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strasen11

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Reactions

reaction1

TGFb > ∅

reaction10

Active_Rec_endo > TGFb_R2_endo + TGFb_In

reaction11

Active_Rec_endo > TGFb_R1_endo + TGFb_R2_endo

reaction12

TGFb_R1_endo > ∅

reaction13

TGFb_R2_endo > ∅

reaction14

Active_Rec + S7 > Inactive_Rec

reaction15

Inactive_Rec > Active_Rec + S7

reaction16

Inactive_Rec > TGFb_R1_endo + TGFb_R2_endo + S7

reaction17

Inactive_Rec > TGFb_R1_endo + TGFb_In + S7

reaction18

TGFb_R1_surface > TGFb_R1_endo

reaction19

TGFb_R2_surface > TGFb_R2_endo

reaction2

TGFb_R2_surface > ∅

reaction20

TGFb_R1_endo > TGFb_R1_surface

reaction21

TGFb_R2_endo > TGFb_R2_surface

reaction22

Active_Rec > Active_Rec_endo

reaction23

Active_Rec_endo > TGFb_R1_endo + TGFb_R2_endo + TGFb_In

reaction24

TGFb_In > ∅

reaction25

TGFb > ∅

reaction26

S2_c > pS2_c

reaction27

{2.0}pS2_c + S4_c > pS2_pS2_S4_c

reaction28

pS2_pS2_S4_c > {2.0}pS2_c + S4_c

reaction29

{2.0}pS2_n + S4_n > pS2_pS2_S4_n

reaction3

∅ > Active_R2

reaction30

pS2_pS2_S4_n > {2.0}pS2_n + S4_n

reaction31

{3.0}pS2_c > pS2_pS2_pS2_c

reaction32

pS2_pS2_pS2_c > {3.0}pS2_c

reaction33

{3.0}pS2_n > pS2_pS2_pS2_n

reaction34

pS2_pS2_pS2_n > {3.0}pS2_n

reaction35

S2_c > S2_n

reaction36

S2_n > S2_c

reaction37

S4_c > S4_n

reaction38

S4_n > S4_c

reaction39

pS2_c > pS2_n

reaction4

Active_R2 > ∅

reaction40

pS2_n > pS2_c

reaction41

pS2_pS2_S4_c > pS2_pS2_S4_n

reaction42

pS2_pS2_pS2_c > pS2_pS2_pS2_n

reaction43

pS2_n > S2_n

reaction44

pS2_pS2_S4_n > pS2_n + S2_n + S4_n

reaction45

∅ > S2_c

reaction46

∅ > S4_c

reaction47

∅ > TGFb_R1_surface

reaction48

∅ > TGFb_R2_surface

reaction5

∅ > TGFb_R2_surface

reaction51

∅ > Smad7mRNA1

reaction52

Smad7mRNA1 > Smad7mRNA

reaction53

∅ > S7

reaction54

S2_c > ∅

reaction55

S2_n > ∅

reaction56

pS2_n > ∅

reaction57

pS2_c > ∅

reaction58

S4_c > ∅

reaction59

S4_n > ∅

reaction6

∅ > TGFb

reaction60

pS2_pS2_S4_c > pS2_c + S4_c

reaction61

pS2_pS2_S4_c > {2.0}pS2_c

reaction62

pS2_pS2_pS2_c > {2.0}pS2_c

reaction63

pS2_pS2_S4_n > pS2_n + S4_n

reaction64

pS2_pS2_S4_n > {2.0}pS2_n

reaction65

pS2_pS2_pS2_n > {2.0}pS2_n

reaction66

Smad7mRNA1 > ∅

reaction67

Smad7mRNA > ∅

reaction68

S7 > ∅

reaction7

TGFb_R1_surface + Active_R2 > Active_Rec

reaction8

Active_Rec > TGFb_R1_surface + Active_R2

reaction9

Active_Rec_endo > TGFb_R1_endo + TGFb_In

Parameters

Global parameters

DRB*

K_mran*

R1_total_C6*

R2_total_C6*

S2_export_from_nuc_C6*

S2_import_to_nuc_C6*

S2_total_C6*

S4_export_from_nuc_C6*

S4_import_to_nuc_C6*

S4_total_C6*

S7KD*

Trimer_import_to_nuc*

export_cytoplasm*

hill_fact1*

index_active_Rec_internalize_C6*

index_induced_R2_deg*

index_induced_ligand_deg*

index_k_out_1_relative_speed_C6*

index_k_out_2_relative_speed_C6*

index_kb_R1*

index_kb_R2*

index_kb_homotrimer*

index_kf_homotrimer*

index_seq_kb*

index_trimer_dephos*

k_Dephos_C6*

k_S7_protein_C6*

k_disso_Active_Rec*

k_in_R1_C6*

k_in_R2_C6*

k_induced_S7_production_C6*

k_medium*

k_phosphorylation*

kb_trimmer*

kdeg_R1*

kdeg_R2*

kdeg_S2*

kdeg_S4*

kdeg_S7*

kf_R1_activation*

kf_R2_activation*

kf_Seq_S7_Rec*

kf_trimmer*

kin_deg_Ligand*

kmRNA1deg_S7*

kmRNAdeg_S7*

kout_deg_Ligand_100pM*

mRNA_prod_C6*

cyt*

nuc*

Initial values

Active_R2*

Active_Rec*

Active_Rec_endo*

Inactive_Rec*

S2_c

S2_n

S4_c

S4_n

Smad7mRNA

Smad7mRNA1

TGFb*

TGFb_In*

TGFb_R1_endo

TGFb_R1_surface

TGFb_R2_endo

TGFb_R2_surface

pS2_c*

pS2_n*

pS2_pS2_S4_c*

pS2_pS2_S4_n*

pS2_pS2_pS2_c*

pS2_pS2_pS2_n*

Functions and Rules

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_reaction39_5(S2_import_to_nuc_C6, cyt, pS2_c) = cyt * S2_import_to_nuc_C6 * pS2_c

Function_for_reaction40_5(S2_export_from_nuc_C6, nuc, pS2_n) = nuc * S2_export_from_nuc_C6 * pS2_n

Function_for_reaction5_0(Active_R2, index_kb_R2, kf_R2_activation) = Active_R2 * index_kb_R2 * kf_R2_activation

Function_for_reaction17_0(Inactive_Rec, index_induced_R2_deg, kdeg_R2) = Inactive_Rec * index_induced_R2_deg * kdeg_R2

Function_for_reaction33_2(index_kf_homotrimer, kf_trimmer, pS2_n) = index_kf_homotrimer * kf_trimmer * pow(pS2_n, 3)

Function_for_reaction53_2(Smad7mRNA, k_S7_protein_C6) = Smad7mRNA * k_S7_protein_C6

Function_for_reaction16_0(Inactive_Rec, index_induced_ligand_deg, kin_deg_Ligand) = Inactive_Rec * index_induced_ligand_deg * kin_deg_Ligand

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_reaction1_0(TGFb, TGFb_R2_surface, k_medium, kf_R2_activation) = TGFb * TGFb_R2_surface * kf_R2_activation / k_medium

Function_for_reaction22_4(Active_Rec, index_active_Rec_internalize_C6, k_in_R1_C6) = Active_Rec * index_active_Rec_internalize_C6 * k_in_R1_C6

Function_for_reaction37_5(S4_c, S4_import_to_nuc_C6, cyt) = cyt * S4_c * S4_import_to_nuc_C6

Function_for_reaction38_5(S4_export_from_nuc_C6, S4_n, nuc) = nuc * S4_n * S4_export_from_nuc_C6

Function_for_reaction2_0(TGFb, TGFb_R2_surface, kf_R2_activation) = TGFb * TGFb_R2_surface * 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_reaction36_5(S2_export_from_nuc_C6, S2_n, nuc) = nuc * S2_n * S2_export_from_nuc_C6

Function_for_reaction34_2(index_kb_homotrimer, kb_trimmer, pS2_pS2_pS2_n) = index_kb_homotrimer * kb_trimmer * pS2_pS2_pS2_n

Function_for_reaction52_3(Smad7mRNA1, export_cytoplasm, nuc) = nuc * Smad7mRNA1 * export_cytoplasm

Function_for_reaction26_0(Active_Rec_endo, S2_c, k_phosphorylation) = Active_Rec_endo * S2_c * k_phosphorylation

Function_for_reaction42_0(Trimer_import_to_nuc, cyt, pS2_pS2_pS2_c) = cyt * Trimer_import_to_nuc * pS2_pS2_pS2_c

Function_for_reaction32_3(index_kb_homotrimer, kb_trimmer, pS2_pS2_pS2_c) = index_kb_homotrimer * kb_trimmer * pS2_pS2_pS2_c

Function_for_reaction41_2(Trimer_import_to_nuc, cyt, pS2_pS2_S4_c) = cyt * Trimer_import_to_nuc * pS2_pS2_S4_c

Function_for_reaction4_0(Active_R2, index_kb_R2, kf_R2_activation) = Active_R2 * index_kb_R2 * kf_R2_activation

Function_for_reaction51_4(DRB, K_mran, S7KD, hill_fact1, k_induced_S7_production_C6, mRNA_prod_C6, pS2_pS2_S4_n) = DRB * S7KD * (mRNA_prod_C6 + k_induced_S7_production_C6 * pow(pS2_pS2_S4_n, hill_fact1) / (pow(K_mran, hill_fact1) + pow(pS2_pS2_S4_n, hill_fact1)))

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_reaction35_5(S2_c, S2_import_to_nuc_C6, cyt) = cyt * S2_c * S2_import_to_nuc_C6

Function_for_reaction21_4(TGFb_R2_endo, index_k_out_2_relative_speed_C6, k_in_R2_C6) = TGFb_R2_endo * index_k_out_2_relative_speed_C6 * k_in_R2_C6

Function_for_reaction47_5(R1_total_C6, index_k_out_1_relative_speed_C6, k_in_R1_C6, kdeg_R1) = R1_total_C6 * k_in_R1_C6 * pow(kdeg_R1, 2) / (k_in_R1_C6 * kdeg_R1 + pow(kdeg_R1, 2) + index_k_out_1_relative_speed_C6 * k_in_R1_C6 * kdeg_R1)

Function_for_reaction20_4(TGFb_R1_endo, index_k_out_1_relative_speed_C6, k_in_R1_C6) = TGFb_R1_endo * index_k_out_1_relative_speed_C6 * k_in_R1_C6

Function_for_reaction46_5(S4_export_from_nuc_C6, S4_import_to_nuc_C6, S4_total_C6, kdeg_S4) = S4_total_C6 * (S4_import_to_nuc_C6 * kdeg_S4 + S4_export_from_nuc_C6 * kdeg_S4 + pow(kdeg_S4, 2)) / (2 * S4_import_to_nuc_C6 + S4_export_from_nuc_C6 + kdeg_S4)

Function_for_reaction44_5(index_trimer_dephos, k_Dephos_C6, pS2_pS2_S4_n) = index_trimer_dephos * k_Dephos_C6 * pS2_pS2_S4_n

Function_for_reaction48_2(R2_total_C6, index_k_out_2_relative_speed_C6, k_in_R2_C6, kdeg_R2) = R2_total_C6 * k_in_R2_C6 * pow(kdeg_R2, 2) / (k_in_R2_C6 * kdeg_R2 + pow(kdeg_R2, 2) + index_k_out_2_relative_speed_C6 * k_in_R2_C6 * kdeg_R2)

Function_for_reaction45_5(S2_export_from_nuc_C6, S2_import_to_nuc_C6, S2_total_C6, kdeg_S2) = S2_total_C6 * (S2_import_to_nuc_C6 * kdeg_S2 + S2_export_from_nuc_C6 * kdeg_S2 + pow(kdeg_S2, 2)) / (2 * S2_import_to_nuc_C6 + S2_export_from_nuc_C6 + kdeg_S2)

Function_for_reaction8_0(Active_Rec, index_kb_R1, kf_R1_activation) = Active_Rec * index_kb_R1 * kf_R1_activation

Events

Constraints

Note that constraints are not enforced in simulations. It remains the responsibility of the user to verify that simulation results satisfy these constraints.

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JWS Online documentation

Active_R2 (Active_R2)
Active_Rec (Active_Rec)
Active_Rec_endo (Active_Rec_endo)
Inactive_Rec (Inactive_Rec)
S2_c (S2_c)
S2_n (S2_n)
S4_c (S4_c)
S4_n (S4_n)
S7 (S7)
Smad7mRNA (Smad7mRNA)
Smad7mRNA1 (Smad7mRNA1)
TGFb (TGFb)
TGFb_In (TGFb_In)
TGFb_R1_endo (TGFb_R1_endo)
TGFb_R1_surface (TGFb_R1_surface)
TGFb_R2_endo (TGFb_R2_endo)
TGFb_R2_surface (TGFb_R2_surface)
pS2_c (pS2_c)
pS2_n (pS2_n)
pS2_pS2_S4_c (pS2_pS2_S4_c)
pS2_pS2_S4_n (pS2_pS2_S4_n)
pS2_pS2_pS2_c (pS2_pS2_pS2_c)
pS2_pS2_pS2_n (pS2_pS2_pS2_n)

reaction1 (reaction1)
reaction10 (reaction10)
reaction11 (reaction11)
reaction12 (reaction12)
reaction13 (reaction13)
reaction14 (reaction14)
reaction15 (reaction15)
reaction16 (reaction16)
reaction17 (reaction17)
reaction18 (reaction18)
reaction19 (reaction19)
reaction2 (reaction2)
reaction20 (reaction20)
reaction21 (reaction21)
reaction22 (reaction22)
reaction23 (reaction23)
reaction24 (reaction24)
reaction25 (reaction25)
reaction26 (reaction26)
reaction27 (reaction27)
reaction28 (reaction28)
reaction29 (reaction29)
reaction3 (reaction3)
reaction30 (reaction30)
reaction31 (reaction31)
reaction32 (reaction32)
reaction33 (reaction33)
reaction34 (reaction34)
reaction35 (reaction35)
reaction36 (reaction36)
reaction37 (reaction37)
reaction38 (reaction38)
reaction39 (reaction39)
reaction4 (reaction4)
reaction40 (reaction40)
reaction41 (reaction41)
reaction42 (reaction42)
reaction43 (reaction43)
reaction44 (reaction44)
reaction45 (reaction45)
reaction46 (reaction46)
reaction47 (reaction47)
reaction48 (reaction48)
reaction5 (reaction5)
reaction51 (reaction51)
reaction52 (reaction52)
reaction53 (reaction53)
reaction54 (reaction54)
reaction55 (reaction55)
reaction56 (reaction56)
reaction57 (reaction57)
reaction58 (reaction58)
reaction59 (reaction59)
reaction6 (reaction6)
reaction60 (reaction60)
reaction61 (reaction61)
reaction62 (reaction62)
reaction63 (reaction63)
reaction64 (reaction64)
reaction65 (reaction65)
reaction66 (reaction66)
reaction67 (reaction67)
reaction68 (reaction68)
reaction7 (reaction7)
reaction8 (reaction8)
reaction9 (reaction9)

strasen11

Reactions

reaction1

reaction10

reaction11

reaction12

reaction13

reaction14

reaction15

reaction16

reaction17

reaction18

reaction19

reaction2

reaction20

reaction21

reaction22

reaction23

reaction24

reaction25

reaction26

reaction27

reaction28

reaction29

reaction3

reaction30

reaction31

reaction32

reaction33

reaction34

reaction35

reaction36

reaction37

reaction38

reaction39

reaction4

reaction40

reaction41

reaction42

reaction43

reaction44

reaction45

reaction46

reaction47

reaction48

reaction5

reaction51

reaction52

reaction53

reaction54

reaction55

reaction56

reaction57

reaction58

reaction59

reaction6

reaction60

reaction61

reaction62

reaction63

reaction64

reaction65

reaction66

reaction67

reaction68

reaction7

reaction8

reaction9

Parameters

Fixed species

Initial values

Functions and Rules

Assignment rules

Function definitions

Events

Constraints