goldbeter6
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000079) Biomodels notes: This model is according to the paper of A model for the dynamics of human weight cycling by A. Goldbeter 2006.The figure3 (A) and (B) have been reproduced by Copasi 4.0.19 (development) and SBMLodeSolver. The writer of the paper did not specify any units for the metabolites, so the creator of the model did not define the units as well. Both Q and R are normalized to vary between 0 and 1. Reproduction of figures 3 A and B from the original publication using Copasi 4.5. The units in fig 3 are not correct. JWS Online curation: Figure 3A was curated.
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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 | |
|---|---|---|
| — | 604800.0 second | |
| — | 1.0 dimensionless |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| body | body | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| P | P | 0.0 | body (body) | ✘ | |
| Q | Q | 0.0 | body (body) | ✘ | |
| R | R | 0.0 | body (body) | ✘ |
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_0 | Increase of P | ∅ > P body * function_0(a, Q) | |||
| reaction_1 | Decrease of P | P > ∅ function_1(V, P, Km) | |||
| reaction_2 | Increase of Q | ∅ > Q function_2(V1, Q, K1) | |||
| reaction_3 | Decrease of Q | Q > ∅ function_3(V2, R, Q, K2) | |||
| reaction_4 | Increase of R | ∅ > R function_4(P, V3, R, k3) | |||
| reaction_5 | Decrease of R | R > ∅ function_1(V, R, Km) |
| Id | Value |
|---|
| Id | Value | Reaction | |
|---|---|---|---|
| Km | 0.01 | reaction_5 (Decrease of R) | |
| k3 | 0.01 | reaction_4 (Increase of R) | |
| a | 0.1 | reaction_0 (Increase of P) | |
| V | 0.1 | reaction_1 (Decrease of P) | |
| Km | 0.2 | reaction_1 (Decrease of P) | |
| V1 | 1.0 | reaction_2 (Increase of Q) | |
| K1 | 0.01 | reaction_2 (Increase of Q) | |
| V2 | 1.5 | reaction_3 (Decrease of Q) | |
| K2 | 0.01 | reaction_3 (Decrease of Q) | |
| V3 | 6.0 | reaction_4 (Increase of R) | |
| V | 2.5 | reaction_5 (Decrease of R) |
| Definition |
|---|
| Definition |
|---|
| Definition |
|---|
| Definition | |
|---|---|
| function_4(P, V3, R, k3) = P * V3 * (1 - R) / (k3 + (1 - R)) | |
| function_0(a, Q) = a * Q | |
| function_1(V, substrate, Km) = V * substrate / (Km + substrate) | |
| function_2(V1, Q, K1) = V1 * (1 - Q) / (K1 + (1 - Q)) | |
| function_3(V2, R, Q, K2) = V2 * R * Q / (K2 + Q) |
| Trigger | Assignments |
|---|