nakakuki2
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000251) Biomodels notes: reproduction of the 10 nM HRG stimlations depicted in figures 4BCD of the original publication. The results were obtained using SBML ODESolver. JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.
None
None
None
None
None
None
| Simulation | |
|---|---|
| nakakuki2010_Fig4 |
Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.
| Name | Definition | |
|---|---|---|
| — | 0.001 litre | |
| — | 60.0 second | |
| — | 0.001 mole |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| compartment | compartment | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| DUSP | DUSP | 0.0 | compartment (compartment) | ✘ | |
| cFOS | cFOS | 0.0 | compartment (compartment) | ✘ | |
| cFOSm | cFOSmRNA | 0.0 | compartment (compartment) | ✘ | |
| cFOSp | cFOS preRNA | 0.0 | compartment (compartment) | ✘ | |
| pRSKn | pRSKn | 0.0 | compartment (compartment) | ✘ | |
| pcFOS | pc-FOS | 0.0 | compartment (compartment) | ✘ | |
| ppERKc | ppERK(cytosol) | 0.0 | compartment (compartment) | ✔ | |
| ppERKn | ppERK(nucleus) | 0.0 | compartment (compartment) | ✘ | |
| x1 | x1 | 0.0 | compartment (compartment) | ✘ | |
| x2 | x2 | 0.0 | compartment (compartment) | ✘ |
Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.
| Definition |
|---|
| Id | Name | Objective coefficient | Reaction Equation and Kinetic Law | Flux bounds | |
|---|---|---|---|---|---|
| reaction_1 | 1 PhIM 1 | ∅ > x1 compartment * (-x1 / tau1 + K1 * L / tau1) | |||
| reaction_2 | 1 PhIM 2 | ∅ > x2 compartment * (-x2 / tau2 + K2 * L / tau2) | |||
| reaction_3 | 2a ppERKn | ∅ > ppERKn compartment * (k1 * ppERKc - k2 * ppERKn - k3 * DUSP * ppERKn) | |||
| reaction_4 | 2b DUSP | ∅ > DUSP compartment * k * ppERKn | |||
| reaction_5 | 3 pRSKn | ∅ > pRSKn compartment * (k4 * ppERKn - k5 * pRSKn) | |||
| reaction_6 | 4 cFOSp | ∅ > cFOSp compartment * (pow(ppERKn * pRSKn, n) / (pow(k6, n) + pow(ppERKn * pRSKn, n)) - k7 * cFOSp) | |||
| reaction_7 | 5 cFOSm | ∅ > cFOSm compartment * (k7 * cFOSp - k8 * cFOSm) | |||
| reaction_8 | 6 cFOS | ∅ > cFOS compartment * (k9 * cFOSm - k10 * cFOS - k11 * cFOS * ppERKc + k13 * pcFOS) | |||
| reaction_9 | 7 pcFOS | ∅ > pcFOS compartment * (k11 * cFOS * ppERKc - k12 * pcFOS - k13 * pcFOS) |
| Id | Value | |
|---|---|---|
| K1 | 1.09 | |
| K2 | 2.89 | |
| L | 1.0 | |
| k11 | 0.11 | |
| k13 | 0.06 | |
| k7 | 0.5 | |
| tau1 | 3.07 | |
| tau2 | 472.0 |
| Id | Value | Reaction | |
|---|---|---|---|
| k1 | 15.0 | reaction_3 (2a ppERKn) | |
| k2 | 50.0 | reaction_3 (2a ppERKn) | |
| k3 | 14.0 | reaction_3 (2a ppERKn) | |
| k | 1.0 | reaction_4 (2b DUSP) | |
| k4 | 0.1 | reaction_5 (3 pRSKn) | |
| k5 | 0.15 | reaction_5 (3 pRSKn) | |
| k6 | 0.13 | reaction_6 (4 cFOSp) | |
| n | 1.1 | reaction_6 (4 cFOSp) | |
| k8 | 0.08 | reaction_7 (5 cFOSm) | |
| k10 | 0.3 | reaction_8 (6 cFOS) | |
| k9 | 0.3 | reaction_8 (6 cFOS) | |
| k12 | 0.001 | reaction_9 (7 pcFOS) |
| Definition | |
|---|---|
| ppERKc = x1 - x2 |
| Definition |
|---|
| Definition |
|---|
| Definition |
|---|
| Trigger | Assignments |
|---|