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_surface + TGFb_R2_surface + S7
reaction17
reaction17
Inactive_Rec > TGFb_R1_surface + 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
S2_c > pS2_c
reaction26
reaction26
{2.0}pS2_c + S4_c > pS2_pS2_S4_c
reaction27
reaction27
pS2_pS2_S4_c > {2.0}pS2_c + S4_c
reaction28
reaction28
{2.0}pS2_n + S4_n > pS2_pS2_S4_n
reaction29
reaction29
pS2_pS2_S4_n > {2.0}pS2_n + S4_n
reaction3
reaction3
∅ > Active_R2
reaction30
reaction30
{3.0}pS2_c > pS2_pS2_pS2_c
reaction31
reaction31
{3.0}pS2_n > pS2_pS2_pS2_n
reaction32
reaction32
pS2_pS2_pS2_n > {3.0}pS2_n
reaction33
reaction33
pS2_pS2_pS2_c > {3.0}pS2_c
reaction34
reaction34
S2_c > S2_n
reaction35
reaction35
S2_n > S2_c
reaction36
reaction36
S4_c > S4_n
reaction37
reaction37
S4_n > S4_c
reaction38
reaction38
pS2_c > pS2_n
reaction39
reaction39
pS2_n > pS2_c
reaction4
reaction4
Active_R2 > ∅
reaction40
reaction40
pS2_pS2_S4_c > pS2_pS2_S4_n
reaction41
reaction41
pS2_pS2_pS2_c > pS2_pS2_pS2_n
reaction42
reaction42
pS2_n > S2_n
reaction43
reaction43
pS2_pS2_S4_n > pS2_n + S2_n + S4_n
reaction44
reaction44
∅ > S2_c
reaction45
reaction45
∅ > S4_c
reaction46
reaction46
∅ > TGFb_R1_surface
reaction47
reaction47
∅ > TGFb_R2_surface
reaction5
reaction5
∅ > TGFb_R2_surface
reaction50
reaction50
∅ > Smad7mRNA1
reaction51
reaction51
Smad7mRNA1 > Smad7mRNA
reaction52
reaction52
∅ > S7
reaction53
reaction53
S2_c > ∅
reaction54
reaction54
S2_n > ∅
reaction55
reaction55
pS2_n > ∅
reaction56
reaction56
pS2_c > ∅
reaction57
reaction57
S4_c > ∅
reaction58
reaction58
S4_n > ∅
reaction59
reaction59
pS2_pS2_S4_c > pS2_c + S4_c
reaction6
reaction6
∅ > TGFb
reaction60
reaction60
pS2_pS2_S4_c > {2.0}pS2_c
reaction61
reaction61
pS2_pS2_pS2_c > {2.0}pS2_c
reaction62
reaction62
pS2_pS2_S4_n > pS2_n + S4_n
reaction63
reaction63
pS2_pS2_S4_n > {2.0}pS2_n
reaction64
reaction64
pS2_pS2_pS2_n > {2.0}pS2_n
reaction65
reaction65
Smad7mRNA1 > ∅
reaction66
reaction66
Smad7mRNA > ∅
reaction67
reaction67
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 = offset_DRB + scale_DRB * ((2.0 * pS2_pS2_S4_n + S2_n + pS2_n + 3.0 * pS2_pS2_pS2_n) / (2.0 * pS2_pS2_S4_c + S2_c + pS2_c + 3.0 * pS2_pS2_pS2_c))
Function definitions
Function_for_reaction25(Active_Rec_endo, S2_c, k_phosphorylation) = Active_Rec_endo * S2_c * k_phosphorylation
Function_for_reaction41(Trimer_import_to_nuc, cyt, pS2_pS2_pS2_c) = cyt * Trimer_import_to_nuc * pS2_pS2_pS2_c
Function_for_reaction52(Smad7mRNA, k_S7_protein) = Smad7mRNA * k_S7_protein
Function_for_reaction39(S2_export_from_nuc, nuc, pS2_n) = nuc * S2_export_from_nuc * pS2_n
Function_for_reaction1(TGFb, TGFb_R2_surface, k_medium, kf_R2_activation) = TGFb * TGFb_R2_surface * kf_R2_activation / k_medium
Function_for_reaction35(S2_export_from_nuc, S2_n, nuc) = nuc * S2_n * S2_export_from_nuc
Function_for_reaction6(Active_R2, index_kb_R2, k_medium, kf_R2_activation) = Active_R2 * index_kb_R2 * kf_R2_activation / k_medium
Function_for_reaction43(index_trimer_dephos, k_Dephos, pS2_pS2_S4_n) = index_trimer_dephos * k_Dephos * pS2_pS2_S4_n
Function_for_reaction33(index_kb_homotrimer, kb_trimmer, pS2_pS2_pS2_c) = index_kb_homotrimer * kb_trimmer * pS2_pS2_pS2_c
Function_for_reaction31_0(index_kf_homotrimer, kf_trimmer, pS2_n) = index_kf_homotrimer * kf_trimmer * pow(pS2_n, 3)
Function_for_reaction51(Smad7mRNA1, export_cytoplasm, nuc) = nuc * Smad7mRNA1 * export_cytoplasm
Function_for_reaction30(index_kf_homotrimer, kf_trimmer, pS2_c) = index_kf_homotrimer * kf_trimmer * pow(pS2_c, 3)
Function_for_reaction38(S2_import_to_nuc, cyt, pS2_c) = cyt * S2_import_to_nuc * pS2_c
Function_for_reaction37(S4_export_from_nuc, S4_n, nuc) = nuc * S4_n * S4_export_from_nuc
Function_for_reaction36(S4_c, S4_import_to_nuc, cyt) = cyt * S4_c * S4_import_to_nuc
Function_for_reaction34(S2_c, S2_import_to_nuc, cyt) = cyt * S2_c * S2_import_to_nuc
Function_for_reaction3(TGFb, TGFb_R2_surface, kf_R2_activation) = TGFb * TGFb_R2_surface * kf_R2_activation
Function_for_reaction40(Trimer_import_to_nuc, cyt, pS2_pS2_S4_c) = cyt * Trimer_import_to_nuc * pS2_pS2_S4_c
Function_for_reaction5(Active_R2, index_kb_R2, kf_R2_activation) = Active_R2 * index_kb_R2 * kf_R2_activation
Function_for_reaction8(Active_Rec, index_kb_R1, kf_R1_activation) = Active_Rec * index_kb_R1 * kf_R1_activation
Function_for_reaction15(Inactive_Rec, index_seq_kb, kf_Seq_S7_Rec) = Inactive_Rec * index_seq_kb * kf_Seq_S7_Rec
Function_for_reaction47_0(R2_total, index_k_out_2_relative_speed, k_in_2, kdeg_R2) = R2_total * k_in_2 * pow(kdeg_R2, 2) / (k_in_2 * kdeg_R2 + pow(kdeg_R2, 2) + index_k_out_2_relative_speed * k_in_2 * kdeg_R2)
Function_for_reaction50_1_0(DRB, K_mran, hill_fact1, k_induced_S7_production, mRNA_prod, pS2_pS2_S4_n) = DRB * (mRNA_prod + k_induced_S7_production * pow(pS2_pS2_S4_n, hill_fact1) / (pow(K_mran, hill_fact1) + pow(pS2_pS2_S4_n, hill_fact1)))
Function_for_reaction32(index_kb_homotrimer, kb_trimmer, pS2_pS2_pS2_n) = index_kb_homotrimer * kb_trimmer * pS2_pS2_pS2_n
Function_for_reaction17(Inactive_Rec, index_induced_R2_deg, kdeg_R2) = Inactive_Rec * index_induced_R2_deg * kdeg_R2
Function_for_reaction16(Inactive_Rec, index_induced_ligand_deg, kin_deg_Ligand) = Inactive_Rec * index_induced_ligand_deg * kin_deg_Ligand
Function_for_reaction46_0(R1_total, index_k_out_1_relative_speed, k_in_1, kdeg_R1) = R1_total * k_in_1 * pow(kdeg_R1, 2) / (k_in_1 * kdeg_R1 + pow(kdeg_R1, 2) + index_k_out_1_relative_speed * k_in_1 * kdeg_R1)
Function_for_reaction4(Active_R2, index_kb_R2, kf_R2_activation) = Active_R2 * index_kb_R2 * kf_R2_activation
Function_for_reaction22(Active_Rec, index_active_Rec_internalize, k_in_1) = Active_Rec * index_active_Rec_internalize * k_in_1
Function_for_reaction21(TGFb_R2_endo, index_k_out_2_relative_speed, k_in_2) = TGFb_R2_endo * index_k_out_2_relative_speed * k_in_2
Function_for_reaction2(TGFb, TGFb_R2_surface, kf_R2_activation) = TGFb * TGFb_R2_surface * kf_R2_activation
Function_for_reaction45_0(S4_export_from_nuc, S4_import_to_nuc, S4_total, kdeg_S4) = S4_total * (S4_import_to_nuc * kdeg_S4 + S4_export_from_nuc * kdeg_S4 + pow(kdeg_S4, 2)) / (2 * S4_import_to_nuc + S4_export_from_nuc + kdeg_S4)
Function_for_reaction44_0(S2_export_from_nuc, S2_import_to_nuc, S2_total, kdeg_S2) = S2_total * (S2_import_to_nuc * kdeg_S2 + S2_export_from_nuc * kdeg_S2 + pow(kdeg_S2, 2)) / (2 * S2_import_to_nuc + S2_export_from_nuc + kdeg_S2)
Function_for_reaction20(TGFb_R1_endo, index_k_out_1_relative_speed, k_in_1) = TGFb_R1_endo * index_k_out_1_relative_speed * k_in_1
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.