mcauley1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000434) Biomodels notes: Figure 1b of the reference publication has been reproduced here. The figure in the paper has been generated using MathSBML. The author has generated the SBML file using Copasi, and finds that with the same intial conditions and parameter sets, LDLC enters a slightly higher steady statem, when running the simulation using Copasi. This is reflected in this curation figure, generated using SBML odeSolver. The model was simulated using SBML odeSolver and the plot was generated using Gnuplot. JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. A global parameter 'multiplier' was added, and added to reaction 1. To reproduce Fig 1B the values for 'multiplier' needs to be set to 0.6667, 1, 1.3333, 1.6667, 2 and 2.3333 for DC values of 200, 300, 400, 500, 600 and 700 mg/day respectively.
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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 | |
|---|---|---|
| — | 1.0 dimensionless | |
| — | 86400.0 second | |
| — | 1.0 dimensionless |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| Excreted | Excreted | 3.0 | 1.0 volume | |
| HepaticTissue | HepaticTissue | 3.0 | 1.0 volume | |
| Intake | Intake | 3.0 | 1.0 volume | |
| Intestine | Intestine | 3.0 | 1.0 volume | |
| PeripheralTissue | PeripheralTissue | 3.0 | 1.0 volume | |
| Plasma | Plasma | 3.0 | 1.0 volume |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| species_1 | DC | 304.0 <substance_units>/volume | Intake (Intake) | ✔ | |
| species_10 | NHDL | 100.0 <substance_units>/volume | Plasma (Plasma) | ✘ | |
| species_11 | PFC | 57516.0 <substance_units>/volume | PeripheralTissue (PeripheralTissue) | ✘ | |
| species_12 | HCS | 0.0 <substance_units>/volume | HepaticTissue (HepaticTissue) | ✔ | |
| species_13 | HCE | 10000.0 <substance_units>/volume | HepaticTissue (HepaticTissue) | ✘ | |
| species_14 | ACAT | 100.0 <substance_units>/volume | HepaticTissue (HepaticTissue) | ✘ | |
| species_15 | CEH | 100.0 <substance_units>/volume | HepaticTissue (HepaticTissue) | ✘ | |
| species_16 | HNHDLS | 0.0 <substance_units>/volume | HepaticTissue (HepaticTissue) | ✔ | |
| species_17 | VLDLC | 20.0 <substance_units>/volume | Plasma (Plasma) | ✘ | |
| species_18 | HLDLRs | 100.0 <substance_units>/volume | HepaticTissue (HepaticTissue) | ✘ | |
| species_19 | HLDLRsS | 600.0 <substance_units>/volume | HepaticTissue (HepaticTissue) | ✔ | |
| species_2 | IC | 3150.0 <substance_units>/volume | Intestine (Intestine) | ✘ | |
| species_20 | HLDLRD | 0.0 <substance_units>/volume | HepaticTissue (HepaticTissue) | ✘ | |
| species_21 | IDLC | 20.0 <substance_units>/volume | Plasma (Plasma) | ✘ | |
| species_22 | LPL | 100.0 <substance_units>/volume | Plasma (Plasma) | ✘ | |
| species_23 | LDLC | 100.0 <substance_units>/volume | Plasma (Plasma) | ✘ | |
| species_24 | HSL | 100.0 <substance_units>/volume | Plasma (Plasma) | ✘ | |
| species_25 | PLDLRs | 100.0 <substance_units>/volume | PeripheralTissue (PeripheralTissue) | ✘ | |
| species_26 | PLDLRsS | 575.16 <substance_units>/volume | PeripheralTissue (PeripheralTissue) | ✔ | |
| species_27 | PLDLRD | 0.0 <substance_units>/volume | PeripheralTissue (PeripheralTissue) | ✘ | |
| species_28 | PCE | 9363.0 <substance_units>/volume | PeripheralTissue (PeripheralTissue) | ✘ | |
| species_29 | PSS | 0.0 <substance_units>/volume | PeripheralTissue (PeripheralTissue) | ✘ | |
| species_3 | ICS | 0.0 <substance_units>/volume | Intestine (Intestine) | ✔ | |
| species_30 | HDLC | 45.0 <substance_units>/volume | Plasma (Plasma) | ✘ | |
| species_31 | LCAT | 100.0 <substance_units>/volume | Plasma (Plasma) | ✘ | |
| species_32 | PCS | 0.0 <substance_units>/volume | PeripheralTissue (PeripheralTissue) | ✔ | |
| species_33 | CETP | 100.0 <substance_units>/volume | Plasma (Plasma) | ✘ | |
| species_34 | SRB1 | 100.0 <substance_units>/volume | HepaticTissue (HepaticTissue) | ✘ | |
| species_4 | HBS | 400.0 <substance_units>/volume | HepaticTissue (HepaticTissue) | ✘ | |
| species_5 | IBS | 467.0 <substance_units>/volume | Intestine (Intestine) | ✘ | |
| species_6 | EBS | 0.0 <substance_units>/volume | Excreted (Excreted) | ✘ | |
| species_7 | HFC | 60000.0 <substance_units>/volume | HepaticTissue (HepaticTissue) | ✘ | |
| species_8 | EC | 0.0 <substance_units>/volume | Excreted (Excreted) | ✘ | |
| species_9 | INHDLS | 0.0 <substance_units>/volume | Plasma (Plasma) | ✔ |
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 | Ingestion | species_1 > species_2 k1 * species_1 * multiplier | |||
| reaction_10 | Billary Cholesterol Release | species_7 > species_2 function_6(BCRmax, BCRt, species_7, BS) | |||
| reaction_11 | Hepatic Cholesterol Synthesis | species_12 > species_7 function_7(HCSmax, species_7, HCSt, HS) | |||
| reaction_12 | Hepatic Cholesterol Storage | species_7 > species_13 function_8(k9, species_14, species_7) | |||
| reaction_13 | Release of Stored Cholesterol | species_13 > species_7 function_9(k10, species_15, species_13) | |||
| reaction_14 | Hepatic Nascent HDL Synthesis | species_16 > species_10 function_10(k11, species_11) | |||
| reaction_15 | VLDL Cholesterol Formation | species_7 > species_17 k1 * species_7 | |||
| reaction_16 | Hepatic LDLR Synthesis | species_19 > species_18 function_11(khrs, species_19, species_7) | |||
| reaction_17 | Hepatic LDL Receptor Degradation | species_18 > species_20 k1 * species_18 | |||
| reaction_18 | VLDL Cholesterol ReUptake | species_17 > species_7 k1 * species_17 | |||
| reaction_19 | IDL Cholesterol Formation | species_17 > species_21 function_12(k15, species_17, species_22) | |||
| reaction_2 | Intestinal Cholesterol Synthesis | species_3 > species_2 function_1(ICSmax, species_2, ICt, IS) | |||
| reaction_20 | IDL Cholesterol ReUptake | species_21 > species_7 k1 * species_21 | |||
| reaction_21 | LDL Cholesterol Formation | species_21 > species_23 function_13(k17, species_21, species_24) | |||
| reaction_22 | Receptor Dependent Hepatic Uptake | species_23 > species_7 function_14(k18, species_23, species_18) | |||
| reaction_23 | Receptor Independent Hepatic Uptake | species_23 > species_7 k1 * species_23 | |||
| reaction_24 | Receptor Dependent Peripheral Uptake | species_23 > species_11 function_15(k20, species_25, species_23) | |||
| reaction_25 | Receptor Independent Peripheral Uptake | species_23 > species_11 k1 * species_23 | |||
| reaction_26 | Peripheral LDLR Synthesis | species_26 > species_25 function_16(kprs, species_26, species_11) | |||
| reaction_27 | Peripheral LDL Receptor Degradation | species_25 > species_27 k1 * species_25 | |||
| reaction_28 | Peripheral Cholesterol Storage | species_11 > species_28 function_17(k23, species_14, species_11) | |||
| reaction_29 | Release of Stored Peripheral Cholesterol | species_28 > species_11 function_18(k24, species_15, species_28) | |||
| reaction_3 | Bile Salt Release | species_4 > species_5 k1 * species_4 | |||
| reaction_30 | Peripheral Steroid Production | species_11 > species_29 k1 * species_11 | |||
| reaction_31 | HDL Cholesterol Formation | species_11 + species_10 > species_30 function_19(k26, species_11, species_10, species_31) | |||
| reaction_32 | Peripheral Cholesterol Synthesis | species_32 > species_11 function_20(PCSmax, species_11, PPCt, PCSS) | |||
| reaction_33 | CETP Mediated Transfer To VLDL | species_30 > species_17 function_21(k27, species_30, species_33) | |||
| reaction_34 | CETP Mediated TransferTo LDL | species_30 > species_23 function_22(k28, species_30, species_33) | |||
| reaction_35 | Reverse Cholesterol Transport | species_30 > species_7 function_23(k29, species_30, species_34) | |||
| reaction_4 | Bile Salt Return | species_5 > species_4 k1 * species_5 | |||
| reaction_5 | Bile Salt Excretion | species_5 > species_6 k1 * species_5 | |||
| reaction_6 | Bile Salt Synthesis | species_7 > species_4 function_2(k5, species_7, species_4) | |||
| reaction_7 | Cholesterol Absorption | species_2 > species_7 function_3(k6, species_2, species_5) | |||
| reaction_8 | Cholesterol Excretion | species_2 > species_8 function_4(k7, species_2, species_5) | |||
| reaction_9 | Intestinal Nascent HDL Synthesis | species_9 > species_10 function_5(k8, species_11) |
| Id | Value | |
|---|---|---|
| multiplier | 1.0 |
| Id | Value | Reaction | |
|---|---|---|---|
| BCRmax | 2000.0 | reaction_10 (Billary Cholesterol Release) | |
| k1 | 1.0 | reaction_1 (Ingestion) | |
| ICSmax | 100.0 | reaction_2 (Intestinal Cholesterol Synthesis) | |
| ICt | 3120.0 | reaction_2 (Intestinal Cholesterol Synthesis) | |
| IS | 5.0 | reaction_2 (Intestinal Cholesterol Synthesis) | |
| k1 | 6.0 | reaction_3 (Bile Salt Release) | |
| k1 | 4.29 | reaction_4 (Bile Salt Return) | |
| k1 | 0.856 | reaction_5 (Bile Salt Excretion) | |
| k5 | 2.66 | reaction_6 (Bile Salt Synthesis) | |
| k6 | 0.0005286 | reaction_7 (Cholesterol Absorption) | |
| k7 | 0.0005286 | reaction_8 (Cholesterol Excretion) | |
| k8 | 0.0005 | reaction_9 (Intestinal Nascent HDL Synthesis) | |
| BCRt | 55326.0 | reaction_10 (Billary Cholesterol Release) | |
| BS | 5.0 | reaction_10 (Billary Cholesterol Release) | |
| HCSmax | 500.0 | reaction_11 (Hepatic Cholesterol Synthesis) | |
| HCSt | 93925.0 | reaction_11 (Hepatic Cholesterol Synthesis) | |
| HS | 5.0 | reaction_11 (Hepatic Cholesterol Synthesis) | |
| k9 | 1.0 | reaction_12 (Hepatic Cholesterol Storage) | |
| k10 | 5.998 | reaction_13 (Release of Stored Cholesterol) | |
| k11 | 0.005 | reaction_14 (Hepatic Nascent HDL Synthesis) | |
| k1 | 0.016 | reaction_15 (VLDL Cholesterol Formation) | |
| khrs | 100.0 | reaction_16 (Hepatic LDLR Synthesis) | |
| k1 | 0.01 | reaction_17 (Hepatic LDL Receptor Degradation) | |
| k1 | 0.0496 | reaction_18 (VLDL Cholesterol ReUptake) | |
| k15 | 0.43 | reaction_19 (IDL Cholesterol Formation) | |
| k1 | 0.054 | reaction_20 (IDL Cholesterol ReUptake) | |
| k17 | 0.38 | reaction_21 (LDL Cholesterol Formation) | |
| k18 | 0.068 | reaction_22 (Receptor Dependent Hepatic Uptake) | |
| k1 | 0.005 | reaction_23 (Receptor Independent Hepatic Uptake) | |
| k20 | 0.00675 | reaction_24 (Receptor Dependent Peripheral Uptake) | |
| k1 | 0.000005 | reaction_25 (Receptor Independent Peripheral Uptake) | |
| kprs | 100.0 | reaction_26 (Peripheral LDLR Synthesis) | |
| k1 | 0.01 | reaction_27 (Peripheral LDL Receptor Degradation) | |
| k23 | 0.017386 | reaction_28 (Peripheral Cholesterol Storage) | |
| k24 | 0.1068 | reaction_29 (Release of Stored Peripheral Cholesterol) | |
| k1 | 0.0005 | reaction_30 (Peripheral Steroid Production) | |
| k26 | 0.000015 | reaction_31 (HDL Cholesterol Formation) | |
| PCSmax | 500.0 | reaction_32 (Peripheral Cholesterol Synthesis) | |
| PPCt | 80342.0 | reaction_32 (Peripheral Cholesterol Synthesis) | |
| PCSS | 5.0 | reaction_32 (Peripheral Cholesterol Synthesis) | |
| k27 | 0.01 | reaction_33 (CETP Mediated Transfer To VLDL) | |
| k28 | 0.001 | reaction_34 (CETP Mediated TransferTo LDL) | |
| k29 | 0.05 | reaction_35 (Reverse Cholesterol Transport) |
| Definition |
|---|
| Definition |
|---|
| Definition |
|---|
| Definition | |
|---|---|
| function_4(k7, IC, IBS) = k7 * IC * IBS | |
| function_5(k8, PFC) = k8 * PFC | |
| function_6(BCRmax, BCRt, HFC, BS) = BCRmax / (1 + pow(BCRt / HFC, BS)) | |
| function_10(k11, PFC) = k11 * PFC | |
| function_8(k9, ACAT, HFC) = k9 * ACAT * HFC | |
| function_16(kprs, PLDLRsS, PFC) = kprs * PLDLRsS / PFC | |
| function_15(k20, PLDLRs, LDLC) = k20 * PLDLRs * LDLC | |
| function_14(k18, LDLC, HLDLRs) = k18 * LDLC * HLDLRs | |
| function_13(k17, IDLC, HSL) = k17 * IDLC * HSL | |
| function_12(k15, VLDLC, LPL) = k15 * VLDLC * LPL | |
| function_11(khrs, HLDLRsS, HFC) = khrs * HLDLRsS / HFC | |
| function_1(ICSmax, IC, ICt, IS) = ICSmax / (1 + pow(IC / ICt, IS)) | |
| function_2(k5, HFC, HBS) = k5 * HFC / HBS | |
| function_3(k6, IC, IBS) = k6 * IC * IBS | |
| function_7(HCSmax, HFC, HCSt, HS) = HCSmax / (1 + pow(HFC / HCSt, HS)) | |
| function_9(k10, CEH, HCE) = k10 * CEH * HCE | |
| function_23(k29, HDLC, SRB1) = k29 * HDLC * SRB1 | |
| function_22(k28, HDLC, CETP) = k28 * HDLC * CETP | |
| function_21(k27, HDLC, CETP) = k27 * HDLC * CETP | |
| function_20(PCSmax, PFC, PPCt, PCSS) = PCSmax / (1 + pow(PFC / PPCt, PCSS)) | |
| function_19(k26, PFC, NHDL, LCAT) = k26 * PFC * NHDL * LCAT | |
| function_18(k24, CEH, PCE) = k24 * CEH * PCE | |
| function_17(k23, ACAT, PFC) = k23 * ACAT * PFC |
| Trigger | Assignments |
|---|