nyman3
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000423) Biomodels notes: The model reproduces figure 5b,5c and 5d of the reference publication. The y-axis of the plots in the paper are rescaled. To reproduce the plot in the paper, 1) multiply model variable measIRp by a scaling factor of 31.8, 2) multiply model variable measIRS1 by a scaling factor of 21.2 and 3) multiply model variable IRmem by a scaling factor of 10. The model simulation was done using Copasi v4.8 (Build 35). The data were obtained from Copasi and plotted using Gnuplot. JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.
None
None
None
None
None
None
| Simulation | |
|---|---|
| nyman2012_Fig5 |
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 |
|---|
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| default | default | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| IR | IR | 8.94067597532632 | default (default) | ✘ | |
| IRS | IRS | 9.43998194225544 | default (default) | ✘ | |
| IRSiP | IRSiP | 0.560018057744573 | default (default) | ✘ | |
| IRi | IRi | 0.00000483863890758515 | default (default) | ✘ | |
| IRiP | IRiP | 0.424076631823384 | default (default) | ✘ | |
| IRins | IRins | 0.59688996214639 | default (default) | ✘ | |
| IRp | IRp | 0.0383525925240207 | default (default) | ✘ | |
| X | X | 9.99635886407151 | default (default) | ✘ | |
| Xp | Xp | 0.00364113592848386 | default (default) | ✘ |
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 | v1a | IR > IRins k1a * ins * IR + k1aBasic * IR | |||
| v1b | v1b | IRins > IR k1b * IRins | |||
| v1c | v1c | IRins > IRp k1c * IRins | |||
| v1d | v1d | IRp > IRiP k1d * IRp | |||
| v1e | v1e | IRiP > IRi IRiP * (k1e + k1f * Xp / (1 + Xp)) | |||
| v1g | v1g | IRp > IR k1g * IRp | |||
| v1r | v1r | IRi > IR k1r * IRi | |||
| v2 | v2 | IRS > IRSiP k21 * IRS * (IRp + k22 * IRiP) / (1 + km23 * Xp) | |||
| v3 | v3 | X > Xp k3 * X * IRSiP | |||
| vm2 | vm2 | IRSiP > IRS km2 * IRSiP | |||
| vm3 | vm3 | Xp > X km3 * Xp |
| Id | Value | |
|---|---|---|
| IRmem | 0.0 | |
| ins | 100.0 | |
| k1a | 0.153418 | |
| k1aBasic | 0.0383389 | |
| k1b | 0.0000034699 | |
| k1c | 0.574266 | |
| k1d | 4.78844 | |
| k1e | 0.0000525027 | |
| k1f | 119.353 | |
| k1g | 4.14899 | |
| k1r | 37954.7 | |
| k21 | 538004.0 | |
| k22 | 0.0000017252 | |
| k3 | 0.0000862917 | |
| km2 | 262759.0 | |
| km23 | 88.9096 | |
| km3 | 0.132671 | |
| measIRS1 | 0.0 | |
| measIRp | 0.0 |
| Id | Value | Reaction |
|---|
| Definition | |
|---|---|
| IRmem = (IRp + IRins + IR) * 10.0 | |
| measIRp = (IRp + IRiP) * 31.8 | |
| measIRS1 = IRSiP * 21.2 |
| Definition |
|---|
| Definition |
|---|
| Definition |
|---|
| Trigger | Assignments |
|---|