goldbeter3
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000004) Biomodels notes: This model represents the inactive forms of CDC-2 Kinase and Cyclin Protease as separate species, unlike the ODEs in the published paper, in which the equations for the inactive forms are substituted into the equations for the active forms using a mass conservation rule M+MI=1,X+XI=1. Mass is still conserved in this model through the explicit reactions M<->MI and X<->XI. The terms in the kinetic laws are identical to the corresponding terms in the kinetic laws in the published paper. JWS Online curation: This model reproduces Figure 3, similar to goldbeter2.
None
None
None
None
None
None
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 |
|---|
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| cell | cell | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| C | Cyclin | 0.01 | cell (cell) | ✘ | |
| M | Active CDC-2 Kinase | 0.01 | cell (cell) | ✘ | |
| MI | Inactive CDC-2 Kinase | 0.99 | cell (cell) | ✘ | |
| X | Active Cyclin Protease | 0.01 | cell (cell) | ✘ | |
| XI | Inactive Cyclin Protease | 0.99 | cell (cell) | ✘ |
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 | |
|---|---|---|---|---|---|
| reaction1 | creation of cyclin | ∅ > C cell * vi | |||
| reaction2 | default degradation of cyclin | C > ∅ C * cell * kd | |||
| reaction3 | cdc2 kinase triggered degration of cyclin | C > ∅ C * cell * vd * X * pow(C + Kd, -1) | |||
| reaction4 | activation of cdc2 kinase | MI > M cell * MI * V1 * pow(K1 + MI, -1) | |||
| reaction5 | deactivation of cdc2 kinase | M > MI cell * M * V2 * pow(K2 + M, -1) | |||
| reaction6 | activation of cyclin protease | XI > X cell * V3 * XI * pow(K3 + XI, -1) | |||
| reaction7 | deactivation of cyclin protease | X > XI cell * V4 * X * pow(K4 + X, -1) |
| Id | Value | |
|---|---|---|
| Kc | 0.5 | |
| V1 | 0.0 | |
| V3 | 0.0 | |
| VM1 | 3.0 | |
| VM3 | 1.0 |
| Id | Value | Reaction | |
|---|---|---|---|
| vd | 0.25 | reaction3 (cdc2 kinase triggered degration of cyclin) | |
| vi | 0.025 | reaction1 (creation of cyclin) | |
| kd | 0.01 | reaction2 (default degradation of cyclin) | |
| Kd | 0.02 | reaction3 (cdc2 kinase triggered degration of cyclin) | |
| K1 | 0.005 | reaction4 (activation of cdc2 kinase) | |
| V2 | 1.5 | reaction5 (deactivation of cdc2 kinase) | |
| K2 | 0.005 | reaction5 (deactivation of cdc2 kinase) | |
| K3 | 0.005 | reaction6 (activation of cyclin protease) | |
| K4 | 0.005 | reaction7 (deactivation of cyclin protease) | |
| V4 | 0.5 | reaction7 (deactivation of cyclin protease) |
| Definition | |
|---|---|
| V3 = M * VM3 | |
| V1 = C * VM1 * pow(C + Kc, -1.0) |
| Definition |
|---|
| Definition |
|---|
| Definition |
|---|
| Trigger | Assignments |
|---|