yao1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000318) Biomodels notes: Bifurcation diagram as in fig. 1B of the original publication. The diagram was computed using SBW and its Auto2000 frontend (http://sys-bio.org/fbergman/files/latest/SetupAutoWrapper.exe) and gnuplot. JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.
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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 | |
|---|---|---|
| — | 1e-06 mole | |
| — | 3600.0 second | |
| — | 2.7777777777777777e-10 mole litre^(-1.0) second^(-1.0) | |
| — | 1e-06 mole litre^(-1.0) | |
| — | 0.0002777777777777778 second^(-1.0) | |
| — | 277.77777777777777 mole^(-1.0) litre second^(-1.0) | |
| — | 1.0 dimensionless |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| cell | cell | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| CD | CycD | 0.0 | cell (cell) | ✘ | |
| CE | CycE | 0.0 | cell (cell) | ✘ | |
| EF | E2F | 0.0 | cell (cell) | ✘ | |
| MC | Myc | 0.0 | cell (cell) | ✘ | |
| RB | Rb | 0.0 | cell (cell) | ✘ | |
| RE | Rb-E2F complex | 0.55 | cell (cell) | ✘ | |
| RP | phosphorylated Rb | 0.0 | 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 | |
|---|---|---|---|---|---|
| r1 | — | ∅ > MC cell * (kM * S / (KS + S)) | |||
| r10 | — | RP > RB cell * (kkRBUP * RP / (Kp + RP)) | |||
| r11 | — | MC > ∅ cell * dMC * MC | |||
| r12 | — | EF > ∅ cell * dEF * EF | |||
| r13 | — | CE > ∅ cell * dCE * CE | |||
| r14 | — | CD > ∅ cell * dCD * CD | |||
| r15 | — | RB > ∅ cell * dRB * RB | |||
| r16 | — | RP > ∅ cell * dRP * RP | |||
| r17 | — | RE > ∅ cell * dRE * RE | |||
| r2 | — | ∅ > CD cell * (kkCDS * S / (KS + S)) | |||
| r3 | — | ∅ > EF cell * (kkEF * MC * EF / ((KMC + MC) * (KEF + EF)) + kkb * MC / (KMC + MC)) | |||
| r4 | — | ∅ > CE cell * (kkCE * EF / (KEF + EF)) | |||
| r5 | — | ∅ > CD cell * (kkCD * MC / (KMC + MC)) | |||
| r6 | — | ∅ > RB cell * kkRB | |||
| r7 | — | RE > EF + RP cell * (kkRBPP * CD * RE / (KD + RE) + kkRBPP * CE * RE / (KE + RE)) | |||
| r8 | — | EF + RB > RE cell * kkRE * RB * EF | |||
| r9 | — | RB > RP cell * (kkRBP * CD * RB / (KD + RB) + kkRBP2 * CE * RB / (KE + RB)) |
| Id | Value | |
|---|---|---|
| S | 1.0 dimensionless |
| Id | Value | Reaction | |
|---|---|---|---|
| KS | 0.5 dimensionless | r1 | |
| kM | 1.0 uM per hr | r1 | |
| KS | 0.5 dimensionless | r2 | |
| kkCDS | 0.45 uM per hr | r2 | |
| KEF | 0.15 uM | r3 | |
| KMC | 0.15 uM | r3 | |
| kkEF | 0.4 uM per hr | r3 | |
| kkb | 0.003 uM per hr | r3 | |
| KEF | 0.15 uM | r4 | |
| kkCE | 0.35 uM per hr | r4 | |
| KMC | 0.15 uM | r5 | |
| kkCD | 0.03 uM per hr | r5 | |
| kkRB | 0.18 uM per hr | r6 | |
| KD | 0.92 uM | r7 | |
| KE | 0.92 uM | r7 | |
| kkRBPP | 18.0 per hr | r7 | |
| kkRE | 180.0 per_uM per hr | r8 | |
| KD | 0.92 uM | r9 | |
| KE | 0.92 uM | r9 | |
| kkRBP | 18.0 per hr | r9 | |
| kkRBP2 | 18.0 per hr | r9 | |
| Kp | 0.01 uM | r10 | |
| kkRBUP | 3.6 uM per hr | r10 | |
| dMC | 0.7 per hr | r11 | |
| dEF | 0.25 per hr | r12 | |
| dCE | 1.5 per hr | r13 | |
| dCD | 1.5 per hr | r14 | |
| dRB | 0.06 per hr | r15 | |
| dRP | 0.06 per hr | r16 | |
| dRE | 0.03 per hr | r17 |
| Definition |
|---|
| Definition |
|---|
| Definition |
|---|
| Definition |
|---|
| Trigger | Assignments | |
|---|---|---|
| gt(time, 0) | S = 20 | |
| gt(time, 5) | S = 1 |