ferreira1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000053) Biomodels notes: The model should reproduce the figure 2F of the article. The equation 7 has been split into equations 7a-7c, in order to take into account the different flux rates of Lysine and CML formation from Schiff. The model was tested in Jarnac (SBML L2 V1) and Copasi (SBML L2 V3). The model reproduces the time profiles of Amadori and CML for oxidative conditions as shown in Fig 2 F. Please note that the variables are expressed as a fraction of total lysine. 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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| Simulation | |
|---|---|
| ferreira2003_Fig2F |
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 | |
|---|---|---|
| — | 3600.0 second |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| compartment | — | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| Amadori | — | 0.0 | compartment | ✘ | |
| CML | — | 0.0 | compartment | ✘ | |
| Glucose | — | 0.25 | compartment | ✘ | |
| Glyoxal | — | 0.0 | compartment | ✘ | |
| Lysine | — | 0.0034 | compartment | ✘ | |
| Schiff | — | 0.0 | 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 | |
|---|---|---|---|---|---|
| v1a | — | Lysine + Glucose > Schiff compartment * p1 * k1a * Glucose * Lysine | |||
| v1b | — | Schiff > Lysine + Glucose compartment * k1b * Schiff | |||
| v2a | — | Schiff > Amadori compartment * p2 * k2a * Schiff | |||
| v2b | — | Amadori > Schiff compartment * p2 * k2b * Amadori | |||
| v3 | — | Glucose > Glyoxal compartment * ox * p3 * k3 * pow(Glucose / 0.25, 0.36) | |||
| v4 | — | Amadori > CML compartment * ox * p4 * k4 * Amadori | |||
| v5 | — | Lysine + Glyoxal > CML compartment * ox * p5 * k5 * Glyoxal * Lysine | |||
| v5b | — | Glyoxal > ∅ compartment * k5b * Glyoxal | |||
| v6 | — | Schiff > CML compartment * ox * p6 * k3 * pow(Schiff / 0.25, 0.36) | |||
| v7a | — | ∅ > Lysine compartment * 0.05 * ox * p7 * k3 * pow(Schiff / 0.25, 0.36) | |||
| v7b | — | ∅ > Glyoxal compartment * 0.005 * ox * p7 * k3 * pow(Schiff / 0.25, 0.36) | |||
| v7c | — | Schiff > ∅ compartment * ox * p7 * k3 * pow(Schiff / 0.25, 0.36) |
| Id | Value | |
|---|---|---|
| Fraction_Amadori | 0.0 | |
| Fraction_CML | 0.0 |
| Id | Value | Reaction | |
|---|---|---|---|
| p1 | 0.115 | v1a | |
| k1a | 0.09 | v1a | |
| k1b | 0.36 | v1b | |
| p2 | 0.75 | v2a | |
| k2a | 0.033 | v2a | |
| p2 | 0.75 | v2b | |
| k2b | 0.0012 | v2b | |
| ox | 1.0 | v3 | |
| p3 | 1.0 | v3 | |
| k3 | 0.000000792 | v3 | |
| ox | 1.0 | v4 | |
| p4 | 1.0 | v4 | |
| k4 | 0.000086 | v4 | |
| ox | 1.0 | v5 | |
| p5 | 1.0 | v5 | |
| k5 | 0.019 | v5 | |
| k5b | 0.0017 | v5b | |
| ox | 1.0 | v6 | |
| p6 | 2.7 | v6 | |
| k3 | 0.000000792 | v6 | |
| ox | 1.0 | v7a | |
| p7 | 60.0 | v7a | |
| k3 | 0.000000792 | v7a | |
| ox | 1.0 | v7b | |
| p7 | 60.0 | v7b | |
| k3 | 0.000000792 | v7b | |
| ox | 1.0 | v7c | |
| p7 | 60.0 | v7c | |
| k3 | 0.000000792 | v7c |
| Definition | |
|---|---|
| Fraction_Amadori = Amadori / 0.0034 | |
| Fraction_CML = CML / 0.0034 |
| Definition |
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| Definition |
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| Definition |
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| Trigger | Assignments |
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