ehrenstein2
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000553) Biomodels notes: Figure 1 has been reproduced here. Time course of the decline in acetylcholine is plotted ranging different values for k2 parameter. The simulation was done using Copasi v4.12 (Build 81) and the plots were generated using Gnuplot. The Copasi file of the model with simulation settings can be downloaded from the below link. 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 | |
|---|---|---|
| — | 0.001 litre | |
| — | 86400.0 second | |
| — | 0.001 mole |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| Brain | Brain | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| a | a | 50.0 | Brain (Brain) | ✘ | |
| aRel | aRel | 1.0 | Brain (Brain) | ✔ | |
| b | b | 0.0 | Brain (Brain) | ✘ |
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 | |
|---|---|---|---|---|---|
| Abeta_formation_from_APP | Abeta formation from APP | ∅ > b Brain * Constant_flux__irreversible(k2) | |||
| Decrease_in_the_extracellular_concentration_of_beta_amyloid | Decrease in the extracellular concentration of beta-amyloid | b > ∅ Brain * Decrease_in_the_extracellular_concentration_of_beta_amyloid_0(k4, b) | |||
| Effect_of_extracellular_ACh | Effect of extracellular ACh | b > ∅ Brain * Effect_of_extracellular_ACh_0(k3, a) | |||
| Loss_of_intracellular_choline | Loss of intracellular choline | a > ∅ Brain * Loss_of_intracellular_choline_0(k1, a, b) |
| Id | Value | |
|---|---|---|
| k1 | 0.007 | |
| k2 | 0.33 | |
| k3 | 0.0042 | |
| k4 | 0.01 |
| Id | Value | Reaction |
|---|
| Definition | |
|---|---|
| aRel = a / 50.0 |
| Definition |
|---|
| Definition |
|---|
| Definition | |
|---|---|
| Decrease_in_the_extracellular_concentration_of_beta_amyloid_0(k4, b) = k4 * b | |
| Effect_of_extracellular_ACh_0(k3, a) = k3 * a | |
| Loss_of_intracellular_choline_0(k1, a, b) = k1 * a * b | |
| Constant_flux__irreversible(v) = v |
| Trigger | Assignments |
|---|