fisher2
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000122) Biomodels notes: The plot corresponds to Fig 4a of the paper. Simulation result obtained from MathSBML. 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 | |
|---|---|
| fisher2006_Fig4A |
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 | |
|---|---|---|
| — | 1e-06 mole |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| cytosol | cytosol | 3.0 | 0.000000000000269 | |
| nucleus | nucleus | 3.0 | 0.000000000000113 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| Act_C_Cyt | Active Calcineurin in cytosol | 0.0000091 | cytosol (cytosol) | ✘ | |
| Act_C_Nuc | Active Calcineurin in Nucleus | 0.0000505 | nucleus (nucleus) | ✘ | |
| Ca_Cyt | Calcium in Cytosol | 1.0 | cytosol (cytosol) | ✔ | |
| Ca_Nuc | Calcium in Nucleus | 1.0 | nucleus (nucleus) | ✔ | |
| Inact_C_Cyt | Inactive Calcineurin in cytosol | 0.0097108 | cytosol (cytosol) | ✘ | |
| Inact_C_Nuc | Inactive Calcineurin in nucleus | 0.049198 | nucleus (nucleus) | ✘ | |
| NFAT_Act_C_Cyt | NFAT Calcineurin complex in cytosol | 0.0000061 | cytosol (cytosol) | ✘ | |
| NFAT_Act_C_Nuc | NFAT Calcineurin complex in nucleus | 0.0009477 | nucleus (nucleus) | ✘ | |
| NFAT_Cyt | NFAT_Cyt | 0.0001101 | cytosol (cytosol) | ✘ | |
| NFAT_Nuc | NFAT_nuc | 0.0005219 | nucleus (nucleus) | ✘ | |
| NFAT_Pi_Act_C_Cyt | Phosphorylated NFAT Calcineurin complex in cytosol | 0.0000022 | cytosol (cytosol) | ✘ | |
| NFAT_Pi_Act_C_Nuc | Phosphorylated NFAT Calcineurin complex in nucleus | 0.0000025 | nucleus (nucleus) | ✘ | |
| NFAT_Pi_Cyt | Phosphorylated NFAT in cytosol | 0.0094397 | cytosol (cytosol) | ✘ | |
| NFAT_Pi_Nuc | Phosphorylated NFAT in nucleus | 0.0002272 | nucleus (nucleus) | ✘ |
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 | |
|---|---|---|---|---|---|
| R1 | Calcineurin dpdnt NFAT dephosphorylation | NFAT_Pi_Nuc + Act_C_Nuc = Act_C_Nuc + NFAT_Nuc nucleus * (k1 * NFAT_Pi_Nuc - k2 * NFAT_Nuc) | |||
| R10 | Phosphorylated NFAT transport | NFAT_Pi_Cyt = NFAT_Pi_Nuc cytosol * k3 * NFAT_Pi_Cyt - nucleus * k4 * NFAT_Pi_Nuc | |||
| R11 | NFAT Calcineurin complex disassembly | NFAT_Act_C_Cyt = Act_C_Cyt + NFAT_Cyt cytosol * (k15 * NFAT_Act_C_Cyt - k16 * NFAT_Cyt * Act_C_Cyt) | |||
| R12 | Calcineurin dpdnt NFAT dephosphorylation | NFAT_Pi_Cyt + Act_C_Cyt = Act_C_Cyt + NFAT_Cyt cytosol * (k1 * NFAT_Pi_Cyt - k2 * NFAT_Cyt) | |||
| R13 | Calcineurin activation | {3.0}Ca_Cyt + Inact_C_Cyt = Act_C_Cyt cytosol * (k19 * Inact_C_Cyt * pow(Ca_Cyt, 3) - k20 * Act_C_Cyt) | |||
| R14 | Calcineurin activation | {3.0}Ca_Nuc + Inact_C_Nuc = Act_C_Nuc nucleus * (k19 * Inact_C_Nuc * pow(Ca_Nuc, 3) - k20 * Act_C_Nuc) | |||
| R15 | Inactive Calcineurin transport | Inact_C_Cyt = Inact_C_Nuc cytosol * k5 * Inact_C_Cyt - nucleus * k6 * Inact_C_Nuc | |||
| R16 | Calcium transport | Ca_Cyt = Ca_Nuc cytosol * k21 * Ca_Cyt - nucleus * k22 * Ca_Nuc | |||
| R17 | Phosphorylated NFAT Calcineurin complex transport | NFAT_Pi_Act_C_Cyt = NFAT_Pi_Act_C_Nuc cytosol * k7 * NFAT_Pi_Act_C_Cyt - nucleus * k8 * NFAT_Pi_Act_C_Nuc | |||
| R2 | NFAT Calcineurin complex formation | Act_C_Nuc + NFAT_Nuc = NFAT_Act_C_Nuc nucleus * (k16 * NFAT_Nuc * Act_C_Nuc - k15 * NFAT_Act_C_Nuc) | |||
| R3 | NFAT transport | NFAT_Nuc = NFAT_Cyt nucleus * k18 * NFAT_Nuc - cytosol * k17 * NFAT_Cyt | |||
| R4 | Active Calcineurin transport | Act_C_Nuc = Act_C_Cyt nucleus * k6 * Act_C_Nuc - cytosol * k5 * Act_C_Cyt | |||
| R5 | NFAT Calcineurin complex phosphorylation | NFAT_Act_C_Nuc = NFAT_Pi_Act_C_Nuc nucleus * (k14 * NFAT_Act_C_Nuc - k13 * NFAT_Pi_Act_C_Nuc) | |||
| R6 | Phosphorylated NFAT Calcineurin complex disassembly | NFAT_Pi_Act_C_Nuc = Act_C_Nuc + NFAT_Pi_Nuc nucleus * (k12 * NFAT_Pi_Act_C_Nuc - k11 * NFAT_Pi_Nuc * Act_C_Nuc) | |||
| R7 | NFAT Calcineurin complex transport | NFAT_Act_C_Nuc = NFAT_Act_C_Cyt nucleus * k10 * NFAT_Act_C_Nuc - cytosol * k9 * NFAT_Act_C_Cyt | |||
| R8 | NFAT Calcineurin complex phosphorylation | NFAT_Act_C_Cyt = NFAT_Pi_Act_C_Cyt cytosol * (k14 * NFAT_Act_C_Cyt - k13 * NFAT_Pi_Act_C_Cyt) | |||
| R9 | Phosphorylated NFAT Calcineurin complex disassembly | NFAT_Pi_Act_C_Cyt = Act_C_Cyt + NFAT_Pi_Cyt cytosol * (k12 * NFAT_Pi_Act_C_Cyt - k11 * NFAT_Pi_Cyt * Act_C_Cyt) |
| Id | Value | |
|---|---|---|
| Time_in_Seconds | 100.0 | |
| k1 | 0.0000256 | |
| k10 | 0.005 | |
| k11 | 6.63 | |
| k12 | 0.00168 | |
| k13 | 0.5 | |
| k14 | 0.00256 | |
| k15 | 0.00168 | |
| k16 | 6.63 | |
| k17 | 0.0015 | |
| k18 | 0.00096 | |
| k19 | 1.0 | |
| k2 | 0.00256 | |
| k20 | 1.0 | |
| k21 | 0.21 | |
| k22 | 0.5 | |
| k3 | 0.005 | |
| k4 | 0.5 | |
| k5 | 0.0019 | |
| k6 | 0.00092 | |
| k7 | 0.005 | |
| k8 | 0.5 | |
| k9 | 0.5 |
| Id | Value | Reaction |
|---|
| Definition |
|---|
| Definition |
|---|
| Definition |
|---|
| Definition |
|---|
| Trigger | Assignments | |
|---|---|---|
| and(leq(Time_in_Seconds - time, 0), lt(time, 1500)) | Ca_Cyt = 1; Ca_Nuc = 1; Time_in_Seconds = Time_in_Seconds + 100 | |
| geq(time, 1500) | Ca_Cyt = 0.1; Ca_Nuc = 0.1 | |
| and(leq(Time_in_Seconds - time, 90), lt(time, 1500)) | Ca_Cyt = 0.1; Ca_Nuc = 0.1 |