diff --git a/tutorials/Rdesigneur/chem/CICRspineDend.xml b/tutorials/Rdesigneur/chem/CICRspineDend.xml new file mode 100644 index 00000000..c88150f1 --- /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 + 0.0 + + + + + + + 800.0 + 333.33333333333337 + 23 + black + 2e-11 + 0.0 + + + + + + + 500.0 + 800.0 + 25 + yellow + 2e-11 + 0.0 + + + + + + + 1000.0 + 333.33333333333337 + 61 + black + 0.0 + 0.0 + + + + + + + + CaIP3_3_R_452_0_ + + + + + + + + ConcChannel + 2.0 + 2.0 + 8000.0 + + + + + + + + + + + + + + + kinetics_443_0_ * ( Permeability) * ActIP3R_478_0_ * (CaER_506_0_ - Ca_512_0_) + + + + + + kinetics_443_0_ + Permeability + ActIP3R_478_0_ + + + CaER_506_0_ + Ca_512_0_ + + + + + + + + + + + + ConcChannel + 4.0 + 5.0 + 40.0 + + + + + + + + + + + + + + + compartment_1_532_0_ * ( Permeability) * leakPool_508_0_ * (CaER_506_0_ - Ca_512_0_) + + + + + + compartment_1_532_0_ + Permeability + leakPool_508_0_ + + + CaER_506_0_ + Ca_512_0_ + + + + + + + + + + + + 600.0 + 66.66666666666666 + white + black + + + + + + + + + + + + + kinetics_443_0_ * CaMreac1_486_0__Kf * CaM_458_0_*Ca_512_0_-kinetics_443_0_ * CaMreac1_486_0__Kb * CaMCa_460_0_ + + + + + + + + kinetics_443_0_ + CaMreac1_486_0__Kf + CaM_458_0_ + Ca_512_0_ + + + + kinetics_443_0_ + CaMreac1_486_0__Kb + CaMCa_460_0_ + + + + + + + + + + + + + 700.0 + 133.33333333333331 + white + black + + + + + + + + + + + + + kinetics_443_0_ * CaMreac2_488_0__Kf * CaMCa_460_0_*Ca_512_0_-kinetics_443_0_ * CaMreac2_488_0__Kb * CaMCa2_462_0_ + + + + + + + + kinetics_443_0_ + CaMreac2_488_0__Kf + CaMCa_460_0_ + Ca_512_0_ + + + + kinetics_443_0_ + CaMreac2_488_0__Kb + CaMCa2_462_0_ + + + + + + + + + + + + + 800.0 + 200.0 + white + black + + + + + + + + + + + + + kinetics_443_0_ * CaMreac3_490_0__Kf * CaMCa2_462_0_*Ca_512_0_-kinetics_443_0_ * CaMreac3_490_0__Kb * CaMCa3_464_0_ + + + + + + + + kinetics_443_0_ + CaMreac3_490_0__Kf + CaMCa2_462_0_ + Ca_512_0_ + + + + kinetics_443_0_ + CaMreac3_490_0__Kb + CaMCa3_464_0_ + + + + + + + + + + + + + 900.0 + 266.66666666666663 + white + black + + + + + + + + + + + + + kinetics_443_0_ * CaMreac4_492_0__Kf * CaMCa3_464_0_*Ca_512_0_-kinetics_443_0_ * CaMreac4_492_0__Kb * CaMCa4_466_0_ + + + + + + + + kinetics_443_0_ + CaMreac4_492_0__Kf + CaMCa3_464_0_ + Ca_512_0_ + + + + kinetics_443_0_ + CaMreac4_492_0__Kb + CaMCa4_466_0_ + + + + + + + + + + + + + 500.0 + 600.0 + white + black + + + + + + + + + + + + + kinetics_443_0_ * Reac_494_0__Kf * IP3_R_468_0_*IP3_472_0_-kinetics_443_0_ * Reac_494_0__Kb * IP3_3_R_470_0_ + + + + + + + + kinetics_443_0_ + Reac_494_0__Kf + IP3_R_468_0_ + IP3_472_0_ + + + + kinetics_443_0_ + Reac_494_0__Kb + IP3_3_R_470_0_ + + + + + + + + + + + + + 700.0 + 466.6666666666667 + white + black + + + + + + + + + + + + + kinetics_443_0_ * Reac2_496_0__Kf * IP3_3_R_470_0_*Ca_512_0_-kinetics_443_0_ * Reac2_496_0__Kb * CaIP3_3_R_452_0_ + + + + + + + + kinetics_443_0_ + Reac2_496_0__Kf + IP3_3_R_470_0_ + Ca_512_0_ + + + + kinetics_443_0_ + Reac2_496_0__Kb + CaIP3_3_R_452_0_ + + + + + + + + + + + + + 800.0 + 533.3333333333333 + white + black + + + + + + + + + + + + + kinetics_443_0_ * Reac4_498_0__Kf * CaIP3_3_R_452_0_*Ca_512_0_-kinetics_443_0_ * Reac4_498_0__Kb * Ca2_IP3_3_R_474_0_ + + + + + + + + kinetics_443_0_ + Reac4_498_0__Kf + CaIP3_3_R_452_0_ + Ca_512_0_ + + + + kinetics_443_0_ + Reac4_498_0__Kb + Ca2_IP3_3_R_474_0_ + + + + + + + + + + + + + 100.0 + 66.66666666666666 + white + black + + + + + + + + + + + + kinetics_443_0_ * Reac1_500_0__Kf * Mirror_CaIP3_3_R_476_0_^3-kinetics_443_0_ * Reac1_500_0__Kb * ActIP3R_478_0_ + + + + + + + + kinetics_443_0_ + Reac1_500_0__Kf + + + Mirror_CaIP3_3_R_476_0_ + 3 + + + + + kinetics_443_0_ + Reac1_500_0__Kb + ActIP3R_478_0_ + + + + + + + + + + + + + 900.0 + 400.0 + white + black + + + + + + + + + + + + kinetics_443_0_ * Ca_regn_520_0__Kf * Ca_512_0_-kinetics_443_0_ * Ca_regn_520_0__Kb * CaExtracell_518_0_ + + + + + + + + kinetics_443_0_ + Ca_regn_520_0__Kf + Ca_512_0_ + + + + kinetics_443_0_ + Ca_regn_520_0__Kb + CaExtracell_518_0_ + + + + + + + + + + + + + 500.0 + 200.0 + black + 42 + + + + + + + + + + + + + + + kinetics_443_0_ * ( kcat * Ca_512_0_ * Serca_454_0_/(Km + Ca_512_0_)) + + + + + + kinetics_443_0_ + + + + + kcat + Ca_512_0_ + Serca_454_0_ + + + + Km + Ca_512_0_ + + + + + + + + + + + + + + + + kinetics_443_0_ + kinetics_443_0_ + #FFA500 + + + + + + + kinetics_443_0_ + kinetics_443_0_ + #00a858 + + + + + + + kinetics_443_0_ + kinetics_443_0_ + #FFFF00 + + + + + + diff --git a/tutorials/Rdesigneur/chem/chanPhosph3compt.xml b/tutorials/Rdesigneur/chem/chanPhosph3compt.xml new file mode 100644 index 00000000..95d8f797 --- /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_520_0_ * dephosph_489_0__Kf * chan_p_491_0_ + + + + + + compartment_2_520_0_ + dephosph_489_0__Kf + chan_p_491_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_518_0_ * Ca_bind_CaM_501_0__Kf * CaM_495_0_*Ca_497_0_^2-compartment_1_518_0_ * Ca_bind_CaM_501_0__Kb * Ca_CaM_499_0_ + + + + + + + + compartment_1_518_0_ + Ca_bind_CaM_501_0__Kf + CaM_495_0_ + + + Ca_497_0_ + 2 + + + + + compartment_1_518_0_ + Ca_bind_CaM_501_0__Kb + Ca_CaM_499_0_ + + + + + + + + + + + + + 428.57142857142856 + 160.0 + white + 0 + + + + + + + + + + + + + compartment_1_518_0_ * CaM_bind_CaMKII_505_0__Kf * Ca_CaM_499_0_*CaMKII_503_0_-compartment_1_518_0_ * CaM_bind_CaMKII_505_0__Kb * Ca_CaM_CaMKII_482_0_ + + + + + + + + compartment_1_518_0_ + CaM_bind_CaMKII_505_0__Kf + Ca_CaM_499_0_ + CaMKII_503_0_ + + + + compartment_1_518_0_ + CaM_bind_CaMKII_505_0__Kb + Ca_CaM_CaMKII_482_0_ + + + + + + + + + + + + + Ca_CaM_CaMKII_482_0_ + chan_487_0_ + kinase_cplx_485_0_ + kinase_484_0_ + 1 + 857.1428571428571 + 160.0 + red + blue + + + + + + + + + + + + + compartment_2_520_0_ * ( k1 * Ca_CaM_CaMKII_482_0_*chan_487_0_ - k2 * kinase_cplx_485_0_ ) + + + + + + compartment_2_520_0_ + + + + + k1 + Ca_CaM_CaMKII_482_0_ + chan_487_0_ + + + + k2 + kinase_cplx_485_0_ + + + + + + + + + + + + + + kinase_cplx_485_0_ + Ca_CaM_CaMKII_482_0_ + chan_p_491_0_ + kinase_484_0_ + 2 + 857.1428571428571 + 160.0 + red + blue + + + + + + + + + + + + + compartment_2_520_0_ * k3*kinase_cplx_485_0_ + + + + + + compartment_2_520_0_ + k3 + kinase_cplx_485_0_ + + + + + + + + + + + + + kinetics_473_0_ + kinetics_473_0_ + #FFFF00 + + + + + + + kinetics_473_0_ + kinetics_473_0_ + #f800ff + + + + + + + kinetics_473_0_ + kinetics_473_0_ + #38ff00 + + + + + + + + + diff --git a/tutorials/Rdesigneur/chem/echem.xml b/tutorials/Rdesigneur/chem/echem.xml new file mode 100644 index 00000000..69d5ceca --- /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_549_0_ * remove_Ca_560_0__Kf * Ca_558_0_-kinetics_549_0_ * remove_Ca_560_0__Kb * Ca_ext_562_0_ + + + + + + + + kinetics_549_0_ + remove_Ca_560_0__Kf + Ca_558_0_ + + + + kinetics_549_0_ + remove_Ca_560_0__Kb + Ca_ext_562_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_549_0_ * vesicle_release_564_0__Kf * Ca_558_0_^4*RR_pool_566_0_ + + + + + + kinetics_549_0_ + vesicle_release_564_0__Kf + + + Ca_558_0_ + 4 + + RR_pool_566_0_ + + + + + + + + + + + 500.0 + 266.66666666666663 + white + yellow + + + + + + + + + + + + kinetics_549_0_ * remove_570_0__Kf * glu_572_0_ + + + + + + kinetics_549_0_ + remove_570_0__Kf + glu_572_0_ + + + + + + + + + + + 500.0 + 0.0 + white + yellow + + + + + + + + + + + + kinetics_549_0_ * replenish_vesicle_574_0__Kf * vesicle_pool_568_0_-kinetics_549_0_ * replenish_vesicle_574_0__Kb * RR_pool_566_0_ + + + + + + + + kinetics_549_0_ + replenish_vesicle_574_0__Kf + vesicle_pool_568_0_ + + + + kinetics_549_0_ + replenish_vesicle_574_0__Kb + RR_pool_566_0_ + + + + + + + + + + + + + + + kinetics_549_0_ + kinetics_549_0_ + #FFFF00 + + + + + + + + + + + + + + + + +