deback1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000435) Biomodels notes: Figure 3d of the reference publication has been reproduced here. Xi and Xj denote the expression of pro-endocrine transcription factor Ngn3 (neurogenin-3) in cells i and j, respectively. Yi and Yj denote the expression of transcription factor Ptf1a (Pancreas-specific transcription factor 1 subunit alpha) in cells i and j, respectively. The model was simulated using Copasi v4.8 (Build 35). The plot was generated using 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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| Simulation | |
|---|---|
| deback2012_Fig3D |
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_1 | compartment | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| species_1 | Xi | 0.0 | compartment_1 (compartment) | ✘ | |
| species_2 | Yi | 0.0 | compartment_1 (compartment) | ✘ | |
| species_3 | Xj | 0.0 | compartment_1 (compartment) | ✘ | |
| species_4 | Yj | 0.0 | compartment_1 (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 | Xi expr | ∅ > species_1 compartment_1 * function_1(theta, a, species_3, n) | |||
| reaction_2 | Xi degr | species_1 > ∅ compartment_1 * k1 * species_1 | |||
| reaction_3 | Yi expr | ∅ > species_2 compartment_1 * function_2(theta, b, species_2, species_4, n, c, species_1) | |||
| reaction_4 | Yi degr | species_2 > ∅ compartment_1 * k1 * species_2 | |||
| reaction_5 | Xj expr | ∅ > species_3 compartment_1 * function_1(theta, a, species_1, n) | |||
| reaction_6 | Xj degr | species_3 > ∅ compartment_1 * k1 * species_3 | |||
| reaction_7 | Yj expr | ∅ > species_4 compartment_1 * function_2(theta, b, species_2, species_4, n, c, species_3) | |||
| reaction_8 | Yj degr | species_4 > ∅ compartment_1 * k1 * species_4 |
| Id | Value |
|---|
| Id | Value | Reaction | |
|---|---|---|---|
| theta | 0.0001 | reaction_1 (Xi expr) | |
| a | 1.0 | reaction_1 (Xi expr) | |
| n | 4.0 | reaction_1 (Xi expr) | |
| k1 | 1.0 | reaction_2 (Xi degr) | |
| theta | 0.0001 | reaction_3 (Yi expr) | |
| b | 21.0 | reaction_3 (Yi expr) | |
| n | 4.0 | reaction_3 (Yi expr) | |
| c | 1.0 | reaction_3 (Yi expr) | |
| k1 | 1.0 | reaction_4 (Yi degr) | |
| theta | 0.0001 | reaction_5 (Xj expr) | |
| a | 1.0 | reaction_5 (Xj expr) | |
| n | 4.0 | reaction_5 (Xj expr) | |
| k1 | 1.0 | reaction_6 (Xj degr) | |
| theta | 0.0001 | reaction_7 (Yj expr) | |
| b | 21.0 | reaction_7 (Yj expr) | |
| n | 4.0 | reaction_7 (Yj expr) | |
| c | 1.0 | reaction_7 (Yj expr) | |
| k1 | 1.0 | reaction_8 (Yj degr) |
| Definition |
|---|
| Definition |
|---|
| Definition |
|---|
| Definition | |
|---|---|
| function_1(theta, a, Xj, n) = theta / (theta + a * pow(Xj, n)) | |
| function_2(theta, b, Yi, Yj, n, c, Xi) = (theta + b * pow(Yi * Yj, n)) / (theta + c * pow(Xi, n) + b * pow(Yi * Yj, n)) |
| Trigger | Assignments |
|---|