leloup6
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000171) Biomodels notes: The model has been simulated using copasi 4.3(build 25) For fig 4A one parameter, v_dT_fac, has been changed to 1 and the starting point of the simulation had to be changed to +32 hours to better fit the figure in the publication. JWS Online curation: This model was curated by reproducing Figure 4D.
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| Simulation | |
|---|---|
| leloup1998_Fig4D |
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-09 mole | |
| — | 1e-09 mole litre^(-1.0) | |
| — | 3600.0 second | |
| — | 2.777777777777778e-13 second^(-1.0) mole litre^(-1.0) | |
| — | 0.0002777777777777778 second^(-1.0) | |
| — | 277777.7777777778 second^(-1.0) mole^(-1.0) litre | |
| — | 2.777777777777778e-13 mole second^(-1.0) | |
| — | 1.0 dimensionless | |
| — | 1.0 litre |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| cytoplasm | cytoplasm | 3.0 | 1.0 litre | |
| nucleus | — | 3.0 | 1.0 litre |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| C | PER_TIM complex cytoplasm | 0.18 <substance_units>/litre | cytoplasm (cytoplasm) | ✘ | |
| CN | PER_TIM complex nuclear | 1.2 <substance_units>/litre | nucleus | ✘ | |
| M_P | per mRNA | 0.09 <substance_units>/litre | cytoplasm (cytoplasm) | ✘ | |
| M_T | tim mRNA | 1.41 <substance_units>/litre | cytoplasm (cytoplasm) | ✘ | |
| P0 | PER | 0.02 <substance_units>/litre | cytoplasm (cytoplasm) | ✘ | |
| P1 | PER-p | 0.02 <substance_units>/litre | cytoplasm (cytoplasm) | ✘ | |
| P2 | PER-pp | 0.01 <substance_units>/litre | cytoplasm (cytoplasm) | ✘ | |
| Pt | total PER | <assignment rule> <substance_units>/litre | cytoplasm (cytoplasm) | ✔ | |
| T0 | TIM | 0.54 <substance_units>/litre | cytoplasm (cytoplasm) | ✘ | |
| T1 | TIM-p | 0.79 <substance_units>/litre | cytoplasm (cytoplasm) | ✘ | |
| T2 | TIM-pp | 4.65 <substance_units>/litre | cytoplasm (cytoplasm) | ✘ | |
| Tt | total TIM | <assignment rule> <substance_units>/litre | cytoplasm (cytoplasm) | ✔ |
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 | |
|---|---|---|---|---|---|
| CN_decay | nuclear PER_TIM compl. decay | CN > ∅ kd_CN * CN * nucleus | |||
| C_decay | cytopl. PER_TIM compl. decay | C > ∅ kd_C * C * cytoplasm | |||
| C_form | Per_TIM complex formation | P2 + T2 > C (k3 * T2 * P2 - k4 * C) * cytoplasm | |||
| C_transp | PER_TIM complex shuttling | C = CN k1 * C * cytoplasm - k2 * CN * nucleus | |||
| M_P_decay | per mRNA decay | M_P > ∅ (v_mP / (K_mP + M_P) + kd) * M_P * cytoplasm | |||
| M_T_decay | tim mRNA decay | M_T > ∅ (v_mT / (K_mT + M_T) + kd) * M_T * cytoplasm | |||
| P1_decay | PER-p decay | P1 > ∅ kd * P1 * cytoplasm | |||
| P1_depho | PER-p dephosphorylation | P1 > P0 V_2P * P1 / (K_2P + P1) * cytoplasm | |||
| P1_pho | PER-p phosphorylation | P1 > P2 V_3P * P1 / (K_3P + P1) * cytoplasm | |||
| P2_decay | PER-pp decay | P2 > ∅ kd * P2 * cytoplasm | |||
| P2_depho | PER-pp dephosphorylation | P2 > P1 V_4P * P2 / (K_4P + P2) * cytoplasm | |||
| P2_light_deact | PER-pp light deactivation | P2 > ∅ v_dP * P2 / (K_dP + P2) * cytoplasm | |||
| PER_transl | PER tranlation | ∅ > P0 k_sP * M_P * cytoplasm | |||
| PO_decay | PER decay | P0 > ∅ kd * P0 * cytoplasm | |||
| P_pho | PER phosphorylation | P0 > P1 V_1P * P0 / (K_1P + P0) * cytoplasm | |||
| T0_decay | TIM decay | T0 > ∅ kd * T0 * cytoplasm | |||
| T1_decay | TIM-p decay | T1 > ∅ kd * T1 * cytoplasm | |||
| T1_depho | TIM-p dephosphorylation | T1 > T0 V_2T * T1 / (K_2T + T1) * cytoplasm | |||
| T1_pho | TIM-p phosphorylation | T1 > T2 V_3T * T1 / (K_3T + T1) * cytoplasm | |||
| T2_decay | TIM-pp decay | T2 > ∅ kd * T2 * cytoplasm | |||
| T2_depho | TIM-pp dephosphorylation | T2 > T1 V_4T * T2 / (K_4T + T2) * cytoplasm | |||
| T2_light_deact | TIM-pp light deactivation | T2 > ∅ v_dT * T2 / (K_dT + T2) * cytoplasm | |||
| TIM_transl | TIM translation | ∅ > T0 k_sT * M_T * cytoplasm | |||
| T_pho | TIM phosphorylation | T0 > T1 V_1T * T0 / (K_1T + T0) * cytoplasm | |||
| per_trans | per transkription | ∅ > M_P v_sP * pow(Ki_P, n) / (pow(Ki_P, n) + pow(CN, n)) | |||
| tim_trans | tim transkription | ∅ > M_T v_sT * pow(Ki_T, n) / (pow(Ki_T, n) + pow(CN, n)) |
| Id | Value | |
|---|---|---|
| kd | 0.01 | |
| l_d | 12.0 | |
| n | 4.0 dimensionless | |
| v_dT | 2.0 | |
| v_dT_dark | 2.0 | |
| v_dT_fac | 2.0 dimensionless |
| Id | Value | Reaction | |
|---|---|---|---|
| v_sP | 0.8 | per_trans (per transkription) | |
| Ki_P | 1.0 | per_trans (per transkription) | |
| v_sT | 1.0 | tim_trans (tim transkription) | |
| Ki_T | 1.0 | tim_trans (tim transkription) | |
| v_mT | 0.7 | M_T_decay (tim mRNA decay) | |
| K_mT | 0.2 | M_T_decay (tim mRNA decay) | |
| v_mP | 0.8 | M_P_decay (per mRNA decay) | |
| K_mP | 0.2 | M_P_decay (per mRNA decay) | |
| k_sP | 0.9 | PER_transl (PER tranlation) | |
| k_sT | 0.9 | TIM_transl (TIM translation) | |
| k3 | 1.2 | C_form (Per_TIM complex formation) | |
| k4 | 0.6 | C_form (Per_TIM complex formation) | |
| kd_C | 0.01 | C_decay (cytopl. PER_TIM compl. decay) | |
| kd_CN | 0.01 | CN_decay (nuclear PER_TIM compl. decay) | |
| k1 | 1.2 | C_transp (PER_TIM complex shuttling) | |
| k2 | 0.2 | C_transp (PER_TIM complex shuttling) | |
| V_1P | 8.0 | P_pho (PER phosphorylation) | |
| K_1P | 2.0 | P_pho (PER phosphorylation) | |
| V_3P | 8.0 | P1_pho (PER-p phosphorylation) | |
| K_3P | 2.0 | P1_pho (PER-p phosphorylation) | |
| K_2P | 2.0 | P1_depho (PER-p dephosphorylation) | |
| V_2P | 1.0 | P1_depho (PER-p dephosphorylation) | |
| V_4P | 1.0 | P2_depho (PER-pp dephosphorylation) | |
| K_4P | 2.0 | P2_depho (PER-pp dephosphorylation) | |
| V_1T | 8.0 | T_pho (TIM phosphorylation) | |
| K_1T | 2.0 | T_pho (TIM phosphorylation) | |
| V_3T | 8.0 | T1_pho (TIM-p phosphorylation) | |
| K_3T | 2.0 | T1_pho (TIM-p phosphorylation) | |
| K_2T | 2.0 | T1_depho (TIM-p dephosphorylation) | |
| V_2T | 1.0 | T1_depho (TIM-p dephosphorylation) | |
| V_4T | 1.0 | T2_depho (TIM-pp dephosphorylation) | |
| K_4T | 2.0 | T2_depho (TIM-pp dephosphorylation) | |
| K_dT | 0.2 | T2_light_deact (TIM-pp light deactivation) | |
| v_dP | 2.0 | P2_light_deact (PER-pp light deactivation) | |
| K_dP | 0.2 | P2_light_deact (PER-pp light deactivation) |
| Definition | |
|---|---|
| v_dT = (1.0 + (v_dT_fac - 1.0) * ceil(sin(time / l_d * pi) * 0.9)) * v_dT_dark | |
| Pt = P0 + P1 + P2 + C + CN * nucleus / cytoplasm | |
| Tt = T0 + T1 + T2 + C + CN * nucleus / cytoplasm |
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| Definition |
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| Definition |
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| Trigger | Assignments |
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