neumann1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000243) Biomodels notes: The model reproduces figure 5D of the reference publication. The model as such reproduces the plot corresponding to Anti-CD95 conc. 1500ng/ml (black). To obtain plots corresponding to Anti-CD95 conc. 500ng/ml (blue) and Anti-CD95 conc. 250ng/ml (red), the initial concentration of L should be set as 37.74nM and 18.87nM, respectively. The model was integrated and simulated using Copasi v4.5 (Build 30). JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. Only figures C3, C8, NF-KB:IKB and NF-KB:IKB:P were recreated.
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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 | |
|---|---|---|
| — | 60.0 second | |
| — | 1e-09 mole |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| default | default | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| C3 | C3 | 1.443404 | default (default) | ✘ | |
| C3_star | C3* | 0.0 | default (default) | ✘ | |
| C8 | C8 | 64.47652 | default (default) | ✘ | |
| C8_star | C8* | 0.0 | default (default) | ✘ | |
| FL | FL | 7.398562 | default (default) | ✘ | |
| FS | FS | 5.083923 | default (default) | ✘ | |
| IKK | IKK | 5.772825 | default (default) | ✘ | |
| L | L | 113.22 | default (default) | ✘ | |
| L_RF | L:RF | 0.0 | default (default) | ✘ | |
| L_RF_C8 | L:RF:C8 | 0.0 | default (default) | ✘ | |
| L_RF_C8_FS | L:RF:C8:FS | 0.0 | default (default) | ✘ | |
| L_RF_FL | L:RF:FL | 0.0 | default (default) | ✘ | |
| L_RF_FL_FL | L:RF:FL:FL | 0.0 | default (default) | ✘ | |
| L_RF_FL_FS | L:RF:FL:FS | 0.0 | default (default) | ✘ | |
| L_RF_FS | L:RF:FS | 0.0 | default (default) | ✘ | |
| L_RF_FS_FS | L:RF:FS:FS | 0.0 | default (default) | ✘ | |
| NF_kB_IkB | NF-kB:IkB | 4.739546 | default (default) | ✘ | |
| NF_kB_IkB_P | NF-kB:IkB:P | 0.0 | default (default) | ✘ | |
| NF_kB_star | NF-kB* | 0.0 | default (default) | ✘ | |
| RF | RF | 91.26592 | default (default) | ✘ | |
| p43_FLIP | p43-FLIP | 0.0 | default (default) | ✘ | |
| p43_FLIP_IKK_star | p43-FLIP:IKK* | 0.0 | default (default) | ✘ | |
| p43_p41 | p43/p41 | 0.0 | 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 | |
|---|---|---|---|---|---|
| reaction_1 | reaction_1 | L + RF > L_RF default * k1 * L * RF | |||
| reaction_10 | reaction_10 | L_RF_FL + FS > L_RF_FL_FS default * k7 * L_RF_FL * FS | |||
| reaction_11 | reaction_11 | L_RF_FS + C8 > L_RF_C8_FS default * k5 * L_RF_FS * C8 | |||
| reaction_12 | reaction_12 | L_RF_FS + FL > L_RF_FL_FS default * k6 * L_RF_FS * FL | |||
| reaction_13 | reaction_13 | L_RF_FS + FS > L_RF_FS_FS default * k7 * L_RF_FS * FS | |||
| reaction_14 | reaction_14 | p43_p41 + p43_p41 > C8_star default * k8 * p43_p41 * p43_p41 | |||
| reaction_15 | reaction_15 | C3 + C8_star > C3_star + C8_star default * k9 * C3 * C8_star | |||
| reaction_16 | reaction_16 | C8 + C3_star > p43_p41 + C3_star default * k10 * C8 * C3_star | |||
| reaction_17 | reaction_17 | C8_star > ∅ default * k11 * C8_star | |||
| reaction_18 | reaction_18 | C3_star > ∅ default * k12 * C3_star | |||
| reaction_19 | reaction_19 | p43_FLIP + IKK > p43_FLIP_IKK_star default * k13 * p43_FLIP * IKK | |||
| reaction_2 | reaction_2 | L_RF + C8 > L_RF_C8 default * k2 * L_RF * C8 | |||
| reaction_20 | reaction_20 | NF_kB_IkB + p43_FLIP_IKK_star > NF_kB_IkB_P + p43_FLIP_IKK_star default * k14 * NF_kB_IkB * p43_FLIP_IKK_star | |||
| reaction_21 | reaction_21 | NF_kB_IkB_P > NF_kB_star default * k15 * NF_kB_IkB_P | |||
| reaction_22 | reaction_22 | p43_FLIP_IKK_star > ∅ default * k16 * p43_FLIP_IKK_star | |||
| reaction_23 | reaction_23 | NF_kB_star > ∅ default * k17 * NF_kB_star | |||
| reaction_3 | reaction_3 | L_RF + FL > L_RF_FL default * k3 * L_RF * FL | |||
| reaction_4 | reaction_4 | L_RF + FS > L_RF_FS default * k4 * L_RF * FS | |||
| reaction_5 | reaction_5 | L_RF_C8 + C8 > p43_p41 + p43_p41 default * k5 * L_RF_C8 * C8 | |||
| reaction_6 | reaction_6 | L_RF_C8 + FL > p43_FLIP default * k6 * L_RF_C8 * FL | |||
| reaction_7 | reaction_7 | L_RF_C8 + FS > L_RF_C8_FS default * k7 * L_RF_C8 * FS | |||
| reaction_8 | reaction_8 | L_RF_FL + C8 > p43_FLIP default * k5 * L_RF_FL * C8 | |||
| reaction_9 | reaction_9 | L_RF_FL + FL > L_RF_FL_FL default * k6 * L_RF_FL * FL |
| Id | Value | |
|---|---|---|
| k1 | 1.0 | |
| k10 | 0.1205258 | |
| k11 | 0.02891451 | |
| k12 | 0.1502914 | |
| k13 | 0.0007204261 | |
| k14 | 0.3588224 | |
| k15 | 3.684162 | |
| k16 | 0.02229912 | |
| k17 | 0.0064182 | |
| k2 | 0.0001277248 | |
| k3 | 0.6693316 | |
| k4 | 0.00001 | |
| k5 | 0.0005946569 | |
| k6 | 0.9999999 | |
| k7 | 0.8875063 | |
| k8 | 0.0008044378 | |
| k9 | 0.002249759 |
| Id | Value | Reaction |
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| Definition |
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| Definition |
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| Definition |
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| Definition |
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| Trigger | Assignments |
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