Physiology
Reaction Diagram
Cross-References
Annotations
Structures
PM Universal ID's
PM Text Annotations
cytoplasm Universal ID's
cytoplasm Text Annotations
EC Universal ID's
EC Text Annotations
Species
| Name | Structure | BioNetGen Definition | Depiction |
|---|---|---|---|
| L_EC | EC | Oxo_EC(). | |
| R | PM | M1R(L!-,S228~u!-,S273~u!-,Arr!-,GRK!-,PP1!-,CK2!-,). | |
| RL | PM | Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!-,GRK!-,PP1!-,CK2!-,). | |
| Arrestin | cytoplasm | Arrestin(RLP!-,MEK!-,PP2A!-,). | |
| RLPP_A | PM | Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!-,PP2A!-,). | |
| RLPPA_M | PM | Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!3,PP2A!-,).MEK(Arr!3,ERK!-,). | |
| ERK | cytoplasm | ERK(MEK!-,s~u!-,PP2A!-,PP1!-,). | |
| MEK | cytoplasm | MEK(Arr!-,ERK!-,). | |
| PP2A | cytoplasm | PP2A(Arrestin!-,ERK!-,). | |
| pERK | cytoplasm | pERK(MEK!-,s~p!-,PP2A!-,PP1!-,). | |
| RLppA_ME | PM | Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!3,PP2A!-,).MEK(Arr!3,ERK!4,).ERK(MEK!4,s~u!-,PP2A!-,PP1!-,). | |
| RLppA_MpE | PM | Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!3,PP2A!-,).MEK(Arr!3,ERK!4,).pERK(MEK!4,s~p!-,PP2A!-,PP1!-,). | |
| RL_A | PM | Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!-,PP2A!-,). | |
| RL_A_PP2A | PM | Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!-,PP2A!3,).PP2A(Arrestin!3,ERK!-,). | |
| ERK_KTR_probe | cytoplasm | probe(site~u!-,). | |
| phos_ERK_KTR_probe | cytoplasm | phos_probe(Site0~p!-,). | |
| GRK | PM | GRK(RL!-,). | |
| RLGRK | PM | Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!-,GRK!2,PP1!-,CK2!-,).GRK(RL!2,). | |
| RLGRKpp | PM | Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!-,GRK!2,PP1!-,CK2!-,).GRK(RL!2,). | |
| RLpp | PM | Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!-,GRK!-,PP1!-,CK2!-,). | |
| RL_A_PP2A_pERK | PM | Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!-,PP2A!3,).PP2A(Arrestin!3,ERK!4,).pERK(MEK!-,s~p!-,PP2A!4,PP1!-,). | |
| RL_A_PP2A_ERK | PM | Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!2,GRK!-,PP1!-,CK2!-,).Arrestin(RLP!2,MEK!-,PP2A!3,).PP2A(Arrestin!3,ERK!4,).ERK(MEK!-,s~u!-,PP2A!4,PP1!-,). | |
| RL_PP1_pool | PM | Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!-,GRK!-,PP1!2,CK2!-,).PP1(RL!2,). | |
| PP1 | cytoplasm | PP1(RL!-,). | |
| CK2 | cytoplasm | CK2(RL!-,). | |
| RL_CK2 | PM | Oxo(R!1,).M1R(L!1,S228~u!-,S273~u!-,Arr!-,GRK!-,PP1!-,CK2!2,).CK2(RL!2,). | |
| RLpp_CK2 | PM | Oxo(R!1,).M1R(L!1,S228~p!-,S273~p!-,Arr!-,GRK!-,PP1!-,CK2!2,).CK2(RL!2,). |
L_EC Universal ID's
L_EC Text Annotations
R Universal ID's
R Text Annotations
RL Universal ID's
RL Text Annotations
Arrestin Universal ID's
Arrestin Text Annotations
RLPP_A Universal ID's
RLPP_A Text Annotations
RLPPA_M Universal ID's
RLPPA_M Text Annotations
ERK Universal ID's
ERK Text Annotations
MEK Universal ID's
MEK Text Annotations
PP2A Universal ID's
PP2A Text Annotations
pERK Universal ID's
pERK Text Annotations
RLppA_ME Universal ID's
RLppA_ME Text Annotations
RLppA_MpE Universal ID's
RLppA_MpE Text Annotations
RL_A Universal ID's
RL_A Text Annotations
RL_A_PP2A Universal ID's
RL_A_PP2A Text Annotations
ERK_KTR_probe Universal ID's
ERK_KTR_probe Text Annotations
phos_ERK_KTR_probe Universal ID's
phos_ERK_KTR_probe Text Annotations
GRK Universal ID's
GRK Text Annotations
RLGRK Universal ID's
RLGRK Text Annotations
RLGRKpp Universal ID's
RLGRKpp Text Annotations
RLpp Universal ID's
RLpp Text Annotations
RL_A_PP2A_pERK Universal ID's
RL_A_PP2A_pERK Text Annotations
RL_A_PP2A_ERK Universal ID's
RL_A_PP2A_ERK Text Annotations
RL_PP1_pool Universal ID's
RL_PP1_pool Text Annotations
PP1 Universal ID's
PP1 Text Annotations
CK2 Universal ID's
CK2 Text Annotations
RL_CK2 Universal ID's
RL_CK2 Text Annotations
RLpp_CK2 Universal ID's
RLpp_CK2 Text Annotations
Molecules
| Name | BioNetGen Definition | DEPICTION |
|---|---|---|
| M1R | M1R(L,S228~u~p,S273~u~p,Arr,GRK,PP1,CK2,) | |
| Oxo | Oxo(R,) | |
| Arrestin | Arrestin(RLP,MEK,PP2A,) | |
| MEK | MEK(Arr,ERK,) | |
| ERK | ERK(MEK,s~u,PP2A,PP1,) | |
| pERK | pERK(MEK,s~p,PP2A,PP1,) | |
| Oxo_EC | Oxo_EC() | |
| PP2A | PP2A(Arrestin,ERK,) | |
| probe | probe(site~u,) | |
| phos_probe | phos_probe(Site0~p,) | |
| GRK | GRK(RL,) | |
| PP1 | PP1(RL,) | |
| CK2 | CK2(RL,) |
M1R Universal ID's
M1R Text Annotations
Oxo Universal ID's
Oxo Text Annotations
Arrestin Universal ID's
Arrestin Text Annotations
MEK Universal ID's
MEK Text Annotations
ERK Universal ID's
ERK Text Annotations
pERK Universal ID's
pERK Text Annotations
Oxo_EC Universal ID's
Oxo_EC Text Annotations
PP2A Universal ID's
PP2A Text Annotations
probe Universal ID's
probe Text Annotations
phos_probe Universal ID's
phos_probe Text Annotations
GRK Universal ID's
GRK Text Annotations
PP1 Universal ID's
PP1 Text Annotations
CK2 Universal ID's
CK2 Text Annotations
Observables
| Name | Structure | Count | BNGL Definition | Sequence Type | DEPICTION | ||||
|---|---|---|---|---|---|---|---|---|---|
| O0_M1R_tot | PM | Molecules | M1R(L!-,S228!-,S273!-,Arr!-,GRK!-,PP1!-,CK2!-,). | Multimolecular | |||||
| O0_Oxo_EC | EC | Molecules | Oxo(R!-,). | Multimolecular | |||||
| O0_Arrestin | cytoplasm | Molecules | Arrestin(RLP!-,MEK!-,PP2A!-,). | Multimolecular | |||||
| O0_RLPPA | PM | Molecules | Oxo(R!1,). | M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!-,PP1!-,CK2!-,). | Arrestin(RLP!2,MEK!-,PP2A!-,). | Multimolecular | |||
| O0_MEK | cytoplasm | Molecules | MEK(Arr!-,ERK!-,). | Multimolecular | |||||
| O0_ERK | cytoplasm | Molecules | ERK(MEK!-,s~u!-,PP2A!-,PP1!-,). | Multimolecular | |||||
| O0_pERK | cytoplasm | Molecules | pERK(MEK!-,s~p!-,PP2A!-,PP1!-,). | Multimolecular | |||||
| O0_RLPPA_M | PM | Molecules | Oxo(R!1,). | M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!-,PP1!-,CK2!-,). | Arrestin(RLP!2,MEK!3,PP2A!-,). | MEK(Arr!3,ERK!-,). | Multimolecular | ||
| O0_RLPP | PM | Molecules | Oxo(R!1,). | M1R(L!1,S228~p!-,S273~p!-,Arr!-,GRK!-,PP1!-,CK2!-,). | Multimolecular | ||||
| O0_RLA | PM | Molecules | Oxo(R!1,). | M1R(L!1,S228~u!-,S273~u!-,Arr!2,GRK!-,PP1!-,CK2!-,). | Arrestin(RLP!2,MEK!-,PP2A!-,). | Multimolecular | |||
| O0_Oxo_EC_tot | cytoplasm | Molecules | Oxo_EC(). | Multimolecular | |||||
| O0_PP2A_tot | cytoplasm | Molecules | PP2A(Arrestin!-,ERK!-,). | Multimolecular | |||||
| O0_RLAPP2A | PM | Molecules | Oxo(R!1,). | M1R(L!1,S228~u!-,S273~u!-,Arr!2,GRK!-,PP1!-,CK2!-,). | Arrestin(RLP!2,MEK!-,PP2A!3,). | PP2A(Arrestin!3,ERK!-,). | Multimolecular | ||
| O0_RLppAME | PM | Molecules | Oxo(R!1,). | M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!-,PP1!-,CK2!-,). | Arrestin(RLP!2,MEK!3,PP2A!-,). | MEK(Arr!3,ERK!4,). | ERK(MEK!4,s~u!-,PP2A!?,PP1!?,). | Multimolecular | |
| O0_RLppAMpE | PM | Molecules | Oxo(R!1,). | M1R(L!1,S228~p!-,S273~p!-,Arr!2,GRK!-,PP1!-,CK2!-,). | Arrestin(RLP!2,MEK!3,PP2A!-,). | MEK(Arr!3,ERK!4,). | pERK(MEK!4,s~p!-,PP2A!?,PP1!?,). | Multimolecular | |
| O0_probe_tot | cytoplasm | Molecules | probe(site!?,). | Multimolecular | |||||
| O0_phos_probe_tot | cytoplasm | Molecules | phos_probe(Site0!?,). | Multimolecular | |||||
| O0_GRK_tot | EC | Molecules | GRK(RL!?,). | Multimolecular | |||||
| O0_PP1_tot | cytoplasm | Molecules | PP1(RL!?,). | Multimolecular | |||||
| O0_CK2_tot | cytoplasm | Molecules | CK2(RL!?,). | Multimolecular |
O0_M1R_tot Universal ID's
O0_M1R_tot Text Annotations
O0_Oxo_EC Universal ID's
O0_Oxo_EC Text Annotations
O0_Arrestin Universal ID's
O0_Arrestin Text Annotations
O0_RLPPA Universal ID's
O0_RLPPA Text Annotations
O0_MEK Universal ID's
O0_MEK Text Annotations
O0_ERK Universal ID's
O0_ERK Text Annotations
O0_pERK Universal ID's
O0_pERK Text Annotations
O0_RLPPA_M Universal ID's
O0_RLPPA_M Text Annotations
O0_RLPP Universal ID's
O0_RLPP Text Annotations
O0_RLA Universal ID's
O0_RLA Text Annotations
O0_Oxo_EC_tot Universal ID's
O0_Oxo_EC_tot Text Annotations
O0_PP2A_tot Universal ID's
O0_PP2A_tot Text Annotations
O0_RLAPP2A Universal ID's
O0_RLAPP2A Text Annotations
O0_RLppAME Universal ID's
O0_RLppAME Text Annotations
O0_RLppAMpE Universal ID's
O0_RLppAMpE Text Annotations
O0_probe_tot Universal ID's
O0_probe_tot Text Annotations
O0_phos_probe_tot Universal ID's
O0_phos_probe_tot Text Annotations
O0_GRK_tot Universal ID's
O0_GRK_tot Text Annotations
O0_PP1_tot Universal ID's
O0_PP1_tot Text Annotations
O0_CK2_tot Universal ID's
O0_CK2_tot Text Annotations
Applications
| Name | Properties | Math Type | Annotation |
|---|---|---|---|
| Deterministic |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental |
Deterministic Universal ID's
Deterministic Text Annotations
Specifications (Species) - Deterministic go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| Arrestin | 15.0 [uM] | 0.0 [um2/s] | cytoplasm |
| ERK | 1.0 [uM] | 0.0 [um2/s] | cytoplasm |
| MEK | 1.0 [uM] | 0.0 [um2/s] | cytoplasm |
| PP2A | 5.0 [uM] | 0.0 [um2/s] | cytoplasm |
| pERK | 0.1 [uM] | 0.0 [um2/s] | cytoplasm |
| ERK_KTR_probe | 5.0 [uM] | 0.0 [um2/s] | cytoplasm |
| phos_ERK_KTR_probe | 5.0 [uM] | 0.0 [um2/s] | cytoplasm |
| PP1 | 1.0 [uM] | 0.0 [um2/s] | cytoplasm |
| CK2 | 1.0 [uM] | 0.0 [um2/s] | cytoplasm |
| L_EC | 100.0 [uM] | 0.0 [um2/s] | EC |
| R | 3500.0 [uM] | 0.0 [um2/s] | PM |
| RL | 0.0 [uM] | 0.0 [um2/s] | PM |
| RLPP_A | 0.0 [uM] | 0.0 [um2/s] | PM |
| RLPPA_M | 0.0 [uM] | 0.0 [um2/s] | PM |
| RLppA_ME | 0.0 [uM] | 0.0 [um2/s] | PM |
| RLppA_MpE | 0.0 [uM] | 0.0 [um2/s] | PM |
| RL_A | 0.0 [uM] | 0.0 [um2/s] | PM |
| RL_A_PP2A | 0.0 [uM] | 0.0 [um2/s] | PM |
| GRK | 10.0 [uM] | 0.0 [um2/s] | PM |
| RLGRK | 0.0 [uM] | 0.0 [um2/s] | PM |
| RLGRKpp | 0.0 [uM] | 0.0 [um2/s] | PM |
| RLpp | 0.0 [uM] | 0.0 [um2/s] | PM |
| RL_A_PP2A_pERK | 0.0 [uM] | 0.0 [um2/s] | PM |
| RL_A_PP2A_ERK | 0.0 [uM] | 0.0 [um2/s] | PM |
| RL_PP1_pool | 0.0 [uM] | 0.0 [um2/s] | PM |
| RL_CK2 | 0.0 [uM] | 0.0 [um2/s] | PM |
| RLpp_CK2 | 0.0 [uM] | 0.0 [um2/s] | PM |
Specifications (Reaction) - Deterministic go to Simulations
Simulations - Deterministic go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation0 | 900.0 |
KeepEvery 1 KeepAtMost 1000 |
Deterministic Universal ID's
Deterministic Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry non-spatial334277079
(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0 [um])
| Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
|---|---|---|---|---|---|
| Compartmental | Compartment | PM |
Events
| Name | Variable | Rate Expression |
|---|
Global Parameters
| Name | Expression |
|---|---|
| start | 60.0[s] |
| end | 540.0[s] |
| time | 60.0[s-1] |
| washing_agonist | ((1.0 * (t > 60.0)) && (t < 540.0))[s-1.uM-1] |
| on_set | 1.0[s-1] |
| off_set | (0.0 * (t > 480.0))[1] |
| converting_factor | 0.0[s-1] |
| Dephos_factor | 0.1[s-1.uM-1] |
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Downloads
| Model Format | Model Downloads |
|---|---|
| Virtual Cell Markup Language | VCML File |
| PDF Report | Report |
| COMBINE Archive | OMEX File |
| SEDML | SEDML File |
| File Format | Application Downloads |
| BNGL | Deterministic.bngl |
| SBML | Deterministic.sbml |
| Matlab | Deterministic.m |
| NFSim XML | Deterministic.xml |