reaction1
reaction1
TGFb > ∅
reaction10
reaction10
Active_Rec_endo > TGFb_R2_endo + TGFb_In
reaction11
reaction11
Active_Rec_endo > TGFb_R1_endo + TGFb_R2_endo
reaction12
reaction12
TGFb_R1_endo > ∅
reaction13
reaction13
TGFb_R2_endo > ∅
reaction14
reaction14
Active_Rec + S7 > Inactive_Rec
reaction15
reaction15
Inactive_Rec > Active_Rec + S7
reaction16
reaction16
Inactive_Rec > TGFb_R1_endo + TGFb_R2_endo + S7
reaction17
reaction17
Inactive_Rec > TGFb_R1_endo + TGFb_In + S7
reaction18
reaction18
TGFb_R1_surface > TGFb_R1_endo
reaction19
reaction19
TGFb_R2_surface > TGFb_R2_endo
reaction2
reaction2
TGFb_R2_surface > ∅
reaction20
reaction20
TGFb_R1_endo > TGFb_R1_surface
reaction21
reaction21
TGFb_R2_endo > TGFb_R2_surface
reaction22
reaction22
Active_Rec > Active_Rec_endo
reaction23
reaction23
Active_Rec_endo > TGFb_R1_endo + TGFb_R2_endo + TGFb_In
reaction24
reaction24
TGFb_In > ∅
reaction25
reaction25
TGFb > ∅
reaction26
reaction26
S2_c > pS2_c
reaction27
reaction27
{2.0}pS2_c + S4_c > pS2_pS2_S4_c
reaction28
reaction28
pS2_pS2_S4_c > {2.0}pS2_c + S4_c
reaction29
reaction29
{2.0}pS2_n + S4_n > pS2_pS2_S4_n
reaction3
reaction3
∅ > Active_R2
reaction30
reaction30
pS2_pS2_S4_n > {2.0}pS2_n + S4_n
reaction31
reaction31
{3.0}pS2_c > pS2_pS2_pS2_c
reaction32
reaction32
pS2_pS2_pS2_c > {3.0}pS2_c
reaction33
reaction33
{3.0}pS2_n > pS2_pS2_pS2_n
reaction34
reaction34
pS2_pS2_pS2_n > {3.0}pS2_n
reaction35
reaction35
S2_c > S2_n
reaction36
reaction36
S2_n > S2_c
reaction37
reaction37
S4_c > S4_n
reaction38
reaction38
S4_n > S4_c
reaction39
reaction39
pS2_c > pS2_n
reaction4
reaction4
Active_R2 > ∅
reaction40
reaction40
pS2_n > pS2_c
reaction41
reaction41
pS2_pS2_S4_c > pS2_pS2_S4_n
reaction42
reaction42
pS2_pS2_pS2_c > pS2_pS2_pS2_n
reaction43
reaction43
pS2_n > S2_n
reaction44
reaction44
pS2_pS2_S4_n > pS2_n + S2_n + S4_n
reaction45
reaction45
∅ > S2_c
reaction46
reaction46
∅ > S4_c
reaction47
reaction47
∅ > TGFb_R1_surface
reaction48
reaction48
∅ > TGFb_R2_surface
reaction5
reaction5
∅ > TGFb_R2_surface
reaction51
reaction51
∅ > Smad7mRNA1
reaction52
reaction52
Smad7mRNA1 > Smad7mRNA
reaction53
reaction53
∅ > S7
reaction54
reaction54
S2_c > ∅
reaction55
reaction55
S2_n > ∅
reaction56
reaction56
pS2_n > ∅
reaction57
reaction57
pS2_c > ∅
reaction58
reaction58
S4_c > ∅
reaction59
reaction59
S4_n > ∅
reaction6
reaction6
∅ > TGFb
reaction60
reaction60
pS2_pS2_S4_c > pS2_c + S4_c
reaction61
reaction61
pS2_pS2_S4_c > {2.0}pS2_c
reaction62
reaction62
pS2_pS2_pS2_c > {2.0}pS2_c
reaction63
reaction63
pS2_pS2_S4_n > pS2_n + S4_n
reaction64
reaction64
pS2_pS2_S4_n > {2.0}pS2_n
reaction65
reaction65
pS2_pS2_pS2_n > {2.0}pS2_n
reaction66
reaction66
Smad7mRNA1 > ∅
reaction67
reaction67
Smad7mRNA > ∅
reaction68
reaction68
S7 > ∅
reaction7
reaction7
TGFb_R1_surface + Active_R2 > Active_Rec
reaction8
reaction8
Active_Rec > TGFb_R1_surface + Active_R2
reaction9
reaction9
Active_Rec_endo > TGFb_R1_endo + TGFb_In
Assignment rules
NUC_CYT_SMAD2 = (2.0 * pS2_pS2_S4_n + pS2_n + S2_n + 3.0 * pS2_pS2_pS2_n) / (2.0 * pS2_pS2_S4_c + pS2_c + S2_c + 3.0 * pS2_pS2_pS2_c)
Function definitions
Function_for_reaction53(Smad7mRNA, k_S7_protein_C5) = Smad7mRNA * k_S7_protein_C5
Function_for_reaction35(S2_c, S2_import_to_nuc_C5, cyt) = cyt * S2_c * S2_import_to_nuc_C5
Function_for_reaction21(TGFb_R2_endo, index_k_out_2_relative_speed_C5, k_in_R2_C5) = TGFb_R2_endo * index_k_out_2_relative_speed_C5 * k_in_R2_C5
Function_for_reaction1_0(TGFb, TGFb_R2_surface, k_medium, kf_R2_activation) = TGFb * TGFb_R2_surface * kf_R2_activation / k_medium
Function_for_reaction17_0(Inactive_Rec, index_induced_R2_deg, kdeg_R2) = Inactive_Rec * index_induced_R2_deg * kdeg_R2
Function_for_reaction6_0(Active_R2, index_kb_R2, k_medium, kf_R2_activation) = Active_R2 * index_kb_R2 * kf_R2_activation / k_medium
Function_for_reaction3_0(TGFb, TGFb_R2_surface, kf_R2_activation) = TGFb * TGFb_R2_surface * kf_R2_activation
Function_for_reaction15_0(Inactive_Rec, index_seq_kb, kf_Seq_S7_Rec) = Inactive_Rec * index_seq_kb * kf_Seq_S7_Rec
Function_for_reaction4_0(Active_R2, index_kb_R2, kf_R2_activation) = Active_R2 * index_kb_R2 * kf_R2_activation
Function_for_reaction5_0(Active_R2, index_kb_R2, kf_R2_activation) = Active_R2 * index_kb_R2 * kf_R2_activation
Function_for_reaction31_2(index_kf_homotrimer, kf_trimmer, pS2_c) = index_kf_homotrimer * kf_trimmer * pow(pS2_c, 3)
Function_for_reaction26_0(Active_Rec_endo, S2_c, k_phosphorylation) = Active_Rec_endo * S2_c * k_phosphorylation
Function_for_reaction52_3(Smad7mRNA1, export_cytoplasm, nuc) = nuc * Smad7mRNA1 * export_cytoplasm
Function_for_reaction32_3(index_kb_homotrimer, kb_trimmer, pS2_pS2_pS2_c) = index_kb_homotrimer * kb_trimmer * pS2_pS2_pS2_c
Function_for_reaction37(S4_c, S4_import_to_nuc_C5, cyt) = cyt * S4_c * S4_import_to_nuc_C5
Function_for_reaction48(R2_total_C5, index_k_out_2_relative_speed_C5, k_in_R2_C5, kdeg_R2) = R2_total_C5 * k_in_R2_C5 * pow(kdeg_R2, 2) / (k_in_R2_C5 * kdeg_R2 + pow(kdeg_R2, 2) + index_k_out_2_relative_speed_C5 * k_in_R2_C5 * kdeg_R2)
Function_for_reaction38(S4_export_from_nuc_C5, S4_n, nuc) = nuc * S4_n * S4_export_from_nuc_C5
Function_for_reaction44(index_trimer_dephos, k_Dephos_C5, pS2_pS2_S4_n) = index_trimer_dephos * k_Dephos_C5 * pS2_pS2_S4_n
Function_for_reaction22(Active_Rec, index_active_Rec_internalize_C5, k_in_R1_C5) = Active_Rec * index_active_Rec_internalize_C5 * k_in_R1_C5
Function_for_reaction36(S2_export_from_nuc_C5, S2_n, nuc) = nuc * S2_n * S2_export_from_nuc_C5
Function_for_reaction40(S2_export_from_nuc_C5, nuc, pS2_n) = nuc * S2_export_from_nuc_C5 * pS2_n
Function_for_reaction42_0(Trimer_import_to_nuc, cyt, pS2_pS2_pS2_c) = cyt * Trimer_import_to_nuc * pS2_pS2_pS2_c
Function_for_reaction33_2(index_kf_homotrimer, kf_trimmer, pS2_n) = index_kf_homotrimer * kf_trimmer * pow(pS2_n, 3)
Function_for_reaction41_2(Trimer_import_to_nuc, cyt, pS2_pS2_S4_c) = cyt * Trimer_import_to_nuc * pS2_pS2_S4_c
Function_for_reaction51(K_mran, S7KD, hill_fact1, k_induced_S7_production_C5, mRNA_prod_C5, pS2_pS2_S4_n) = S7KD * (mRNA_prod_C5 + k_induced_S7_production_C5 * pow(pS2_pS2_S4_n, hill_fact1) / (pow(K_mran, hill_fact1) + pow(pS2_pS2_S4_n, hill_fact1)))
Function_for_reaction45(S2_export_from_nuc_C5, S2_import_to_nuc_C5, S2_total_C5, kdeg_S2) = S2_total_C5 * (S2_import_to_nuc_C5 * kdeg_S2 + S2_export_from_nuc_C5 * kdeg_S2 + pow(kdeg_S2, 2)) / (2 * S2_import_to_nuc_C5 + S2_export_from_nuc_C5 + kdeg_S2)
Function_for_reaction47(R1_total_C5, index_k_out_1_relative_speed_C5, k_in_R1_C5, kdeg_R1) = R1_total_C5 * k_in_R1_C5 * pow(kdeg_R1, 2) / (k_in_R1_C5 * kdeg_R1 + pow(kdeg_R1, 2) + index_k_out_1_relative_speed_C5 * k_in_R1_C5 * kdeg_R1)
Function_for_reaction46(S4_export_from_nuc_C5, S4_import_to_nuc_C5, S4_total_C5, kdeg_S4) = S4_total_C5 * (S4_import_to_nuc_C5 * kdeg_S4 + S4_export_from_nuc_C5 * kdeg_S4 + pow(kdeg_S4, 2)) / (2 * S4_import_to_nuc_C5 + S4_export_from_nuc_C5 + kdeg_S4)
Function_for_reaction34_2(index_kb_homotrimer, kb_trimmer, pS2_pS2_pS2_n) = index_kb_homotrimer * kb_trimmer * pS2_pS2_pS2_n
Function_for_reaction39(S2_import_to_nuc_C5, cyt, pS2_c) = cyt * S2_import_to_nuc_C5 * pS2_c
Function_for_reaction20(TGFb_R1_endo, index_k_out_1_relative_speed_C5, k_in_R1_C5) = TGFb_R1_endo * index_k_out_1_relative_speed_C5 * k_in_R1_C5
Function_for_reaction8_0(Active_Rec, index_kb_R1, kf_R1_activation) = Active_Rec * index_kb_R1 * kf_R1_activation
Function_for_reaction16_0(Inactive_Rec, index_induced_ligand_deg, kin_deg_Ligand) = Inactive_Rec * index_induced_ligand_deg * kin_deg_Ligand
Function_for_reaction2_0(TGFb, TGFb_R2_surface, kf_R2_activation) = TGFb * TGFb_R2_surface * kf_R2_activation
Note that constraints are not enforced in simulations. It remains the responsibility of the user to verify that simulation results satisfy these constraints.
No manuscript information is available for this model.
No additional notes are available for this model.