kowald1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000108) Biomodels notes: This model is according to the paper from Axel Kowald Alternative pathways as mechanism for the negative effects associated with overexpression of superoxide dismutase. Reactions from 1 to 17 are listed in the paper, note that for clarity species whose concentrations are assumed to be constant (e.g.water, oxygen,protons, metal ions) are omitted from the diagram. In the paper, v16 is a fast reaction, but we do not use fast reaction in the model. Figure2 has been reproduced by both SBMLodeSolver and Copasi4.0.20(development) . Figure 3 has been obtained with Copasi4.0.20(development) using parameter scan. The steady-state of [LOO*] a little bit lower than showed on the paper, I guess it may be the simulation method used in the paper use fast reaction and also the reaction (5) listed on Page 831 on the paper is slightly different from equation (2) on Page 832. The rest of them are the quite the same. 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 | |
|---|---|
| kowald2006_Fig2 |
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 | |
|---|---|---|---|---|
| compartment_0000001 | cell | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| species_0000001 | O2*- | 0.0 | compartment_0000001 (cell) | ✘ | |
| species_0000002 | Cu(II)ZnSOD | 0.000005 | compartment_0000001 (cell) | ✘ | |
| species_0000006 | H2O2 | 0.0 | compartment_0000001 (cell) | ✘ | |
| species_0000007 | LOO* | 0.0 | compartment_0000001 (cell) | ✘ | |
| species_0000008 | HO* | 0.0 | compartment_0000001 (cell) | ✘ | |
| species_0000009 | LOOH | 0.0 | compartment_0000001 (cell) | ✘ | |
| species_0000011 | L* | 0.0 | compartment_0000001 (cell) | ✘ | |
| species_0000016 | SODtotal | 0.00001 | compartment_0000001 (cell) | ✘ | |
| species_0000017 | Cat | 0.00001 | compartment_0000001 (cell) | ✘ |
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 | |
|---|---|---|---|---|---|
| fast | v16 | species_0000001 = ∅ k10 * HO2star * compartment_0000001 | |||
| reaction_0 | v2 | species_0000001 + species_0000002 > ∅ compartment_0000001 * k2 * species_0000001 * species_0000002 | |||
| reaction_0000001 | v1 | ∅ > species_0000001 compartment_0000001 * k1 | |||
| reaction_1 | v3 | species_0000001 > species_0000006 + species_0000002 compartment_0000001 * k3 * species_0000001 * Cu_I_ZnSOD | |||
| reaction_10 | v13a | ∅ > species_0000002 compartment_0000001 * k13a * Cu_I_ZnSOD | |||
| reaction_11 | v13b | species_0000002 > ∅ compartment_0000001 * k13b * species_0000002 | |||
| reaction_12 | v17 | species_0000011 > species_0000007 compartment_0000001 * k17 * species_0000011 | |||
| reaction_13 | v18 | species_0000007 > species_0000011 + species_0000009 compartment_0000001 * k18 * species_0000007 | |||
| reaction_14 | v19 | {2.0}species_0000007 > ∅ compartment_0000001 * k19 * pow(species_0000007, 2) | |||
| reaction_2 | v4 | species_0000001 + species_0000007 > species_0000009 compartment_0000001 * k4 * species_0000001 * species_0000007 | |||
| reaction_3 | v5 | species_0000001 + species_0000006 > {2.0}species_0000008 compartment_0000001 * k5 * species_0000001 * species_0000006 | |||
| reaction_4 | v6 | species_0000006 > {2.0}species_0000008 compartment_0000001 * k6 * species_0000006 * species_0000002 | |||
| reaction_5 | v7 | species_0000006 > ∅ compartment_0000001 * k7 * species_0000006 * species_0000017 | |||
| reaction_6 | v9 | species_0000008 > ∅ compartment_0000001 * k9 * species_0000008 | |||
| reaction_7 | v10 | ∅ > species_0000011 + species_0000006 compartment_0000001 * k10 * HO2star | |||
| reaction_8 | v11 | species_0000008 > species_0000011 compartment_0000001 * k11 * species_0000008 | |||
| reaction_9 | v12 | species_0000009 > ∅ compartment_0000001 * k12 * species_0000009 |
| Id | Value | |
|---|---|---|
| Cu_I_ZnSOD | 0.0 | |
| HO2star | 0.0 | |
| k1 | 0.00000066 | |
| k10 | 1000.0 | |
| k11 | 250000000.0 | |
| k12 | 0.38 | |
| k13a | 0.0087 | |
| k13b | 0.0087 | |
| k17 | 30000.0 | |
| k18 | 7.0 | |
| k19 | 88000.0 | |
| k2 | 1600000000.0 | |
| k3 | 1600000000.0 | |
| k4 | 100000.0 | |
| k5 | 20000.0 | |
| k6 | 1.0 | |
| k7 | 34000000.0 | |
| k9 | 1000000.0 |
| Id | Value | Reaction |
|---|
| Definition | |
|---|---|
| Cu_I_ZnSOD = species_0000016 - species_0000002 | |
| HO2star = species_0000001 / 100.0 |
| Definition |
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| Definition |
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| Definition |
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| Trigger | Assignments |
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