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Commit 3622be4c authored by Santiago Ospina De Los Ríos's avatar Santiago Ospina De Los Ríos
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Update liver test to include membrane 

This test was initially committed by mistake. It included zero reactions on the membrane as a test. This includes the full version to be tested with the jacobian test.
parent 3a6a6055
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1 merge request!39Resolve "Improve testing on jacobians"
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Stage: build
Stage: unit_tests
Stage: system_tests
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test/test_NFkappaB.mini
+ 349
− 167
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......@@ -7,7 +7,7 @@ __name = test_NFkappaB
[grid]
dimension = 2
file = grids/test_cell.msh
file = grids/test_cell_membrane.msh
initial_level = 0
[model]
......@@ -25,8 +25,8 @@ increase_factor = 1.1
[model.compartments]
cytoplasm = 0
#membrane = 1
nucleus = 1
cytoplasm_nucleus = 1
nucleus = 2
[model.writer]
file_path = {__name}
......@@ -53,70 +53,70 @@ IkBa_mRNA_cytoplasm = -4.97223415385606*IkBa_mRNA_cytoplasm
IkBa_cytoplasm = -0.036018623190168*IkBa_cytoplasm + 18.7354723520005*IkBa_mRNA_cytoplasm/(0.238680093564444 + IkBa_mRNA_cytoplasm) - 6608.22068729695*IKKb_p*IkBa_cytoplasm/(0.112460269242964 + IkBa_cytoplasm) - 1.0*(-0.0245628310133508*p65_IkB_cytoplasm + 8.18761033778361*p65_cytoplasm*IkBa_cytoplasm)
[model.cytoplasm.reaction.jacobian]
dp65_cytoplasm_dp65_cytoplasm = -8.18761033778361*IkBa_cytoplasm
dp65_cytoplasm_dIkBa_p = 0
dp65_cytoplasm_dIKKb = 0
dp65_cytoplasm_dIKKb_p = 7342.46743032994*p65_IkB_cytoplasm/(3.13820291340728 + p65_IkB_cytoplasm)
dp65_cytoplasm_dTNFa = 0
dp65_cytoplasm_dp65_IkB_cytoplasm = 0.0605814542035188 + 7342.46743032994*IKKb_p/(3.13820291340728 + p65_IkB_cytoplasm) - 7342.46743032994*IKKb_p*p65_IkB_cytoplasm/(3.13820291340728 + p65_IkB_cytoplasm)^2
dp65_cytoplasm_dIkBa_mRNA_cytoplasm = 0
dp65_cytoplasm_dIkBa_cytoplasm = -8.18761033778361*p65_cytoplasm
dIkBa_p_dp65_cytoplasm = 0
dIkBa_p_dIkBa_p = -35.9999481926134
dIkBa_p_dIKKb = 0
dIkBa_p_dIKKb_p = 6608.22068729695*IkBa_cytoplasm/(0.112460269242964 + IkBa_cytoplasm) + 7342.46743032994*p65_IkB_cytoplasm/(3.13820291340728 + p65_IkB_cytoplasm)
dIkBa_p_dTNFa = 0
dIkBa_p_dp65_IkB_cytoplasm = 0.0 + 7342.46743032994*IKKb_p/(3.13820291340728 + p65_IkB_cytoplasm) - 7342.46743032994*IKKb_p*p65_IkB_cytoplasm/(3.13820291340728 + p65_IkB_cytoplasm)^2
dIkBa_p_dIkBa_mRNA_cytoplasm = 0
dIkBa_p_dIkBa_cytoplasm = 0.0 + 6608.22068729695*IKKb_p/(0.112460269242964 + IkBa_cytoplasm) - 6608.22068729695*IKKb_p*IkBa_cytoplasm/(0.112460269242964 + IkBa_cytoplasm)^2
dIKKb_dp65_cytoplasm = 0
dIKKb_dIkBa_p = 0
dIKKb_dIKKb = -0.1238783595 - 3.65474756811715*TNFa/((1.47829 + IKKb)*(99.9998605315951 + TNFa)) + 3.65474756811715*TNFa*IKKb/((1.47829 + IKKb)^2*(99.9998605315951 + TNFa))
dIKKb_dIKKb_p = 27.7868307830501
dIKKb_dTNFa = 0.0 - 3.65474756811715*IKKb/((1.47829 + IKKb)*(99.9998605315951 + TNFa)) + 3.65474756811715*TNFa*IKKb/((1.47829 + IKKb)*(99.9998605315951 + TNFa)^2)
dIKKb_dp65_IkB_cytoplasm = 0
dIKKb_dIkBa_mRNA_cytoplasm = 0
dIKKb_dIkBa_cytoplasm = 0
dIKKb_p_dp65_cytoplasm = 0
dIKKb_p_dIkBa_p = 0
dIKKb_p_dIKKb = 0.1238783595 + 3.65474756811715*TNFa/((1.47829 + IKKb)*(99.9998605315951 + TNFa)) - 3.65474756811715*TNFa*IKKb/((1.47829 + IKKb)^2*(99.9998605315951 + TNFa))
dIKKb_p_dIKKb_p = -27.7868307830501
dIKKb_p_dTNFa = 0.0 + 3.65474756811715*IKKb/((1.47829 + IKKb)*(99.9998605315951 + TNFa)) - 3.65474756811715*TNFa*IKKb/((1.47829 + IKKb)*(99.9998605315951 + TNFa)^2)
dIKKb_p_dp65_IkB_cytoplasm = 0
dIKKb_p_dIkBa_mRNA_cytoplasm = 0
dIKKb_p_dIkBa_cytoplasm = 0
dTNFa_dp65_cytoplasm = 0
dTNFa_dIkBa_p = 0
dTNFa_dIKKb = 0
dTNFa_dIKKb_p = 0
dTNFa_dTNFa = -0.9
dTNFa_dp65_IkB_cytoplasm = 0
dTNFa_dIkBa_mRNA_cytoplasm = 0
dTNFa_dIkBa_cytoplasm = 0
dp65_IkB_cytoplasm_dp65_cytoplasm = 8.18761033778361*IkBa_cytoplasm
dp65_IkB_cytoplasm_dIkBa_p = 0
dp65_IkB_cytoplasm_dIKKb = 0
dp65_IkB_cytoplasm_dIKKb_p = -7342.46743032994*p65_IkB_cytoplasm/(3.13820291340728 + p65_IkB_cytoplasm)
dp65_IkB_cytoplasm_dTNFa = 0
dp65_IkB_cytoplasm_dp65_IkB_cytoplasm = -0.0605814542035188 - 7342.46743032994*IKKb_p/(3.13820291340728 + p65_IkB_cytoplasm) + 7342.46743032994*IKKb_p*p65_IkB_cytoplasm/(3.13820291340728 + p65_IkB_cytoplasm)^2
dp65_IkB_cytoplasm_dIkBa_mRNA_cytoplasm = 0
dp65_IkB_cytoplasm_dIkBa_cytoplasm = 8.18761033778361*p65_cytoplasm
dIkBa_mRNA_cytoplasm_dp65_cytoplasm = 0
dIkBa_mRNA_cytoplasm_dIkBa_p = 0
dIkBa_mRNA_cytoplasm_dIKKb = 0
dIkBa_mRNA_cytoplasm_dIKKb_p = 0
dIkBa_mRNA_cytoplasm_dTNFa = 0
dIkBa_mRNA_cytoplasm_dp65_IkB_cytoplasm = 0
dIkBa_mRNA_cytoplasm_dIkBa_mRNA_cytoplasm = -4.97223415385606
dIkBa_mRNA_cytoplasm_dIkBa_cytoplasm = 0
dIkBa_cytoplasm_dp65_cytoplasm = -8.18761033778361*IkBa_cytoplasm
dIkBa_cytoplasm_dIkBa_p = 0
dIkBa_cytoplasm_dIKKb = 0
dIkBa_cytoplasm_dIKKb_p = -6608.22068729695*IkBa_cytoplasm/(0.112460269242964 + IkBa_cytoplasm)
dIkBa_cytoplasm_dTNFa = 0
dIkBa_cytoplasm_dp65_IkB_cytoplasm = 0.0245628310133508
dIkBa_cytoplasm_dIkBa_mRNA_cytoplasm = 0.0 - 18.7354723520005*IkBa_mRNA_cytoplasm/(0.238680093564444 + IkBa_mRNA_cytoplasm)^2 + 18.7354723520005*(0.238680093564444 + IkBa_mRNA_cytoplasm)^(-1)
dIkBa_cytoplasm_dIkBa_cytoplasm = -0.036018623190168 - 8.18761033778361*p65_cytoplasm - 6608.22068729695*IKKb_p/(0.112460269242964 + IkBa_cytoplasm) + 6608.22068729695*IKKb_p*IkBa_cytoplasm/(0.112460269242964 + IkBa_cytoplasm)^2
dp65_cytoplasm__dp65_cytoplasm = -8.18761033778361*IkBa_cytoplasm
dp65_cytoplasm__dIkBa_p = 0
dp65_cytoplasm__dIKKb = 0
dp65_cytoplasm__dIKKb_p = 7342.46743032994*p65_IkB_cytoplasm/(3.13820291340728 + p65_IkB_cytoplasm)
dp65_cytoplasm__dTNFa = 0
dp65_cytoplasm__dp65_IkB_cytoplasm = 0.0605814542035188 + 7342.46743032994*IKKb_p/(3.13820291340728 + p65_IkB_cytoplasm) - 7342.46743032994*IKKb_p*p65_IkB_cytoplasm/(3.13820291340728 + p65_IkB_cytoplasm)^2
dp65_cytoplasm__dIkBa_mRNA_cytoplasm = 0
dp65_cytoplasm__dIkBa_cytoplasm = -8.18761033778361*p65_cytoplasm
dIkBa_p__dp65_cytoplasm = 0
dIkBa_p__dIkBa_p = -35.9999481926134
dIkBa_p__dIKKb = 0
dIkBa_p__dIKKb_p = 6608.22068729695*IkBa_cytoplasm/(0.112460269242964 + IkBa_cytoplasm) + 7342.46743032994*p65_IkB_cytoplasm/(3.13820291340728 + p65_IkB_cytoplasm)
dIkBa_p__dTNFa = 0
dIkBa_p__dp65_IkB_cytoplasm = 0.0 + 7342.46743032994*IKKb_p/(3.13820291340728 + p65_IkB_cytoplasm) - 7342.46743032994*IKKb_p*p65_IkB_cytoplasm/(3.13820291340728 + p65_IkB_cytoplasm)^2
dIkBa_p__dIkBa_mRNA_cytoplasm = 0
dIkBa_p__dIkBa_cytoplasm = 0.0 + 6608.22068729695*IKKb_p/(0.112460269242964 + IkBa_cytoplasm) - 6608.22068729695*IKKb_p*IkBa_cytoplasm/(0.112460269242964 + IkBa_cytoplasm)^2
dIKKb__dp65_cytoplasm = 0
dIKKb__dIkBa_p = 0
dIKKb__dIKKb = -0.1238783595 - 3.65474756811715*TNFa/((1.47829 + IKKb)*(99.9998605315951 + TNFa)) + 3.65474756811715*TNFa*IKKb/((1.47829 + IKKb)^2*(99.9998605315951 + TNFa))
dIKKb__dIKKb_p = 27.7868307830501
dIKKb__dTNFa = 0.0 - 3.65474756811715*IKKb/((1.47829 + IKKb)*(99.9998605315951 + TNFa)) + 3.65474756811715*TNFa*IKKb/((1.47829 + IKKb)*(99.9998605315951 + TNFa)^2)
dIKKb__dp65_IkB_cytoplasm = 0
dIKKb__dIkBa_mRNA_cytoplasm = 0
dIKKb__dIkBa_cytoplasm = 0
dIKKb_p__dp65_cytoplasm = 0
dIKKb_p__dIkBa_p = 0
dIKKb_p__dIKKb = 0.1238783595 + 3.65474756811715*TNFa/((1.47829 + IKKb)*(99.9998605315951 + TNFa)) - 3.65474756811715*TNFa*IKKb/((1.47829 + IKKb)^2*(99.9998605315951 + TNFa))
dIKKb_p__dIKKb_p = -27.7868307830501
dIKKb_p__dTNFa = 0.0 + 3.65474756811715*IKKb/((1.47829 + IKKb)*(99.9998605315951 + TNFa)) - 3.65474756811715*TNFa*IKKb/((1.47829 + IKKb)*(99.9998605315951 + TNFa)^2)
dIKKb_p__dp65_IkB_cytoplasm = 0
dIKKb_p__dIkBa_mRNA_cytoplasm = 0
dIKKb_p__dIkBa_cytoplasm = 0
dTNFa__dp65_cytoplasm = 0
dTNFa__dIkBa_p = 0
dTNFa__dIKKb = 0
dTNFa__dIKKb_p = 0
dTNFa__dTNFa = -0.9
dTNFa__dp65_IkB_cytoplasm = 0
dTNFa__dIkBa_mRNA_cytoplasm = 0
dTNFa__dIkBa_cytoplasm = 0
dp65_IkB_cytoplasm__dp65_cytoplasm = 8.18761033778361*IkBa_cytoplasm
dp65_IkB_cytoplasm__dIkBa_p = 0
dp65_IkB_cytoplasm__dIKKb = 0
dp65_IkB_cytoplasm__dIKKb_p = -7342.46743032994*p65_IkB_cytoplasm/(3.13820291340728 + p65_IkB_cytoplasm)
dp65_IkB_cytoplasm__dTNFa = 0
dp65_IkB_cytoplasm__dp65_IkB_cytoplasm = -0.0605814542035188 - 7342.46743032994*IKKb_p/(3.13820291340728 + p65_IkB_cytoplasm) + 7342.46743032994*IKKb_p*p65_IkB_cytoplasm/(3.13820291340728 + p65_IkB_cytoplasm)^2
dp65_IkB_cytoplasm__dIkBa_mRNA_cytoplasm = 0
dp65_IkB_cytoplasm__dIkBa_cytoplasm = 8.18761033778361*p65_cytoplasm
dIkBa_mRNA_cytoplasm__dp65_cytoplasm = 0
dIkBa_mRNA_cytoplasm__dIkBa_p = 0
dIkBa_mRNA_cytoplasm__dIKKb = 0
dIkBa_mRNA_cytoplasm__dIKKb_p = 0
dIkBa_mRNA_cytoplasm__dTNFa = 0
dIkBa_mRNA_cytoplasm__dp65_IkB_cytoplasm = 0
dIkBa_mRNA_cytoplasm__dIkBa_mRNA_cytoplasm = -4.97223415385606
dIkBa_mRNA_cytoplasm__dIkBa_cytoplasm = 0
dIkBa_cytoplasm__dp65_cytoplasm = -8.18761033778361*IkBa_cytoplasm
dIkBa_cytoplasm__dIkBa_p = 0
dIkBa_cytoplasm__dIKKb = 0
dIkBa_cytoplasm__dIKKb_p = -6608.22068729695*IkBa_cytoplasm/(0.112460269242964 + IkBa_cytoplasm)
dIkBa_cytoplasm__dTNFa = 0
dIkBa_cytoplasm__dp65_IkB_cytoplasm = 0.0245628310133508
dIkBa_cytoplasm__dIkBa_mRNA_cytoplasm = 0.0 - 18.7354723520005*IkBa_mRNA_cytoplasm/(0.238680093564444 + IkBa_mRNA_cytoplasm)^2 + 18.7354723520005*(0.238680093564444 + IkBa_mRNA_cytoplasm)^(-1)
dIkBa_cytoplasm__dIkBa_cytoplasm = -0.036018623190168 - 8.18761033778361*p65_cytoplasm - 6608.22068729695*IKKb_p/(0.112460269242964 + IkBa_cytoplasm) + 6608.22068729695*IKKb_p*IkBa_cytoplasm/(0.112460269242964 + IkBa_cytoplasm)^2
[model.cytoplasm.diffusion]
p65_cytoplasm = 1
......@@ -128,70 +128,6 @@ p65_IkB_cytoplasm = 1
IkBa_mRNA_cytoplasm = 1
IkBa_cytoplasm = 1
############################ Model for membrane ############################
[model.membrane.initial]
u_0 = 0
u_1 = 0
u_2 = 0
u_3 = 0
u_4 = 0
u_5 = 0
[model.membrane.reaction]
u_0 = 0
u_1 = 0
u_2 = 0
u_3 = 0
u_4 = 0
u_5 = 0
[model.membrane.reaction.jacobian]
du_0_du_0 = 0
du_0_du_1 = 0
du_0_du_2 = 0
du_0_du_3 = 0
du_0_du_4 = 0
du_0_du_5 = 0
du_1_du_0 = 0
du_1_du_1 = 0
du_1_du_2 = 0
du_1_du_3 = 0
du_1_du_4 = 0
du_1_du_5 = 0
du_2_du_0 = 0
du_2_du_1 = 0
du_2_du_2 = 0
du_2_du_3 = 0
du_2_du_4 = 0
du_2_du_5 = 0
du_3_du_0 = 0
du_3_du_1 = 0
du_3_du_2 = 0
du_3_du_3 = 0
du_3_du_4 = 0
du_3_du_5 = 0
du_4_du_0 = 0
du_4_du_1 = 0
du_4_du_2 = 0
du_4_du_3 = 0
du_4_du_4 = 0
du_4_du_5 = 0
du_5_du_0 = 0
du_5_du_1 = 0
du_5_du_2 = 0
du_5_du_3 = 0
du_5_du_4 = 0
du_5_du_5 = 0
[model.membrane.diffusion]
u_0 = 100
u_1 = 100
u_2 = 100
u_3 = 100
u_4 = 100
u_5 = 100
############################ Model for nucleus ############################
[model.nucleus.initial]
IkBa_mRNA_2 = 5.14124
p65_nucleus = 0.0832677
......@@ -209,42 +145,42 @@ IkBa_mRNA_nucleus = 5.00900035911484*IkBa_mRNA_2 - 0.497223415385606*IkBa_mRNA_n
IkBa_mRNA_1 = -5.00900035911484*IkBa_mRNA_1 + 1.0*(0.0036897759857015 + 309.229298924907*p65_nucleus)
[model.nucleus.reaction.jacobian]
dIkBa_mRNA_2_dIkBa_mRNA_2 = -5.00900035911484
dIkBa_mRNA_2_dp65_nucleus = 0
dIkBa_mRNA_2_dIkBa_nucleus = 0
dIkBa_mRNA_2_dp65_IkB_nucleus = 0
dIkBa_mRNA_2_dIkBa_mRNA_nucleus = 0
dIkBa_mRNA_2_dIkBa_mRNA_1 = 5.00900035911484
dp65_nucleus_dIkBa_mRNA_2 = 0
dp65_nucleus_dp65_nucleus = -8.18761033778361*IkBa_nucleus
dp65_nucleus_dIkBa_nucleus = -8.18761033778361*p65_nucleus
dp65_nucleus_dp65_IkB_nucleus = 0.0605814542035188
dp65_nucleus_dIkBa_mRNA_nucleus = 0
dp65_nucleus_dIkBa_mRNA_1 = 0
dIkBa_nucleus_dIkBa_mRNA_2 = 0
dIkBa_nucleus_dp65_nucleus = -8.18761033778361*IkBa_nucleus
dIkBa_nucleus_dIkBa_nucleus = -0.036018623190168 - 8.18761033778361*p65_nucleus
dIkBa_nucleus_dp65_IkB_nucleus = 0.0245628310133508
dIkBa_nucleus_dIkBa_mRNA_nucleus = 0
dIkBa_nucleus_dIkBa_mRNA_1 = 0
dp65_IkB_nucleus_dIkBa_mRNA_2 = 0
dp65_IkB_nucleus_dp65_nucleus = 8.18761033778361*IkBa_nucleus
dp65_IkB_nucleus_dIkBa_nucleus = 8.18761033778361*p65_nucleus
dp65_IkB_nucleus_dp65_IkB_nucleus = -0.0605814542035188
dp65_IkB_nucleus_dIkBa_mRNA_nucleus = 0
dp65_IkB_nucleus_dIkBa_mRNA_1 = 0
dIkBa_mRNA_nucleus_dIkBa_mRNA_2 = 5.00900035911484
dIkBa_mRNA_nucleus_dp65_nucleus = 0
dIkBa_mRNA_nucleus_dIkBa_nucleus = 0
dIkBa_mRNA_nucleus_dp65_IkB_nucleus = 0
dIkBa_mRNA_nucleus_dIkBa_mRNA_nucleus = -0.497223415385606
dIkBa_mRNA_nucleus_dIkBa_mRNA_1 = 0
dIkBa_mRNA_1_dIkBa_mRNA_2 = 0
dIkBa_mRNA_1_dp65_nucleus = 309.229298924907
dIkBa_mRNA_1_dIkBa_nucleus = 0
dIkBa_mRNA_1_dp65_IkB_nucleus = 0
dIkBa_mRNA_1_dIkBa_mRNA_nucleus = 0
dIkBa_mRNA_1_dIkBa_mRNA_1 = -5.00900035911484
dIkBa_mRNA_2__dIkBa_mRNA_2 = -5.00900035911484
dIkBa_mRNA_2__dp65_nucleus = 0
dIkBa_mRNA_2__dIkBa_nucleus = 0
dIkBa_mRNA_2__dp65_IkB_nucleus = 0
dIkBa_mRNA_2__dIkBa_mRNA_nucleus = 0
dIkBa_mRNA_2__dIkBa_mRNA_1 = 5.00900035911484
dp65_nucleus__dIkBa_mRNA_2 = 0
dp65_nucleus__dp65_nucleus = -8.18761033778361*IkBa_nucleus
dp65_nucleus__dIkBa_nucleus = -8.18761033778361*p65_nucleus
dp65_nucleus__dp65_IkB_nucleus = 0.0605814542035188
dp65_nucleus__dIkBa_mRNA_nucleus = 0
dp65_nucleus__dIkBa_mRNA_1 = 0
dIkBa_nucleus__dIkBa_mRNA_2 = 0
dIkBa_nucleus__dp65_nucleus = -8.18761033778361*IkBa_nucleus
dIkBa_nucleus__dIkBa_nucleus = -0.036018623190168 - 8.18761033778361*p65_nucleus
dIkBa_nucleus__dp65_IkB_nucleus = 0.0245628310133508
dIkBa_nucleus__dIkBa_mRNA_nucleus = 0
dIkBa_nucleus__dIkBa_mRNA_1 = 0
dp65_IkB_nucleus__dIkBa_mRNA_2 = 0
dp65_IkB_nucleus__dp65_nucleus = 8.18761033778361*IkBa_nucleus
dp65_IkB_nucleus__dIkBa_nucleus = 8.18761033778361*p65_nucleus
dp65_IkB_nucleus__dp65_IkB_nucleus = -0.0605814542035188
dp65_IkB_nucleus__dIkBa_mRNA_nucleus = 0
dp65_IkB_nucleus__dIkBa_mRNA_1 = 0
dIkBa_mRNA_nucleus__dIkBa_mRNA_2 = 5.00900035911484
dIkBa_mRNA_nucleus__dp65_nucleus = 0
dIkBa_mRNA_nucleus__dIkBa_nucleus = 0
dIkBa_mRNA_nucleus__dp65_IkB_nucleus = 0
dIkBa_mRNA_nucleus__dIkBa_mRNA_nucleus = -0.497223415385606
dIkBa_mRNA_nucleus__dIkBa_mRNA_1 = 0
dIkBa_mRNA_1__dIkBa_mRNA_2 = 0
dIkBa_mRNA_1__dp65_nucleus = 309.229298924907
dIkBa_mRNA_1__dIkBa_nucleus = 0
dIkBa_mRNA_1__dp65_IkB_nucleus = 0
dIkBa_mRNA_1__dIkBa_mRNA_nucleus = 0
dIkBa_mRNA_1__dIkBa_mRNA_1 = -5.00900035911484
[model.nucleus.diffusion]
IkBa_mRNA_2 = 1
......@@ -253,3 +189,249 @@ IkBa_nucleus = 1
p65_IkB_nucleus = 1
IkBa_mRNA_nucleus = 1
IkBa_mRNA_1 = 1
[model.cytoplasm_nucleus.initial]
p65_cytoplasm = 0.00166609
IkBa_p = 0.234611
IKKb = 0.298668
IKKb_p = 0.00133151
TNFa = 0
p65_IkB_cytoplasm = 0.0411269
IkBa_mRNA_cytoplasm = 0.199202
IkBa_cytoplasm = 1.95156
IkBa_mRNA_2 = 5.14124
p65_nucleus = 0.0832677
IkBa_nucleus = 3.90313
p65_IkB_nucleus = 0.00411473
IkBa_mRNA_nucleus = 0.000133495
IkBa_mRNA_1 = 5.14124
[model.cytoplasm_nucleus.reaction]
p65_cytoplasm = 0.036018623190168*p65_IkB_cytoplasm + 7342.46743032994*IKKb_p*p65_IkB_cytoplasm/(3.13820291340728 + p65_IkB_cytoplasm) - 5e-07*(1.80000128637887*p65_cytoplasm - 0.0360000257275774*p65_nucleus) - 1.0*(-0.0245628310133508*p65_IkB_cytoplasm + 8.18761033778361*p65_cytoplasm*IkBa_cytoplasm)
IkBa_p = -35.9999481926134*IkBa_p + 7342.46743032994*IKKb_p*p65_IkB_cytoplasm/(3.13820291340728 + p65_IkB_cytoplasm) + 6608.22068729695*IKKb_p*IkBa_cytoplasm/(0.112460269242964 + IkBa_cytoplasm)
IKKb = -0.1238783595*IKKb + 27.7868307830501*IKKb_p - 3.65474756811715*TNFa*IKKb/((1.47829 + IKKb)*(99.9998605315951 + TNFa))
IKKb_p = 0.1238783595*IKKb - 27.7868307830501*IKKb_p + 3.65474756811715*TNFa*IKKb/((1.47829 + IKKb)*(99.9998605315951 + TNFa))
TNFa = -0.9*TNFa
p65_IkB_cytoplasm = -0.036018623190168*p65_IkB_cytoplasm - 7342.46743032994*IKKb_p*p65_IkB_cytoplasm/(3.13820291340728 + p65_IkB_cytoplasm) + 5e-07*(-0.0652157388428865*p65_IkB_cytoplasm + 0.652157388428865*p65_IkB_nucleus) + 1.0*(-0.0245628310133508*p65_IkB_cytoplasm + 8.18761033778361*p65_cytoplasm*IkBa_cytoplasm)
IkBa_mRNA_cytoplasm = -4.97223415385606*IkBa_mRNA_cytoplasm + 1.79992399621555e-05*IkBa_mRNA_nucleus
IkBa_cytoplasm = -0.036018623190168*IkBa_cytoplasm + 18.7354723520005*IkBa_mRNA_cytoplasm/(0.238680093564444 + IkBa_mRNA_cytoplasm) - 6608.22068729695*IKKb_p*IkBa_cytoplasm/(0.112460269242964 + IkBa_cytoplasm) - 5e-07*(3.7128132073999*IkBa_cytoplasm - 1.85640660369995*IkBa_nucleus) - 1.0*(-0.0245628310133508*p65_IkB_cytoplasm + 8.18761033778361*p65_cytoplasm*IkBa_cytoplasm)
IkBa_mRNA_2 = 5.00900035911484*IkBa_mRNA_1 - 5.00900035911484*IkBa_mRNA_2
p65_nucleus = 0.036018623190168*p65_IkB_nucleus + 5e-07*(1.80000128637887*p65_cytoplasm - 0.0360000257275774*p65_nucleus) - 1.0*(-0.0245628310133508*p65_IkB_nucleus + 8.18761033778361*IkBa_nucleus*p65_nucleus)
IkBa_nucleus = -0.036018623190168*IkBa_nucleus + 5e-07*(3.7128132073999*IkBa_cytoplasm - 1.85640660369995*IkBa_nucleus) - 1.0*(-0.0245628310133508*p65_IkB_nucleus + 8.18761033778361*IkBa_nucleus*p65_nucleus)
p65_IkB_nucleus = -0.036018623190168*p65_IkB_nucleus - 5e-07*(-0.0652157388428865*p65_IkB_cytoplasm + 0.652157388428865*p65_IkB_nucleus) + 1.0*(-0.0245628310133508*p65_IkB_nucleus + 8.18761033778361*IkBa_nucleus*p65_nucleus)
IkBa_mRNA_nucleus = 5.00900035911484*IkBa_mRNA_2 - 0.497241414625568*IkBa_mRNA_nucleus
IkBa_mRNA_1 = -5.00900035911484*IkBa_mRNA_1 + 1.0*(0.0036897759857015 + 309.229298924907*p65_nucleus)
[model.cytoplasm_nucleus.reaction.jacobian]
dp65_cytoplasm__dp65_cytoplasm = -9.00000643189435e-07 - 8.18761033778361*IkBa_cytoplasm
dp65_cytoplasm__dIkBa_p = 0
dp65_cytoplasm__dIKKb = 0
dp65_cytoplasm__dIKKb_p = 7342.46743032994*p65_IkB_cytoplasm/(3.13820291340728 + p65_IkB_cytoplasm)
dp65_cytoplasm__dTNFa = 0
dp65_cytoplasm__dp65_IkB_cytoplasm = 0.0605814542035188 + 7342.46743032994*IKKb_p/(3.13820291340728 + p65_IkB_cytoplasm) - 7342.46743032994*IKKb_p*p65_IkB_cytoplasm/(3.13820291340728 + p65_IkB_cytoplasm)^2
dp65_cytoplasm__dIkBa_mRNA_cytoplasm = 0
dp65_cytoplasm__dIkBa_cytoplasm = -8.18761033778361*p65_cytoplasm
dp65_cytoplasm__dIkBa_mRNA_2 = 0
dp65_cytoplasm__dp65_nucleus = 1.80000128637887e-08
dp65_cytoplasm__dIkBa_nucleus = 0
dp65_cytoplasm__dp65_IkB_nucleus = 0
dp65_cytoplasm__dIkBa_mRNA_nucleus = 0
dp65_cytoplasm__dIkBa_mRNA_1 = 0
dIkBa_p__dp65_cytoplasm = 0
dIkBa_p__dIkBa_p = -35.9999481926134
dIkBa_p__dIKKb = 0
dIkBa_p__dIKKb_p = 6608.22068729695*IkBa_cytoplasm/(0.112460269242964 + IkBa_cytoplasm) + 7342.46743032994*p65_IkB_cytoplasm/(3.13820291340728 + p65_IkB_cytoplasm)
dIkBa_p__dTNFa = 0
dIkBa_p__dp65_IkB_cytoplasm = 0.0 + 7342.46743032994*IKKb_p/(3.13820291340728 + p65_IkB_cytoplasm) - 7342.46743032994*IKKb_p*p65_IkB_cytoplasm/(3.13820291340728 + p65_IkB_cytoplasm)^2
dIkBa_p__dIkBa_mRNA_cytoplasm = 0
dIkBa_p__dIkBa_cytoplasm = 0.0 + 6608.22068729695*IKKb_p/(0.112460269242964 + IkBa_cytoplasm) - 6608.22068729695*IKKb_p*IkBa_cytoplasm/(0.112460269242964 + IkBa_cytoplasm)^2
dIkBa_p__dIkBa_mRNA_2 = 0
dIkBa_p__dp65_nucleus = 0
dIkBa_p__dIkBa_nucleus = 0
dIkBa_p__dp65_IkB_nucleus = 0
dIkBa_p__dIkBa_mRNA_nucleus = 0
dIkBa_p__dIkBa_mRNA_1 = 0
dIKKb__dp65_cytoplasm = 0
dIKKb__dIkBa_p = 0
dIKKb__dIKKb = -0.1238783595 - 3.65474756811715*TNFa/((1.47829 + IKKb)*(99.9998605315951 + TNFa)) + 3.65474756811715*TNFa*IKKb/((1.47829 + IKKb)^2*(99.9998605315951 + TNFa))
dIKKb__dIKKb_p = 27.7868307830501
dIKKb__dTNFa = 0.0 - 3.65474756811715*IKKb/((1.47829 + IKKb)*(99.9998605315951 + TNFa)) + 3.65474756811715*TNFa*IKKb/((1.47829 + IKKb)*(99.9998605315951 + TNFa)^2)
dIKKb__dp65_IkB_cytoplasm = 0
dIKKb__dIkBa_mRNA_cytoplasm = 0
dIKKb__dIkBa_cytoplasm = 0
dIKKb__dIkBa_mRNA_2 = 0
dIKKb__dp65_nucleus = 0
dIKKb__dIkBa_nucleus = 0
dIKKb__dp65_IkB_nucleus = 0
dIKKb__dIkBa_mRNA_nucleus = 0
dIKKb__dIkBa_mRNA_1 = 0
dIKKb_p__dp65_cytoplasm = 0
dIKKb_p__dIkBa_p = 0
dIKKb_p__dIKKb = 0.1238783595 + 3.65474756811715*TNFa/((1.47829 + IKKb)*(99.9998605315951 + TNFa)) - 3.65474756811715*TNFa*IKKb/((1.47829 + IKKb)^2*(99.9998605315951 + TNFa))
dIKKb_p__dIKKb_p = -27.7868307830501
dIKKb_p__dTNFa = 0.0 + 3.65474756811715*IKKb/((1.47829 + IKKb)*(99.9998605315951 + TNFa)) - 3.65474756811715*TNFa*IKKb/((1.47829 + IKKb)*(99.9998605315951 + TNFa)^2)
dIKKb_p__dp65_IkB_cytoplasm = 0
dIKKb_p__dIkBa_mRNA_cytoplasm = 0
dIKKb_p__dIkBa_cytoplasm = 0
dIKKb_p__dIkBa_mRNA_2 = 0
dIKKb_p__dp65_nucleus = 0
dIKKb_p__dIkBa_nucleus = 0
dIKKb_p__dp65_IkB_nucleus = 0
dIKKb_p__dIkBa_mRNA_nucleus = 0
dIKKb_p__dIkBa_mRNA_1 = 0
dTNFa__dp65_cytoplasm = 0
dTNFa__dIkBa_p = 0
dTNFa__dIKKb = 0
dTNFa__dIKKb_p = 0
dTNFa__dTNFa = -0.9
dTNFa__dp65_IkB_cytoplasm = 0
dTNFa__dIkBa_mRNA_cytoplasm = 0
dTNFa__dIkBa_cytoplasm = 0
dTNFa__dIkBa_mRNA_2 = 0
dTNFa__dp65_nucleus = 0
dTNFa__dIkBa_nucleus = 0
dTNFa__dp65_IkB_nucleus = 0
dTNFa__dIkBa_mRNA_nucleus = 0
dTNFa__dIkBa_mRNA_1 = 0
dp65_IkB_cytoplasm__dp65_cytoplasm = 8.18761033778361*IkBa_cytoplasm
dp65_IkB_cytoplasm__dIkBa_p = 0
dp65_IkB_cytoplasm__dIKKb = 0
dp65_IkB_cytoplasm__dIKKb_p = -7342.46743032994*p65_IkB_cytoplasm/(3.13820291340728 + p65_IkB_cytoplasm)
dp65_IkB_cytoplasm__dTNFa = 0
dp65_IkB_cytoplasm__dp65_IkB_cytoplasm = -0.0605814868113882 - 7342.46743032994*IKKb_p/(3.13820291340728 + p65_IkB_cytoplasm) + 7342.46743032994*IKKb_p*p65_IkB_cytoplasm/(3.13820291340728 + p65_IkB_cytoplasm)^2
dp65_IkB_cytoplasm__dIkBa_mRNA_cytoplasm = 0
dp65_IkB_cytoplasm__dIkBa_cytoplasm = 8.18761033778361*p65_cytoplasm
dp65_IkB_cytoplasm__dIkBa_mRNA_2 = 0
dp65_IkB_cytoplasm__dp65_nucleus = 0
dp65_IkB_cytoplasm__dIkBa_nucleus = 0
dp65_IkB_cytoplasm__dp65_IkB_nucleus = 3.26078694214432e-07
dp65_IkB_cytoplasm__dIkBa_mRNA_nucleus = 0
dp65_IkB_cytoplasm__dIkBa_mRNA_1 = 0
dIkBa_mRNA_cytoplasm__dp65_cytoplasm = 0
dIkBa_mRNA_cytoplasm__dIkBa_p = 0
dIkBa_mRNA_cytoplasm__dIKKb = 0
dIkBa_mRNA_cytoplasm__dIKKb_p = 0
dIkBa_mRNA_cytoplasm__dTNFa = 0
dIkBa_mRNA_cytoplasm__dp65_IkB_cytoplasm = 0
dIkBa_mRNA_cytoplasm__dIkBa_mRNA_cytoplasm = -4.97223415385606
dIkBa_mRNA_cytoplasm__dIkBa_cytoplasm = 0
dIkBa_mRNA_cytoplasm__dIkBa_mRNA_2 = 0
dIkBa_mRNA_cytoplasm__dp65_nucleus = 0
dIkBa_mRNA_cytoplasm__dIkBa_nucleus = 0
dIkBa_mRNA_cytoplasm__dp65_IkB_nucleus = 0
dIkBa_mRNA_cytoplasm__dIkBa_mRNA_nucleus = 1.79992399621555e-05
dIkBa_mRNA_cytoplasm__dIkBa_mRNA_1 = 0
dIkBa_cytoplasm__dp65_cytoplasm = -8.18761033778361*IkBa_cytoplasm
dIkBa_cytoplasm__dIkBa_p = 0
dIkBa_cytoplasm__dIKKb = 0
dIkBa_cytoplasm__dIKKb_p = -6608.22068729695*IkBa_cytoplasm/(0.112460269242964 + IkBa_cytoplasm)
dIkBa_cytoplasm__dTNFa = 0
dIkBa_cytoplasm__dp65_IkB_cytoplasm = 0.0245628310133508
dIkBa_cytoplasm__dIkBa_mRNA_cytoplasm = 0.0 - 18.7354723520005*IkBa_mRNA_cytoplasm/(0.238680093564444 + IkBa_mRNA_cytoplasm)^2 + 18.7354723520005*(0.238680093564444 + IkBa_mRNA_cytoplasm)^(-1)
dIkBa_cytoplasm__dIkBa_cytoplasm = -0.0360204795967717 - 8.18761033778361*p65_cytoplasm - 6608.22068729695*IKKb_p/(0.112460269242964 + IkBa_cytoplasm) + 6608.22068729695*IKKb_p*IkBa_cytoplasm/(0.112460269242964 + IkBa_cytoplasm)^2
dIkBa_cytoplasm__dIkBa_mRNA_2 = 0
dIkBa_cytoplasm__dp65_nucleus = 0
dIkBa_cytoplasm__dIkBa_nucleus = 9.28203301849975e-07
dIkBa_cytoplasm__dp65_IkB_nucleus = 0
dIkBa_cytoplasm__dIkBa_mRNA_nucleus = 0
dIkBa_cytoplasm__dIkBa_mRNA_1 = 0
dIkBa_mRNA_2__dp65_cytoplasm = 0
dIkBa_mRNA_2__dIkBa_p = 0
dIkBa_mRNA_2__dIKKb = 0
dIkBa_mRNA_2__dIKKb_p = 0
dIkBa_mRNA_2__dTNFa = 0
dIkBa_mRNA_2__dp65_IkB_cytoplasm = 0
dIkBa_mRNA_2__dIkBa_mRNA_cytoplasm = 0
dIkBa_mRNA_2__dIkBa_cytoplasm = 0
dIkBa_mRNA_2__dIkBa_mRNA_2 = -5.00900035911484
dIkBa_mRNA_2__dp65_nucleus = 0
dIkBa_mRNA_2__dIkBa_nucleus = 0
dIkBa_mRNA_2__dp65_IkB_nucleus = 0
dIkBa_mRNA_2__dIkBa_mRNA_nucleus = 0
dIkBa_mRNA_2__dIkBa_mRNA_1 = 5.00900035911484
dp65_nucleus__dp65_cytoplasm = 9.00000643189435e-07
dp65_nucleus__dIkBa_p = 0
dp65_nucleus__dIKKb = 0
dp65_nucleus__dIKKb_p = 0
dp65_nucleus__dTNFa = 0
dp65_nucleus__dp65_IkB_cytoplasm = 0
dp65_nucleus__dIkBa_mRNA_cytoplasm = 0
dp65_nucleus__dIkBa_cytoplasm = 0
dp65_nucleus__dIkBa_mRNA_2 = 0
dp65_nucleus__dp65_nucleus = -1.80000128637887e-08 - 8.18761033778361*IkBa_nucleus
dp65_nucleus__dIkBa_nucleus = -8.18761033778361*p65_nucleus
dp65_nucleus__dp65_IkB_nucleus = 0.0605814542035188
dp65_nucleus__dIkBa_mRNA_nucleus = 0
dp65_nucleus__dIkBa_mRNA_1 = 0
dIkBa_nucleus__dp65_cytoplasm = 0
dIkBa_nucleus__dIkBa_p = 0
dIkBa_nucleus__dIKKb = 0
dIkBa_nucleus__dIKKb_p = 0
dIkBa_nucleus__dTNFa = 0
dIkBa_nucleus__dp65_IkB_cytoplasm = 0
dIkBa_nucleus__dIkBa_mRNA_cytoplasm = 0
dIkBa_nucleus__dIkBa_cytoplasm = 1.85640660369995e-06
dIkBa_nucleus__dIkBa_mRNA_2 = 0
dIkBa_nucleus__dp65_nucleus = -8.18761033778361*IkBa_nucleus
dIkBa_nucleus__dIkBa_nucleus = -0.0360195513934699 - 8.18761033778361*p65_nucleus
dIkBa_nucleus__dp65_IkB_nucleus = 0.0245628310133508
dIkBa_nucleus__dIkBa_mRNA_nucleus = 0
dIkBa_nucleus__dIkBa_mRNA_1 = 0
dp65_IkB_nucleus__dp65_cytoplasm = 0
dp65_IkB_nucleus__dIkBa_p = 0
dp65_IkB_nucleus__dIKKb = 0
dp65_IkB_nucleus__dIKKb_p = 0
dp65_IkB_nucleus__dTNFa = 0
dp65_IkB_nucleus__dp65_IkB_cytoplasm = 3.26078694214433e-08
dp65_IkB_nucleus__dIkBa_mRNA_cytoplasm = 0
dp65_IkB_nucleus__dIkBa_cytoplasm = 0
dp65_IkB_nucleus__dIkBa_mRNA_2 = 0
dp65_IkB_nucleus__dp65_nucleus = 8.18761033778361*IkBa_nucleus
dp65_IkB_nucleus__dIkBa_nucleus = 8.18761033778361*p65_nucleus
dp65_IkB_nucleus__dp65_IkB_nucleus = -0.060581780282213
dp65_IkB_nucleus__dIkBa_mRNA_nucleus = 0
dp65_IkB_nucleus__dIkBa_mRNA_1 = 0
dIkBa_mRNA_nucleus__dp65_cytoplasm = 0
dIkBa_mRNA_nucleus__dIkBa_p = 0
dIkBa_mRNA_nucleus__dIKKb = 0
dIkBa_mRNA_nucleus__dIKKb_p = 0
dIkBa_mRNA_nucleus__dTNFa = 0
dIkBa_mRNA_nucleus__dp65_IkB_cytoplasm = 0
dIkBa_mRNA_nucleus__dIkBa_mRNA_cytoplasm = 0
dIkBa_mRNA_nucleus__dIkBa_cytoplasm = 0
dIkBa_mRNA_nucleus__dIkBa_mRNA_2 = 5.00900035911484
dIkBa_mRNA_nucleus__dp65_nucleus = 0
dIkBa_mRNA_nucleus__dIkBa_nucleus = 0
dIkBa_mRNA_nucleus__dp65_IkB_nucleus = 0
dIkBa_mRNA_nucleus__dIkBa_mRNA_nucleus = -0.497241414625568
dIkBa_mRNA_nucleus__dIkBa_mRNA_1 = 0
dIkBa_mRNA_1__dp65_cytoplasm = 0
dIkBa_mRNA_1__dIkBa_p = 0
dIkBa_mRNA_1__dIKKb = 0
dIkBa_mRNA_1__dIKKb_p = 0
dIkBa_mRNA_1__dTNFa = 0
dIkBa_mRNA_1__dp65_IkB_cytoplasm = 0
dIkBa_mRNA_1__dIkBa_mRNA_cytoplasm = 0
dIkBa_mRNA_1__dIkBa_cytoplasm = 0
dIkBa_mRNA_1__dIkBa_mRNA_2 = 0
dIkBa_mRNA_1__dp65_nucleus = 309.229298924907
dIkBa_mRNA_1__dIkBa_nucleus = 0
dIkBa_mRNA_1__dp65_IkB_nucleus = 0
dIkBa_mRNA_1__dIkBa_mRNA_nucleus = 0
dIkBa_mRNA_1__dIkBa_mRNA_1 = -5.00900035911484
[model.cytoplasm_nucleus.diffusion]
p65_cytoplasm = 1
IkBa_p = 1
IKKb = 1
IKKb_p = 1
TNFa = 1
p65_IkB_cytoplasm = 1
IkBa_mRNA_cytoplasm = 1
IkBa_cytoplasm = 1
IkBa_mRNA_2 = 1
p65_nucleus = 1
IkBa_nucleus = 1
p65_IkB_nucleus = 1
IkBa_mRNA_nucleus = 1
IkBa_mRNA_1 = 1
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