kallenberger1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000523) Biomodels notes: This model contain the equations for one "average cell" with median initial concentrations for CD95, FADD, p55, BID, PrNES_mCherry and PrER_mGFP. Figure 4A in the reference publication gives the simulation and experimental results of several cells (80 different cells). As this model is a "average cell" model, trajectories similar to that of Figure 4A has been reproduced, but for the ligand concentration of 500ng/ml (CD95L = 16.6nM (500ng/ml)). The simulation results are checked with the authors. 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 |
|---|
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| cell | cell | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| Bid | Bid | 236.0 | cell (cell) | ✘ | |
| CD95 | CD95 | 116.0 | cell (cell) | ✘ | |
| CD95L | CD95L | 16.6 | cell (cell) | ✘ | |
| DISC | DISC | 0.0 | cell (cell) | ✘ | |
| DISCp55 | DISCp55 | 0.0 | cell (cell) | ✘ | |
| FADD | FADD | 93.0 | cell (cell) | ✘ | |
| PrER | PrER | 0.0 | cell (cell) | ✘ | |
| PrER_mGFP | PrER_mGFP | 5178.0 | cell (cell) | ✘ | |
| PrNES | PrNES | 0.0 | cell (cell) | ✘ | |
| PrNES_mCherry | PrNES_mCherry | 973.0 | cell (cell) | ✘ | |
| mCherry | mCherry | 0.0 | cell (cell) | ✘ | |
| mGFP | mGFP | 0.0 | cell (cell) | ✘ | |
| p18 | p18 | 0.0 | cell (cell) | ✘ | |
| p18inactive | p18inactive | 0.0 | cell (cell) | ✘ | |
| p30 | p30 | 0.0 | cell (cell) | ✘ | |
| p43 | p43 | 0.0 | cell (cell) | ✘ | |
| p55free | p55free | 155.0 | cell (cell) | ✘ | |
| tBid | tBid | 0.0 | cell (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 | |
|---|---|---|---|---|---|
| reaction_1 | — | FADD > DISC kon_FADD * CD95act * FADD * cell | |||
| reaction_10 | — | p18 > p18inactive kdiss_p18 * p18 * cell | |||
| reaction_11 | — | Bid > tBid kBid * Bid * (p43 + p18) * cell | |||
| reaction_12 | — | PrNES_mCherry > PrNES + mCherry kD374probe * PrNES_mCherry * (p43 + p18) * cell | |||
| reaction_13 | — | PrER_mGFP > PrER + mGFP kD374probe * PrER_mGFP * p18 * cell | |||
| reaction_2 | — | DISC > FADD koff_FADD * DISC * cell | |||
| reaction_3 | — | p55free + DISC > DISCp55 kDISC * p55free * DISC * cell | |||
| reaction_4 | — | DISCp55 > p30 kD216 * DISCp55 * cell | |||
| reaction_5 | — | p43 > p18 + DISC kD216 * p43 * cell | |||
| reaction_6 | — | DISCp55 > p43 kD374trans_p55 * DISCp55 * (DISCp55 + p30) * cell | |||
| reaction_7 | — | DISCp55 > p43 kD374trans_p43 * DISCp55 * p43 * cell | |||
| reaction_8 | — | p30 > p18 + DISC kD374trans_p55 * p30 * (DISCp55 + p30) * cell | |||
| reaction_9 | — | p30 > p18 + DISC kD374trans_p43 * p30 * p43 * cell |
| Id | Value | |
|---|---|---|
| CD95act | 0.0 | |
| KDL | 15.421878766215 | |
| KDR | 8.98496674617627 | |
| kBid | 0.00052867403363568 | |
| kD216 | 0.0114186392006403 | |
| kD374probe | 0.00152252549827479 | |
| kD374trans_p43 | 0.00343995957326369 | |
| kD374trans_p55 | 0.000446994772958953 | |
| kDISC | 0.000491828591049766 | |
| kdiss_p18 | 0.0949914492651531 | |
| koff_FADD | 0.00566528253772301 | |
| kon_FADD | 0.000811711012144556 |
| Id | Value | Reaction |
|---|
| Definition | |
|---|---|
| CD95act = pow(CD95, 3.0) * pow(KDL, 2.0) * CD95L / ((CD95L + KDL) * (pow(CD95, 2.0) * pow(KDL, 2.0) + KDR * pow(CD95L, 2.0) + 2.0 * KDR * KDL * CD95L + KDR * pow(KDL, 2.0))) |
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