543_0__Kf * AA_523_0_^2*PKC_530_0_-DEND_627_0_ * activate_PKC_543_0__Kb * act_PKC_525_0_ + + + + + + + + DEND_627_0_ + activate_PKC_543_0__Kf + + + AA_523_0_ + 2 + + PKC_530_0_ + + + + DEND_627_0_ + activate_PKC_543_0__Kb + act_PKC_525_0_ + + + + + + + + + + + + + 837.8378378378378 + 243.47826086956525 + white + 40 + + + + + + + + + + + + DEND_627_0_ * Ca_stim_549_0__Kf * Ca_input_547_0_-DEND_627_0_ * Ca_stim_549_0__Kb * Ca_545_0_ + + + + + + + + DEND_627_0_ + Ca_stim_549_0__Kf + Ca_input_547_0_ + + + + DEND_627_0_ + Ca_stim_549_0__Kb + Ca_545_0_ + + + + + + + + + + + + + 1000.0 + 17.391304347826086 + white + black + + + + + + + + + + + + DEND_627_0_ * basal_phosphatase_551_0__Kf * reg_phosphatase_555_0_ + + + + + + DEND_627_0_ + basal_phosphatase_551_0__Kf + reg_phosphatase_555_0_ + + + + + + + + + + + Use K3 = 21.5 uM here from Stemmer and Klee table 3. kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10 + + + + + 891.8918918918919 + 295.65217391304344 + white + blue + + + + + + + + + + + + + DEND_627_0_ * CaM_Ca3_bind_Ca_564_0__Kf * Ca_545_0_*CaM_Ca3_566_0_-DEND_627_0_ * CaM_Ca3_bind_Ca_564_0__Kb * CaM_Ca4_578_0_ + + + + + + + + DEND_627_0_ + CaM_Ca3_bind_Ca_564_0__Kf + Ca_545_0_ + CaM_Ca3_566_0_ + + + + DEND_627_0_ + CaM_Ca3_bind_Ca_564_0__Kb + CaM_Ca4_578_0_ + + + + + + + + + + + + + Lets use the fast rate consts here. Since the rates are so different, I am not sure whether the order is relevant. These correspond to the TR2C fragment. We use the Martin et al rates here, plus the Drabicowski binding consts. All are scaled by 3X to cell temp. kf = 2e-10 kb = 72 Stemmer _and Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11. If kb=72, kf = 2e-10 (Exactly the same !) 19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into two steps, each binding 1 Ca. This improves numerical stability and is conceptually better too. Overall rates are the same, so each kf and kb is the square root of the earlier ones. So kf = 1.125e-4, kb = 8.4853 + + + + + 567.5675675675675 + 295.65217391304344 + white + blue + + + + + + + + + + + + + DEND_627_0_ * CaM_bind_Ca_568_0__Kf * Ca_545_0_*CaM_562_0_-DEND_627_0_ * CaM_bind_Ca_568_0__Kb * CaM_Ca_576_0_ + + + + + + + + DEND_627_0_ + CaM_bind_Ca_568_0__Kf + Ca_545_0_ + CaM_562_0_ + + + + DEND_627_0_ + CaM_bind_Ca_568_0__Kb + CaM_Ca_576_0_ + + + + + + + + + + + + + K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10 + + + + + 783.7837837837837 + 295.65217391304344 + white + blue + + + + + + + + + + + + + DEND_627_0_ * CaM_Ca2_bind_Ca_572_0__Kf * Ca_545_0_*CaM_Ca2_570_0_-DEND_627_0_ * CaM_Ca2_bind_Ca_572_0__Kb * CaM_Ca3_566_0_ + + + + + + + + DEND_627_0_ + CaM_Ca2_bind_Ca_572_0__Kf + Ca_545_0_ + CaM_Ca2_570_0_ + + + + DEND_627_0_ + CaM_Ca2_bind_Ca_572_0__Kb + CaM_Ca3_566_0_ + + + + + + + + + + + + + Lets use the fast rate consts here. Since the rates are so different, I am not sure whether the order is relevant. These correspond to the TR2C fragment. We use the Martin et al rates here, plus the Drabicowski binding consts. All are scaled by 3X to cell temp. kf = 2e-10 kb = 72 Stemmer _and Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11. If kb=72, kf = 2e-10 (Exactly the same !) 19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into two steps, each binding 1 Ca. This improves numerical stability and is conceptually better too. Overall rates are the same, so each kf and kb is the square root of the earlier ones. So kf = 1.125e-4, kb = 8.4853 + + + + + 675.6756756756756 + 295.65217391304344 + white + blue + + + + + + + + + + + + + DEND_627_0_ * CaM_Ca_bind_Ca_574_0__Kf * Ca_545_0_*CaM_Ca_576_0_-DEND_627_0_ * CaM_Ca_bind_Ca_574_0__Kb * CaM_Ca2_570_0_ + + + + + + + + DEND_627_0_ + CaM_Ca_bind_Ca_574_0__Kf + Ca_545_0_ + CaM_Ca_576_0_ + + + + DEND_627_0_ + CaM_Ca_bind_Ca_574_0__Kb + CaM_Ca2_570_0_ + + + + + + + + + + + + + 243.24324324324326 + 347.82608695652175 + white + black + + + + + + + + + + + + DEND_627_0_ * CaM_x2_580_0__Kf * CaM_562_0_-DEND_627_0_ * CaM_x2_580_0__Kb * CaM_xchange_582_0_ + + + + + + + + DEND_627_0_ + CaM_x2_580_0__Kf + CaM_562_0_ + + + + DEND_627_0_ + CaM_x2_580_0__Kb + CaM_xchange_582_0_ + + + + + + + + + + + + + Use K3 = 21.5 uM here from Stemmer and Klee table 3. kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10 + + + + + 810.8108108108108 + 434.78260869565213 + white + blue + + + + + + + + + + + + + SPINE_629_0_ * CaM_Ca3_bind_Ca_596_0__Kf * Ca_590_0_*CaM_Ca3_598_0_-SPINE_629_0_ * CaM_Ca3_bind_Ca_596_0__Kb * CaM_Ca4_610_0_ + + + + + + + + SPINE_629_0_ + CaM_Ca3_bind_Ca_596_0__Kf + Ca_590_0_ + CaM_Ca3_598_0_ + + + + SPINE_629_0_ + CaM_Ca3_bind_Ca_596_0__Kb + CaM_Ca4_610_0_ + + + + + + + + + + + + + Lets use the fast rate consts here. Since the rates are so different, I am not sure whether the order is relevant. These correspond to the TR2C fragment. We use the Martin et al rates here, plus the Drabicowski binding consts. All are scaled by 3X to cell temp. kf = 2e-10 kb = 72 Stemmer _and Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11. If kb=72, kf = 2e-10 (Exactly the same !) 19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into two steps, each binding 1 Ca. This improves numerical stability and is conceptually better too. Overall rates are the same, so each kf and kb is the square root of the earlier ones. So kf = 1.125e-4, kb = 8.4853 + + + + + 486.4864864864865 + 434.78260869565213 + white + blue + + + + + + + + + + + + + SPINE_629_0_ * CaM_bind_Ca_600_0__Kf * Ca_590_0_*CaM_594_0_-SPINE_629_0_ * CaM_bind_Ca_600_0__Kb * CaM_Ca_608_0_ + + + + + + + + SPINE_629_0_ + CaM_bind_Ca_600_0__Kf + Ca_590_0_ + CaM_594_0_ + + + + SPINE_629_0_ + CaM_bind_Ca_600_0__Kb + CaM_Ca_608_0_ + + + + + + + + + + + + + K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10 + + + + + 702.7027027027027 + 434.78260869565213 + white + blue + + + + + + + + + + + + + SPINE_629_0_ * CaM_Ca2_bind_Ca_604_0__Kf * Ca_590_0_*CaM_Ca2_602_0_-SPINE_629_0_ * CaM_Ca2_bind_Ca_604_0__Kb * CaM_Ca3_598_0_ + + + + + + + + SPINE_629_0_ + CaM_Ca2_bind_Ca_604_0__Kf + Ca_590_0_ + CaM_Ca2_602_0_ + + + + SPINE_629_0_ + CaM_Ca2_bind_Ca_604_0__Kb + CaM_Ca3_598_0_ + + + + + + + + + + + + + Lets use the fast rate consts here. Since the rates are so different, I am not sure whether the order is relevant. These correspond to the TR2C fragment. We use the Martin et al rates here, plus the Drabicowski binding consts. All are scaled by 3X to cell temp. kf = 2e-10 kb = 72 Stemmer _and Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11. If kb=72, kf = 2e-10 (Exactly the same !) 19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into two steps, each binding 1 Ca. This improves numerical stability and is conceptually better too. Overall rates are the same, so each kf and kb is the square root of the earlier ones. So kf = 1.125e-4, kb = 8.4853 + + + + + 594.5945945945946 + 434.78260869565213 + white + blue + + + + + + + + + + + + + SPINE_629_0_ * CaM_Ca_bind_Ca_606_0__Kf * Ca_590_0_*CaM_Ca_608_0_-SPINE_629_0_ * CaM_Ca_bind_Ca_606_0__Kb * CaM_Ca2_602_0_ + + + + + + + + SPINE_629_0_ + CaM_Ca_bind_Ca_606_0__Kf + Ca_590_0_ + CaM_Ca_608_0_ + + + + SPINE_629_0_ + CaM_Ca_bind_Ca_606_0__Kb + CaM_Ca2_602_0_ + + + + + + + + + + + + + 351.35135135135135 + 591.3043478260869 + white + black + + + + + + + + + + + + SPINE_629_0_ * CaM_x2_612_0__Kf * CaM_594_0_-SPINE_629_0_ * CaM_x2_612_0__Kb * CaM_xchange_614_0_ + + + + + + + + SPINE_629_0_ + CaM_x2_612_0__Kf + CaM_594_0_ + + + + SPINE_629_0_ + CaM_x2_612_0__Kb + CaM_xchange_614_0_ + + + + + + + + + + + + + phosphatase_503_0_ + P_MAPK_508_0_ + P_cplx_506_0_ + P_505_0_ + 1 + 891.8918918918919 + 69.56521739130434 + red + 25 + + + + + + + + + + + + + DEND_627_0_ * ( k1 * phosphatase_503_0_*P_MAPK_508_0_ - k2 * P_cplx_506_0_ ) + + + + + + DEND_627_0_ + + + + + k1 + phosphatase_503_0_ + P_MAPK_508_0_ + + + + k2 + P_cplx_506_0_ + + + + + + + + + + + + + + P_cplx_506_0_ + phosphatase_503_0_ + MAPK_519_0_ + P_505_0_ + 2 + 891.8918918918919 + 69.56521739130434 + red + 25 + + + + + + + + + + + + + DEND_627_0_ * k3*P_cplx_506_0_ + + + + + + DEND_627_0_ + k3 + P_cplx_506_0_ + + + + + + + + + + + P_MAPK_508_0_ + APC_532_0_ + PLA2_cplx_511_0_ + PLA2_510_0_ + 1 + 837.8378378378378 + 121.73913043478262 + red + red + + + + + + + + + + + + + DEND_627_0_ * ( k1 * P_MAPK_508_0_*APC_532_0_ - k2 * PLA2_cplx_511_0_ ) + + + + + + DEND_627_0_ + + + + + k1 + P_MAPK_508_0_ + APC_532_0_ + + + + k2 + PLA2_cplx_511_0_ + + + + + + + + + + + + + + PLA2_cplx_511_0_ + P_MAPK_508_0_ + AA_523_0_ + PLA2_510_0_ + 2 + 837.8378378378378 + 121.73913043478262 + red + red + + + + + + + + + + + + + DEND_627_0_ * k3*PLA2_cplx_511_0_ + + + + + + DEND_627_0_ + k3 + PLA2_cplx_511_0_ + + + + + + + + + + + P_MAPK_508_0_ + inact_phosphatase_553_0_ + activate_phosphatase_cplx_514_0_ + activate_phosphatase_513_0_ + 1 + 891.8918918918919 + 17.391304347826086 + red + red + + + + + + + + + + + + + DEND_627_0_ * ( k1 * P_MAPK_508_0_*inact_phosphatase_553_0_ - k2 * activate_phosphatase_cplx_514_0_ ) + + + + + + DEND_627_0_ + + + + + k1 + P_MAPK_508_0_ + inact_phosphatase_553_0_ + + + + k2 + activate_phosphatase_cplx_514_0_ + + + + + + + + + + + + + + activate_phosphatase_cplx_514_0_ + P_MAPK_508_0_ + reg_phosphatase_555_0_ + activate_phosphatase_513_0_ + 2 + 891.8918918918919 + 17.391304347826086 + red + red + + + + + + + + + + + + + DEND_627_0_ * k3*activate_phosphatase_cplx_514_0_ + + + + + + DEND_627_0_ + k3 + activate_phosphatase_cplx_514_0_ + + + + + + + + + + + P_MAPK_508_0_ + channel_584_0_ + phosph_chan_cplx_517_0_ + phosph_chan_516_0_ + 1 + 783.7837837837837 + 69.56521739130434 + red + red + + + + + + + + + + + + + DEND_627_0_ * ( k1 * P_MAPK_508_0_*channel_584_0_ - k2 * phosph_chan_cplx_517_0_ ) + + + + + + DEND_627_0_ + + + + + k1 + P_MAPK_508_0_ + channel_584_0_ + + + + k2 + phosph_chan_cplx_517_0_ + + + + + + + + + + + + + + phosph_chan_cplx_517_0_ + P_MAPK_508_0_ + channel_p_586_0_ + phosph_chan_516_0_ + 2 + 783.7837837837837 + 69.56521739130434 + red + red + + + + + + + + + + + + + DEND_627_0_ * k3*phosph_chan_cplx_517_0_ + + + + + + DEND_627_0_ + k3 + phosph_chan_cplx_517_0_ + + + + + + + + + + + act_PKC_525_0_ + MAPK_519_0_ + MAPKK_cplx_528_0_ + MAPKK_527_0_ + 1 + 918.918918918919 + 156.52173913043478 + red + blue + + + + + + + + + + + + + DEND_627_0_ * ( k1 * act_PKC_525_0_*MAPK_519_0_ - k2 * MAPKK_cplx_528_0_ ) + + + + + + DEND_627_0_ + + + + + k1 + act_PKC_525_0_ + MAPK_519_0_ + + + + k2 + MAPKK_cplx_528_0_ + + + + + + + + + + + + + + MAPKK_cplx_528_0_ + act_PKC_525_0_ + P_MAPK_508_0_ + MAPKK_527_0_ + 2 + 918.918918918919 + 156.52173913043478 + red + blue + + + + + + + + + + + + + DEND_627_0_ * k3*MAPKK_cplx_528_0_ + + + + + + DEND_627_0_ + k3 + MAPKK_cplx_528_0_ + + + + + + + + + + + act_Raf_538_0_ + MAPK_519_0_ + MAPKKK_cplx_541_0_ + MAPKKK_540_0_ + 1 + 972.972972972973 + 156.52173913043478 + red + blue + + + + + + + + + + + + + DEND_627_0_ * ( k1 * act_Raf_538_0_*MAPK_519_0_ - k2 * MAPKKK_cplx_541_0_ ) + + + + + + DEND_627_0_ + + + + + k1 + act_Raf_538_0_ + MAPK_519_0_ + + + + k2 + MAPKKK_cplx_541_0_ + + + + + + + + + + + + + + MAPKKK_cplx_541_0_ + act_Raf_538_0_ + P_MAPK_508_0_ + MAPKKK_540_0_ + 2 + 972.972972972973 + 156.52173913043478 + red + blue + + + + + + + + + + + + + DEND_627_0_ * k3*MAPKKK_cplx_541_0_ + + + + + + DEND_627_0_ + k3 + MAPKKK_cplx_541_0_ + + + + + + + + + + + reg_phosphatase_555_0_ + P_MAPK_508_0_ + P_cplx_558_0_ + P_557_0_ + 1 + 945.9459459459459 + 69.56521739130434 + red + blue + + + + + + + + + + + + + DEND_627_0_ * ( k1 * reg_phosphatase_555_0_*P_MAPK_508_0_ - k2 * P_cplx_558_0_ ) + + + + + + DEND_627_0_ + + + + + k1 + reg_phosphatase_555_0_ + P_MAPK_508_0_ + + + + k2 + P_cplx_558_0_ + + + + + + + + + + + + + + P_cplx_558_0_ + reg_phosphatase_555_0_ + MAPK_519_0_ + P_557_0_ + 2 + 945.9459459459459 + 69.56521739130434 + red + blue + + + + + + + + + + + + + DEND_627_0_ * k3*P_cplx_558_0_ + + + + + + DEND_627_0_ + k3 + P_cplx_558_0_ + + + + + + + + + + + + + PSD_625_0_ + PSD_625_0_ + #FFA500 + + + + + + + + + + + + + + + + + + DEND_627_0_ + DEND_627_0_ + #FFA500 + + + + + + + + + + + + + + + + + + + + SPINE_629_0_ + SPINE_629_0_ + #FFA500 + + + + + + + + + + + + + + + + + + + diff --git a/tutorials/Rdesigneur/chem/CICRspineDend.xml b/tutorials/Rdesigneur/chem/CICRspineDend.xml new file mode 100644 index 00000000..de0281e7 --- /dev/null +++ b/tutorials/Rdesigneur/chem/CICRspineDend.xml @@ -0,0 +1,932 @@ + + + + + + 100.0 + ee + 0.001 + 0.1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CubeMesh + False + + + + + + + CubeMesh + False + + + + + + + CubeMesh + False + + + + + + + + + 1000.0 + 666.6666666666667 + 49 + black + 0.0 + 0.0 + + + + + + + 500.0 + 533.3333333333333 + 20 + black + 0.0 + 0.0 + + + + + + + 500.0 + 133.33333333333331 + 31 + black + 0.0 + 0.0 + + + + + + + 1000.0 + 0.0 + 23 + black + 0.0 + 0.0 + + + + + + + 1000.0 + 66.66666666666666 + 23 + black + 0.0 + 0.0 + + + + + + + 1000.0 + 133.33333333333331 + 55 + black + 0.0 + 0.0 + + + + + + + 1000.0 + 200.0 + 27 + black + 0.0 + 0.0 + + + + + + + 1000.0 + 266.66666666666663 + 55 + black + 0.0 + 0.0 + + + + + + + 400.0 + 666.6666666666667 + 22 + black + 0.0 + 0.0 + + + + + + + 500.0 + 533.3333333333333 + 1 + black + 0.0 + 0.0 + + + + + + + 600.0 + 666.6666666666667 + 53 + black + 0.0 + 0.0 + + + + + + + 800.0 + 666.6666666666667 + 25 + black + 0.0 + 0.0 + + + + + + + 0.0 + 333.33333333333337 + 4 + black + 0.0 + 0.0 + + + + + + + 300.0 + 133.33333333333331 + 8 + black + 0.0 + 0.0 + + + + + + + 300.0 + 0.0 + 8 + black + 0.0 + 0.0 + + + + + + + 200.0 + 666.6666666666667 + 26 + black + 0.0 + 0.0 + + + + + + + 300.0 + 400.0 + 0 + 26 + 0.0 + 0.0 + + + + + + + 500.0 + 333.33333333333337 + 45 + 26 + 0.0 + 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kinetics_1022_0_ + CaMreac1_1065_0__Kf + CaM_1037_0_ + Ca_1091_0_ + + + + kinetics_1022_0_ + CaMreac1_1065_0__Kb + CaMCa_1039_0_ + + + + + + + + + + + + + 700.0 + 133.33333333333331 + white + black + + + + + + + + + + + + + kinetics_1022_0_ * CaMreac2_1067_0__Kf * CaMCa_1039_0_*Ca_1091_0_-kinetics_1022_0_ * CaMreac2_1067_0__Kb * CaMCa2_1041_0_ + + + + + + + + kinetics_1022_0_ + CaMreac2_1067_0__Kf + CaMCa_1039_0_ + Ca_1091_0_ + + + + kinetics_1022_0_ + CaMreac2_1067_0__Kb + CaMCa2_1041_0_ + + + + + + + + + + + + + 800.0 + 200.0 + white + black + + + + + + + + + + + + + kinetics_1022_0_ * CaMreac3_1069_0__Kf * CaMCa2_1041_0_*Ca_1091_0_-kinetics_1022_0_ * CaMreac3_1069_0__Kb * CaMCa3_1043_0_ + + + + + + + + kinetics_1022_0_ + CaMreac3_1069_0__Kf + CaMCa2_1041_0_ + Ca_1091_0_ + + + + kinetics_1022_0_ + CaMreac3_1069_0__Kb + CaMCa3_1043_0_ + + + + + + + + + + + + + 900.0 + 266.66666666666663 + white + black + + + + + + + + + + + + + kinetics_1022_0_ * CaMreac4_1071_0__Kf * CaMCa3_1043_0_*Ca_1091_0_-kinetics_1022_0_ * CaMreac4_1071_0__Kb * CaMCa4_1045_0_ + + + + + + + + kinetics_1022_0_ + CaMreac4_1071_0__Kf + CaMCa3_1043_0_ + Ca_1091_0_ + + + + kinetics_1022_0_ + CaMreac4_1071_0__Kb + CaMCa4_1045_0_ + + + + + + + + + + + + + 500.0 + 600.0 + white + black + + + + + + + + + + + + + kinetics_1022_0_ * Reac_1073_0__Kf * IP3_R_1047_0_*IP3_1051_0_-kinetics_1022_0_ * Reac_1073_0__Kb * IP3_3_R_1049_0_ + + + + + + + + kinetics_1022_0_ + Reac_1073_0__Kf + IP3_R_1047_0_ + IP3_1051_0_ + + + + kinetics_1022_0_ + Reac_1073_0__Kb + IP3_3_R_1049_0_ + + + + + + + + + + + + + 700.0 + 466.6666666666667 + white + black + + + + + + + + + + + + + kinetics_1022_0_ * Reac2_1075_0__Kf * IP3_3_R_1049_0_*Ca_1091_0_-kinetics_1022_0_ * Reac2_1075_0__Kb * CaIP3_3_R_1031_0_ + + + + + + + + kinetics_1022_0_ + Reac2_1075_0__Kf + IP3_3_R_1049_0_ + Ca_1091_0_ + + + + kinetics_1022_0_ + Reac2_1075_0__Kb + CaIP3_3_R_1031_0_ + + + + + + + + + + + + + 800.0 + 533.3333333333333 + white + black 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+ + + + + + + + 500.0 + 200.0 + black + 42 + + + + + + + + + + + + + + + kinetics_1022_0_ * ( kcat * Ca_1091_0_ * Serca_1033_0_/(Km + Ca_1091_0_)) + + + + + + kinetics_1022_0_ + + + + + kcat + Ca_1091_0_ + Serca_1033_0_ + + + + Km + Ca_1091_0_ + + + + + + + + + + + + + + + + kinetics_1022_0_ + kinetics_1022_0_ + #FFA500 + + + + + + + kinetics_1022_0_ + kinetics_1022_0_ + #00a858 + + + + + + + kinetics_1022_0_ + kinetics_1022_0_ + #FFFF00 + + + + + + diff --git a/tutorials/Rdesigneur/chem/CICRwithConcChan.xml b/tutorials/Rdesigneur/chem/CICRwithConcChan.xml new file mode 100644 index 00000000..21493094 --- /dev/null +++ b/tutorials/Rdesigneur/chem/CICRwithConcChan.xml @@ -0,0 +1,802 @@ + + + + + + 100.0 + ee + 0.001 + 0.1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CubeMesh + False + + + + + + + CubeMesh + False + + + + + + + + + 800.0 + 400.0 + 23 + black + 1e-13 + 0.0 + + + + + + + 500.0 + 640.0 + 20 + black + 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ActIP3R_1167_0_ + + + CaER_1141_0_ + CaCyt_1137_0_ + + + + + + + + + + + + ConcChannel + 4.0 + 5.0 + 40.0 + + + + + + + + + + + + + + + compartment_1_1201_0_ * ( Permeability) * leakPool_1187_0_ * (CaER_1141_0_ - CaCyt_1137_0_) + + + + + + compartment_1_1201_0_ + Permeability + leakPool_1187_0_ + + + CaER_1141_0_ + CaCyt_1137_0_ + + + + + + + + + + + + 600.0 + 80.0 + white + black + + + + + + + + + + + + + kinetics_1128_0_ * CaMreac1_1171_0__Kf * CaCyt_1137_0_*CaM_1147_0_-kinetics_1128_0_ * CaMreac1_1171_0__Kb * CaMCa_1149_0_ + + + + + + + + kinetics_1128_0_ + CaMreac1_1171_0__Kf + CaCyt_1137_0_ + CaM_1147_0_ + + + + kinetics_1128_0_ + CaMreac1_1171_0__Kb + CaMCa_1149_0_ + + + + + + + + + + + + + 700.0 + 160.0 + white + black + + + + + + + + + + + + + kinetics_1128_0_ * CaMreac2_1173_0__Kf * CaCyt_1137_0_*CaMCa_1149_0_-kinetics_1128_0_ * CaMreac2_1173_0__Kb * CaMCa2_1151_0_ + + + + + + + + kinetics_1128_0_ + CaMreac2_1173_0__Kf + CaCyt_1137_0_ + CaMCa_1149_0_ + + + + kinetics_1128_0_ + CaMreac2_1173_0__Kb + CaMCa2_1151_0_ + + + + + + + + + + + + + 800.0 + 240.0 + white + black + + + + + + + + + + + + + kinetics_1128_0_ * CaMreac3_1175_0__Kf * CaCyt_1137_0_*CaMCa2_1151_0_-kinetics_1128_0_ * CaMreac3_1175_0__Kb * CaMCa3_1153_0_ + + + + + + + + kinetics_1128_0_ + CaMreac3_1175_0__Kf + CaCyt_1137_0_ + CaMCa2_1151_0_ + + + + kinetics_1128_0_ + CaMreac3_1175_0__Kb + CaMCa3_1153_0_ + + + + + + + + + + + + + 900.0 + 320.0 + white + black + + + + + + + + + + + + + kinetics_1128_0_ * CaMreac4_1177_0__Kf * CaCyt_1137_0_*CaMCa3_1153_0_-kinetics_1128_0_ * CaMreac4_1177_0__Kb * CaMCa4_1155_0_ + + + + + + + + kinetics_1128_0_ + CaMreac4_1177_0__Kf + CaCyt_1137_0_ + CaMCa3_1153_0_ + + + + kinetics_1128_0_ + CaMreac4_1177_0__Kb + CaMCa4_1155_0_ + + + + + + + + + + + + + 500.0 + 720.0 + white + black + + + + + + + + + + + + + kinetics_1128_0_ * Reac_1179_0__Kf * IP3_R_1157_0_*IP3_1161_0_-kinetics_1128_0_ * Reac_1179_0__Kb * IP3_3_R_1159_0_ + + + + + + + + kinetics_1128_0_ + Reac_1179_0__Kf + IP3_R_1157_0_ + IP3_1161_0_ + + + + kinetics_1128_0_ + Reac_1179_0__Kb + IP3_3_R_1159_0_ + + + + + + + + + + + + + 700.0 + 560.0 + white + black + + + + + + + + + + + + + kinetics_1128_0_ * Reac2_1181_0__Kf * CaCyt_1137_0_*IP3_3_R_1159_0_-kinetics_1128_0_ * Reac2_1181_0__Kb * CaIP3_3_R_1139_0_ + + + + + + + + kinetics_1128_0_ + Reac2_1181_0__Kf + CaCyt_1137_0_ + IP3_3_R_1159_0_ + + + + kinetics_1128_0_ + Reac2_1181_0__Kb + CaIP3_3_R_1139_0_ + + + + + + + + + + + + + 800.0 + 640.0 + white + black + + + + + + + + + + + + + kinetics_1128_0_ * Reac4_1183_0__Kf * CaCyt_1137_0_*CaIP3_3_R_1139_0_-kinetics_1128_0_ * Reac4_1183_0__Kb * Ca2_IP3_3_R_1163_0_ + + + + + + + + kinetics_1128_0_ + Reac4_1183_0__Kf + CaCyt_1137_0_ + CaIP3_3_R_1139_0_ + + + + kinetics_1128_0_ + Reac4_1183_0__Kb + Ca2_IP3_3_R_1163_0_ + + + + + + + + + + + + + 100.0 + 80.0 + white + black + + + + + + + + + + + + kinetics_1128_0_ * Reac1_1185_0__Kf * Mirror_CaIP3_3_R_1165_0_^3-kinetics_1128_0_ * Reac1_1185_0__Kb * ActIP3R_1167_0_ + + + + + + + + kinetics_1128_0_ + Reac1_1185_0__Kf + + + Mirror_CaIP3_3_R_1165_0_ + 3 + + + + + kinetics_1128_0_ + Reac1_1185_0__Kb + ActIP3R_1167_0_ + + + + + + + + + + + + + 500.0 + 240.0 + black + 42 + + + + + + + + + + + + + + + kinetics_1128_0_ * ( kcat * CaCyt_1137_0_ * Serca_1143_0_/(Km + CaCyt_1137_0_)) + + + + + + kinetics_1128_0_ + + + + + kcat + CaCyt_1137_0_ + Serca_1143_0_ + + + + Km + CaCyt_1137_0_ + + + + + + + + + + + + + + + + kinetics_1128_0_ + kinetics_1128_0_ + #FFA500 + + + + + + diff --git a/tutorials/Rdesigneur/chem/CaOnly.xml b/tutorials/Rdesigneur/chem/CaOnly.xml new file mode 100644 index 00000000..0bf73efc --- /dev/null +++ b/tutorials/Rdesigneur/chem/CaOnly.xml @@ -0,0 +1,105 @@ + + + + + + 100.0 + ee + 0.001 + 0.1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CubeMesh + False + + + + + + + CubeMesh + False + + + + + + + + + 1000.0 + 0.0 + 23 + black + 2e-11 + 0.0 + + + + + + + 0.0 + 800.0 + 25 + yellow + 2e-11 + 0.0 + + + + + + + + + kinetics_1248_0_ + kinetics_1248_0_ + #FFA500 + + + + + + + kinetics_1248_0_ + kinetics_1248_0_ + #FFFF00 + + + + + + diff --git a/tutorials/Rdesigneur/chem/OSC_different_vols.xml b/tutorials/Rdesigneur/chem/OSC_different_vols.xml new file mode 100644 index 00000000..7a370afa --- /dev/null +++ b/tutorials/Rdesigneur/chem/OSC_different_vols.xml @@ -0,0 +1,736 @@ + + + + + + Compartment + + + + + 2500.0 + ee + 0.005 + 10.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CubeMesh + False + /kinetics + Compartment + + + + + + + CubeMesh + False + /kinetics + Compartment + + + + + + + + + 400.0 + 171.42857142857142 + 4 + yellow + 0.0 + 0.0 + + + + + + + 400.0 + 124.0 + white + black + 0.0 + 0.0 + + + + + + + 100.0 + 314.2857142857143 + 62 + yellow + 0.0 + 0.0 + + + + + + + 800.0 + 171.42857142857142 + 28 + yellow + 0.0 + 0.0 + + + + + + + 700.0 + 295.0 + white + black + 0.0 + 0.0 + + + + + + + 600.0 + 800.0 + 41 + 16 + 0.0 + 0.0 + + + + + + + 500.0 + 428.57142857142856 + 3 + 16 + 0.0 + 0.0 + + + + + + + 500.0 + 495.0 + white + black + 0.0 + 0.0 + + + + + + + 200.0 + 600.0 + 53 + 16 + 0.0 + 0.0 + + + + + + + 1000.0 + 657.1428571428571 + 47 + 16 + 0.0 + 0.0 + + + + + + + 500.0 + 638.0 + white + black + 0.0 + 0.0 + + + + + + + + + + M_686_0_ + M_p_688_0_ + kenz_cplx_691_0_ + kenz_cplx_684_0_ + kenz_cplx_691_0_ + + + + + + + + + 200.0 + 0.0 + white + yellow + + + + + + + + + + + + B_705_0_ * basal_664_0__Kf * M_666_0_ + + + + + + B_705_0_ + basal_664_0__Kf + M_666_0_ + + + + + + + + + + + 900.0 + 371.42857142857144 + white + yellow + + + + + + + + + + + + B_705_0_ * exo_673_0__Kf * M_p_668_0_ + + + + + + B_705_0_ + exo_673_0__Kf + M_p_668_0_ + + + + + + + + + + + 500.0 + 342.85714285714283 + white + 16 + + + + + + + + + + + + A_707_0_ * basal_677_0__Kf * M_686_0_ + + + + + + A_707_0_ + basal_677_0__Kf + M_686_0_ + + + + + + + + + + + 0.0 + 428.57142857142856 + white + 16 + + + + + + + + + + + + A_707_0_ * endo_693_0__Kf * M_686_0_ + + + + + + A_707_0_ + endo_693_0__Kf + M_686_0_ + + + + + + + + + + + P_659_0_ + M_p_668_0_ + kenz_cplx_662_0_ + kenz_661_0_ + 1 + 400.0 + 114.28571428571428 + red + 4 + + + + + + + + + + + + + B_705_0_ * ( k1 * P_659_0_*M_p_668_0_ - k2 * kenz_cplx_662_0_ ) + + + + + + B_705_0_ + + + + + k1 + P_659_0_ + M_p_668_0_ + + + + k2 + kenz_cplx_662_0_ + + + + + + + + + + + + + + kenz_cplx_662_0_ + P_659_0_ + M_666_0_ + kenz_661_0_ + 2 + 400.0 + 114.28571428571428 + red + 4 + + + + + + + + + + + + + B_705_0_ * k3*kenz_cplx_662_0_ + + + + + + B_705_0_ + k3 + kenz_cplx_662_0_ + + + + + + + + + + + M_p_668_0_ + M_666_0_ + kenz_cplx_671_0_ + kenz_670_0_ + 1 + 700.0 + 285.7142857142857 + red + 28 + + + + + + + + + + + + + B_705_0_ * ( k1 * M_p_668_0_*M_666_0_ - k2 * kenz_cplx_671_0_ ) + + + + + + B_705_0_ + + + + + k1 + M_p_668_0_ + M_666_0_ + + + + k2 + kenz_cplx_671_0_ + + + + + + + + + + + + + + kenz_cplx_671_0_ + M_p_668_0_ + M_p_668_0_ + kenz_670_0_ + 2 + 700.0 + 285.7142857142857 + red + 28 + + + + + + + + + + + + B_705_0_ * k3*kenz_cplx_671_0_ + + + + + + B_705_0_ + k3 + kenz_cplx_671_0_ + + + + + + + + + + + P_681_0_ + M_p_688_0_ + kenz_cplx_684_0_ + kenz_683_0_ + 1 + 500.0 + 485.71428571428567 + red + 3 + + + + + + + + + + + + + A_707_0_ * ( k1 * P_681_0_*M_p_688_0_ - k2 * kenz_cplx_684_0_ ) + + + + + + A_707_0_ + + + + + k1 + P_681_0_ + M_p_688_0_ + + + + k2 + kenz_cplx_684_0_ + + + + + + + + + + + + + + kenz_cplx_684_0_ + P_681_0_ + M_686_0_ + kenz_683_0_ + 2 + 500.0 + 485.71428571428567 + red + 3 + + + + + + + + + + + + + A_707_0_ * k3*kenz_cplx_684_0_ + + + + + + A_707_0_ + k3 + kenz_cplx_684_0_ + + + + + + + + + + + M_p_688_0_ + M_686_0_ + kenz_cplx_691_0_ + kenz_690_0_ + 1 + 500.0 + 628.5714285714286 + red + 57 + + + + + + + + + + + + + A_707_0_ * ( k1 * M_p_688_0_*M_686_0_ - k2 * kenz_cplx_691_0_ ) + + + + + + A_707_0_ + + + + + k1 + M_p_688_0_ + M_686_0_ + + + + k2 + kenz_cplx_691_0_ + + + + + + + + + + + + + + kenz_cplx_691_0_ + M_p_688_0_ + M_p_688_0_ + kenz_690_0_ + 2 + 500.0 + 628.5714285714286 + red + 57 + + + + + + + + + + + + A_707_0_ * k3*kenz_cplx_691_0_ + + + + + + A_707_0_ + k3 + kenz_cplx_691_0_ + + + + + + + + + + diff --git a/tutorials/Rdesigneur/chem/chanPhosph3compt.xml b/tutorials/Rdesigneur/chem/chanPhosph3compt.xml new file mode 100644 index 00000000..7fd59712 --- /dev/null +++ b/tutorials/Rdesigneur/chem/chanPhosph3compt.xml @@ -0,0 +1,458 @@ + + + + + + 100.0 + ee + 0.01 + 1.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CubeMesh + False + + + + + + + CubeMesh + False + + + + + + + CubeMesh + False + + + + + + + + + 857.1428571428571 + 80.0 + blue + yellow + 0.0 + 0.0 + + + + + + + 857.1428571428571 + 170.0 + white + black + 0.0 + 0.0 + + + + + + + 714.2857142857143 + 400.0 + 0 + yellow + 0.0 + 0.0 + + + + + + + 1000.0 + 400.0 + 7 + yellow + 0.0 + 0.0 + + + + + + + 0.0 + 640.0 + 55 + 0 + 1e-11 + 0.0 + + + + + + + 285.7142857142857 + 800.0 + blue + 0 + 1e-10 + 0.0 + + + + + + + 428.57142857142856 + 400.0 + blue + 0 + 1e-11 + 0.0 + + + + + + + 142.85714285714286 + 240.0 + 7 + 0 + 0.0 + 0.0 + + + + + + + 285.7142857142857 + 0.0 + blue + 35 + 1e-10 + 0.0 + + + + + + + + + 857.1428571428571 + 560.0 + white + yellow + + + + + + + + + + + + compartment_2_961_0_ * dephosph_930_0__Kf * chan_p_932_0_ + + + + + + compartment_2_961_0_ + dephosph_930_0__Kf + chan_p_932_0_ + + + + + + + + + + + This should actually be 4th order in Ca. Using 2nd order here for simplicity and to lessen numerical stiffness. + + + + + 142.85714285714286 + 480.0 + white + 0 + + + + + + + + + + + + + compartment_1_959_0_ * Ca_bind_CaM_942_0__Kf * CaM_936_0_*Ca_938_0_^2-compartment_1_959_0_ * Ca_bind_CaM_942_0__Kb * Ca_CaM_940_0_ + + + + + + + + compartment_1_959_0_ + Ca_bind_CaM_942_0__Kf + CaM_936_0_ + + + Ca_938_0_ + 2 + + + + + compartment_1_959_0_ + Ca_bind_CaM_942_0__Kb + Ca_CaM_940_0_ + + + + + + + + + + + + + 428.57142857142856 + 160.0 + white + 0 + + + + + + + + + + + + + compartment_1_959_0_ * CaM_bind_CaMKII_946_0__Kf * Ca_CaM_940_0_*CaMKII_944_0_-compartment_1_959_0_ * CaM_bind_CaMKII_946_0__Kb * Ca_CaM_CaMKII_923_0_ + + + + + + + + compartment_1_959_0_ + CaM_bind_CaMKII_946_0__Kf + Ca_CaM_940_0_ + CaMKII_944_0_ + + + + compartment_1_959_0_ + CaM_bind_CaMKII_946_0__Kb + Ca_CaM_CaMKII_923_0_ + + + + + + + + + + + + + Ca_CaM_CaMKII_923_0_ + chan_928_0_ + kinase_cplx_926_0_ + kinase_925_0_ + 1 + 857.1428571428571 + 160.0 + red + blue + + + + + + + + + + + + + compartment_2_961_0_ * ( k1 * Ca_CaM_CaMKII_923_0_*chan_928_0_ - k2 * kinase_cplx_926_0_ ) + + + + + + compartment_2_961_0_ + + + + + k1 + Ca_CaM_CaMKII_923_0_ + chan_928_0_ + + + + k2 + kinase_cplx_926_0_ + + + + + + + + + + + + + + kinase_cplx_926_0_ + Ca_CaM_CaMKII_923_0_ + chan_p_932_0_ + kinase_925_0_ + 2 + 857.1428571428571 + 160.0 + red + blue + + + + + + + + + + + + + compartment_2_961_0_ * k3*kinase_cplx_926_0_ + + + + + + compartment_2_961_0_ + k3 + kinase_cplx_926_0_ + + + + + + + + + + + + + kinetics_914_0_ + kinetics_914_0_ + #FFFF00 + + + + + + + kinetics_914_0_ + kinetics_914_0_ + #f800ff + + + + + + + kinetics_914_0_ + kinetics_914_0_ + #38ff00 + + + + + + + + + diff --git a/tutorials/Rdesigneur/chem/chanPhosphByCaMKII.xml b/tutorials/Rdesigneur/chem/chanPhosphByCaMKII.xml new file mode 100644 index 00000000..3d676b43 --- /dev/null +++ b/tutorials/Rdesigneur/chem/chanPhosphByCaMKII.xml @@ -0,0 +1,398 @@ + + + + + + 100.0 + ee + 0.01 + 1.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CubeMesh + False + + + + + + + + + 0.0 + 622.2222222222223 + 55 + 28 + 1e-11 + 0.0 + + + + + + + 428.57142857142856 + 355.55555555555554 + blue + 28 + 1e-11 + 0.0 + + + + + + + 285.7142857142857 + 800.0 + blue + 28 + 1e-10 + 0.0 + + + + + + + 142.85714285714286 + 177.77777777777777 + 7 + 28 + 0.0 + 0.0 + + + + + + + 857.1428571428571 + 0.0 + blue + 0 + 0.0 + 0.0 + + + + + + + 857.1428571428571 + 98.0 + white + black + 0.0 + 0.0 + + + + + + + 714.2857142857143 + 355.55555555555554 + 0 + black + 0.0 + 0.0 + + + + + + + 1000.0 + 355.55555555555554 + 7 + black + 0.0 + 0.0 + + + + + + + + + 428.57142857142856 + 88.88888888888889 + white + 28 + + + + + + + + + + + + + kinetics_980_0_ * CaM_bind_CaMKII_993_0__Kf * Ca_CaM_989_0_*CaMKII_995_0_-kinetics_980_0_ * CaM_bind_CaMKII_993_0__Kb * Ca_CaM_CaMKII_997_0_ + + + + + + + + kinetics_980_0_ + CaM_bind_CaMKII_993_0__Kf + Ca_CaM_989_0_ + CaMKII_995_0_ + + + + kinetics_980_0_ + CaM_bind_CaMKII_993_0__Kb + Ca_CaM_CaMKII_997_0_ + + + + + + + + + + + + + This should actually be 4th order in Ca. Using 2nd order here for simplicity and to lessen numerical stiffness. + + + + + 142.85714285714286 + 444.44444444444446 + white + 28 + + + + + + + + + + + + + kinetics_980_0_ * Ca_bind_CaM_1006_0__Kf * CaM_987_0_*Ca_991_0_^2-kinetics_980_0_ * Ca_bind_CaM_1006_0__Kb * Ca_CaM_989_0_ + + + + + + + + kinetics_980_0_ + Ca_bind_CaM_1006_0__Kf + CaM_987_0_ + + + Ca_991_0_ + 2 + + + + + kinetics_980_0_ + Ca_bind_CaM_1006_0__Kb + Ca_CaM_989_0_ + + + + + + + + + + + + + 857.1428571428571 + 533.3333333333333 + white + black + + + + + + + + + + + + kinetics_980_0_ * dephosph_1008_0__Kf * chan_p_1004_0_ + + + + + + kinetics_980_0_ + dephosph_1008_0__Kf + chan_p_1004_0_ + + + + + + + + + + + Ca_CaM_CaMKII_997_0_ + chan_1002_0_ + kinase_cplx_1000_0_ + kinase_999_0_ + 1 + 857.1428571428571 + 88.88888888888889 + red + blue + + + + + + + + + + + + + kinetics_980_0_ * ( k1 * Ca_CaM_CaMKII_997_0_*chan_1002_0_ - k2 * kinase_cplx_1000_0_ ) + + + + + + kinetics_980_0_ + + + + + k1 + Ca_CaM_CaMKII_997_0_ + chan_1002_0_ + + + + k2 + kinase_cplx_1000_0_ + + + + + + + + + + + + + + kinase_cplx_1000_0_ + Ca_CaM_CaMKII_997_0_ + chan_p_1004_0_ + kinase_999_0_ + 2 + 857.1428571428571 + 88.88888888888889 + red + blue + + + + + + + + + + + + + kinetics_980_0_ * k3*kinase_cplx_1000_0_ + + + + + + kinetics_980_0_ + k3 + kinase_cplx_1000_0_ + + + + + + + + + + diff --git a/tutorials/Rdesigneur/chem/echem.xml b/tutorials/Rdesigneur/chem/echem.xml new file mode 100644 index 00000000..b50db377 --- /dev/null +++ b/tutorials/Rdesigneur/chem/echem.xml @@ -0,0 +1,316 @@ + + + + + + 100.0 + ee + 0.01 + 1.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CubeMesh + False + + + + + + + + + 0.0 + 666.6666666666667 + 62 + yellow + 0.0 + 0.0 + + + + + + + 1000.0 + 666.6666666666667 + 52 + yellow + 0.0 + 0.0 + + + + + + + 0.0 + 400.0 + 1 + yellow + 0.0 + 0.0 + + + + + + + 1000.0 + 133.33333333333331 + 27 + yellow + 0.0 + 0.0 + + + + + + + 1000.0 + 400.0 + 7 + yellow + 0.0 + 0.0 + + + + + + + + + 500.0 + 800.0 + white + yellow + + + + + + + + + + + + kinetics_1213_0_ * remove_Ca_1224_0__Kf * Ca_1222_0_-kinetics_1213_0_ * remove_Ca_1224_0__Kb * Ca_ext_1226_0_ + + + + + + + + kinetics_1213_0_ + remove_Ca_1224_0__Kf + Ca_1222_0_ + + + + kinetics_1213_0_ + remove_Ca_1224_0__Kb + Ca_ext_1226_0_ + + + + + + + + + + + + + High cooperativity, 4 or higher. Several refs: McDargh and O-Shaughnessy, BioRxiv 2021 Voleti, Jaczynska, Rizo, eLife 2020 Chen.... Scheller, Cell 1999 + + + + + 500.0 + 533.3333333333333 + white + yellow + + + + + + + + + + + + + kinetics_1213_0_ * vesicle_release_1228_0__Kf * Ca_1222_0_^4*RR_pool_1230_0_ + + + + + + kinetics_1213_0_ + vesicle_release_1228_0__Kf + + + Ca_1222_0_ + 4 + + RR_pool_1230_0_ + + + + + + + + + + + 500.0 + 266.66666666666663 + white + yellow + + + + + + + + + + + + kinetics_1213_0_ * remove_1234_0__Kf * glu_1236_0_ + + + + + + kinetics_1213_0_ + remove_1234_0__Kf + glu_1236_0_ + + + + + + + + + + + 500.0 + 0.0 + white + yellow + + + + + + + + + + + + kinetics_1213_0_ * replenish_vesicle_1238_0__Kf * vesicle_pool_1232_0_-kinetics_1213_0_ * replenish_vesicle_1238_0__Kb * RR_pool_1230_0_ + + + + + + + + kinetics_1213_0_ + replenish_vesicle_1238_0__Kf + vesicle_pool_1232_0_ + + + + kinetics_1213_0_ + replenish_vesicle_1238_0__Kb + RR_pool_1230_0_ + + + + + + + + + + + + + + + kinetics_1213_0_ + kinetics_1213_0_ + #FFFF00 + + + + + + + + + + + + + + + + +