chance1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000281) Biomodels notes: Reproduction of figure 3/Graph1 from the original publication. The time course simulation was performed using Copasi 4.6. 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 | |
|---|---|
| chance1960_Fig3 |
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 | |
|---|---|---|
| — | 0.1 second^(-1.0) | |
| — | 0.1 mole^(-1.0) litre second^(-1.0) | |
| — | 0.1 mole^(-2.0) litre^(2.0) second^(-1.0) | |
| — | 1.0 dimensionless |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| cell | cell | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| ADP | (ADP) adenosine diphosphate | 0.0001 | cell (cell) | ✘ | |
| AGP | (AGP) alpha-glycerophosphate | 0.0 | cell (cell) | ✘ | |
| DBP | (DBP) dibromophenol | 0.0 | cell (cell) | ✘ | |
| DGA | (DGA) 1,3 diphosphoglycerate | 0.0 | cell (cell) | ✘ | |
| DHA | (DHA) dihydroxacetone phosphate | 0.0 | cell (cell) | ✘ | |
| DIH | (DIH) intramitochondrial reduced diphospyridine nucleotide | 0.00003 | cell (cell) | ✘ | |
| DIN | (DIN) intramitochondrial diphospyridine nucleotide | 0.00003 | cell (cell) | ✘ | |
| DPH | (DPH) extramitochondrial reduced diphospyridine nucleotide | 0.0001 | cell (cell) | ✘ | |
| DPN | (DPN) extramitochondrial diphospyridine nucleotide | 0.0001 | cell (cell) | ✘ | |
| ENG | (ENG) hexokinase-glucose intermediate | 0.0 | cell (cell) | ✘ | |
| ENZ | (ENZ) hexokinase | 0.00001 | cell (cell) | ✘ | |
| ETG | (ETG) phosphofructokinase intermediate | 0.0 | cell (cell) | ✘ | |
| ETZ | (ETZ) phosphofructokinase | 0.00001 | cell (cell) | ✘ | |
| GAP | (GAP) glyceraldehyde 3-phosphate | 0.0 | cell (cell) | ✘ | |
| GLP | (GLP) glucose 6-phosphate | 0.0 | cell (cell) | ✘ | |
| GLU | (GLU) glucose | 0.0 | cell (cell) | ✘ | |
| GPP | (GPP) hexose diphosphate | 0.0 | cell (cell) | ✘ | |
| LAC | (LAC) lactate | 0.001 | cell (cell) | ✘ | |
| MOB | (MOB) acyl enzyme intermediate of glyceraldehyde 3-phoshphate dehydrogenase | 0.0 | cell (cell) | ✘ | |
| MOD | (MOD) glyceraldehyde 3-phoshphate dehydrogenase-DPN complex | 0.00005 | cell (cell) | ✘ | |
| MOX | (MOX) glyceraldehyde 3-phoshphate dehydrogenase | 0.0 | cell (cell) | ✘ | |
| OXY | (OXY) oxygen | 0.0005 | cell (cell) | ✘ | |
| PGA | (PGA) 3 phosphoglycerate | 0.0 | cell (cell) | ✘ | |
| PID | (PID) inorganic phosphate | 0.004 | cell (cell) | ✘ | |
| PPP | (PPP) enzyme intermediate concerned in ATP utilization | 0.000001 | cell (cell) | ✘ | |
| PUE | (PUE) enzyme concerned in ATP utilization | 0.000002 | cell (cell) | ✘ | |
| PYR | (PYR) pyruvate | 0.001 | cell (cell) | ✘ | |
| TP1 | (TP1) adenosine triphosphate in store 1 (cytoplasm) | 0.0005 | cell (cell) | ✘ | |
| TP2 | (TP2) adenosine triphosphate in store 2 (mitochondria) | 0.0005 | cell (cell) | ✘ | |
| XI | (XI) low energy intermediate in oxidative phosphorylation | 0.00002 | cell (cell) | ✘ | |
| XSI | (XSI) high energy intermediate in oxidative phosphorylation | 0.00002 | cell (cell) | ✘ | |
| XSP | (XSP) phosphorylated intermediate in oxidative phosphorylation | 0.00002 | 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 | |
|---|---|---|---|---|---|
| r_1 | reaction 1 | GLU + ENZ > ENG cell * 1.000000e-06 * k * GLU * ENZ | |||
| r_10 | reaction 10 | MOX + DPN > MOD cell * 1.000000e-06 * k * MOX * DPN | |||
| r_11 | reaction 11 | DGA + ADP > TP1 + PGA cell * 1.000000e-06 * k * DGA * ADP | |||
| r_12 | reaction 12 | PGA + ADP > TP1 + PYR cell * 1.000000e-06 * k * PGA * ADP | |||
| r_13 | reaction 13 | PYR + DPH > LAC + DPN cell * 1.000000e-06 * k * PYR * DPH | |||
| r_14 | reaction 14 | LAC + DPN > PYR + DPH cell * 1.000000e-06 * k * LAC * DPN | |||
| r_15 | reaction 15 | PYR + {4.0}DIN > {4.0}DIH cell * 1.000000e-06 * k * PYR * DIN | |||
| r_16 | reaction 16 | DIH + {3.0}XI + OXY > {3.0}XSI + DIN cell * 1.000000e-06 * k * DIH * XI * OXY | |||
| r_17 | reaction 17 | XSI + PID > XSP cell * 1.000000e-06 * k * XSI * PID | |||
| r_18 | reaction 18 | XSP + ADP > TP2 + XI cell * 1.000000e-06 * k * XSP * ADP | |||
| r_19 | reaction 19 | XSI > XI cell * 1.000000e-06 * k * XSI * DBP | |||
| r_2 | reaction 2 | ENG + TP1 > ADP + GLP + ENZ cell * 1.000000e-06 * k * ENG * TP1 | |||
| r_20 | reaction 20 | TP2 > TP1 cell * 1.000000e-06 * k * TP2 * DBP | |||
| r_21 | reaction 21 | TP1 + PUE > PPP cell * 1.000000e-06 * k * TP1 * PUE | |||
| r_22 | reaction 22 | PPP > ADP + PUE + PID cell * 1.000000e-06 * k * PPP | |||
| r_3 | reaction 3 | GLP + ETZ > ETG cell * 1.000000e-06 * k * GLP * ETZ | |||
| r_4 | reaction 4 | ETG + TP1 > GPP + ETZ + ADP cell * 1.000000e-06 * k * ETG * TP1 | |||
| r_5 | reaction 5 | GPP > GAP + DHA cell * 1.000000e-06 * k * GPP | |||
| r_6 | reaction 6 | DHA + DPH > AGP + DPN cell * 1.000000e-06 * k * DHA * DPH | |||
| r_7 | reaction 7 | AGP + DPN > DHA + DPH cell * 1.000000e-06 * k * AGP * DPN | |||
| r_8 | reaction 8 | GAP + MOD > MOB + DPH cell * 1.000000e-06 * k * GAP * MOD | |||
| r_9 | reaction 9 | MOB + PID > DGA + MOX cell * 1.000000e-06 * k * MOB * PID |
| Id | Value | |
|---|---|---|
| ADP_0 | <assignment rule> dimensionless | |
| AGP_0 | <assignment rule> dimensionless | |
| DBP_0 | <assignment rule> dimensionless | |
| DGA_0 | <assignment rule> dimensionless | |
| DHA_0 | <assignment rule> dimensionless | |
| DIH_0 | <assignment rule> dimensionless | |
| DIN_0 | <assignment rule> dimensionless | |
| DPH_0 | <assignment rule> dimensionless | |
| DPN_0 | <assignment rule> dimensionless | |
| ENG_0 | <assignment rule> dimensionless | |
| ENZ_0 | <assignment rule> dimensionless | |
| ETG_0 | <assignment rule> dimensionless | |
| ETZ_0 | <assignment rule> dimensionless | |
| GAP_0 | <assignment rule> dimensionless | |
| GLP_0 | <assignment rule> dimensionless | |
| GLU_0 | <assignment rule> dimensionless | |
| GPP_0 | <assignment rule> dimensionless | |
| LAC_0 | <assignment rule> dimensionless | |
| MOB_0 | <assignment rule> dimensionless | |
| MOD_0 | <assignment rule> dimensionless | |
| MOX_0 | <assignment rule> dimensionless | |
| OXY_0 | <assignment rule> dimensionless | |
| PGA_0 | <assignment rule> dimensionless | |
| PID_0 | <assignment rule> dimensionless | |
| PPP_0 | <assignment rule> dimensionless | |
| PUE_0 | <assignment rule> dimensionless | |
| PYR_0 | <assignment rule> dimensionless | |
| TP1_0 | <assignment rule> dimensionless | |
| TP2_0 | <assignment rule> dimensionless | |
| XI_0 | <assignment rule> dimensionless | |
| XSI_0 | <assignment rule> dimensionless | |
| XSP_0 | <assignment rule> dimensionless |
| Id | Value | Reaction | |
|---|---|---|---|
| k | 3000000000.0 | r_1 (reaction 1) | |
| k | 10000000000.0 | r_2 (reaction 2) | |
| k | 40000000000.0 | r_3 (reaction 3) | |
| k | 40000000000.0 | r_4 (reaction 4) | |
| k | 100000.0 | r_5 (reaction 5) | |
| k | 2000000000.0 | r_6 (reaction 6) | |
| k | 80000000.0 | r_7 (reaction 7) | |
| k | 600000000000.0 | r_8 (reaction 8) | |
| k | 400000000.0 | r_9 (reaction 9) | |
| k | 6000000000.0 | r_10 (reaction 10) | |
| k | 10000000000.0 | r_11 (reaction 11) | |
| k | 5000000000.0 | r_12 (reaction 12) | |
| k | 500000000.0 | r_13 (reaction 13) | |
| k | 10000000.0 | r_14 (reaction 14) | |
| k | 20000000.0 | r_15 (reaction 15) | |
| k | 7500000000000.0 | r_16 (reaction 16) | |
| k | 400000000.0 | r_17 (reaction 17) | |
| k | 15000000000.0 | r_18 (reaction 18) | |
| k | 120000000.0 | r_19 (reaction 19) | |
| k | 4000000.0 | r_20 (reaction 20) | |
| k | 3000000000.0 | r_21 (reaction 21) | |
| k | 2000000.0 | r_22 (reaction 22) |
| Definition | |
|---|---|
| GPP_0 = GPP / 0.001 | |
| ETG_0 = ETG / 1.000000e-05 | |
| ETZ_0 = ETZ / 1.000000e-05 | |
| GLP_0 = GLP / 0.001 | |
| ADP_0 = ADP / 0.001 | |
| TP1_0 = TP1 / 0.0015 | |
| ENG_0 = ENG / 1.020000e-05 | |
| ENZ_0 = ENZ / 1.020000e-05 | |
| GLU_0 = GLU / 0.003 | |
| MOX_0 = MOX / 5.000000e-05 | |
| MOB_0 = MOB / 0.0001 | |
| MOD_0 = MOD / 5.000000e-05 | |
| AGP_0 = AGP / 0.0013 | |
| PPP_0 = PPP / 3.06 | |
| PUE_0 = PUE / 3.060000e-06 | |
| DBP_0 = DBP / 0.025 | |
| TP2_0 = TP2 / 0.0015 | |
| XSP_0 = XSP / 6.000000e-05 | |
| OXY_0 = OXY / 0.0005 | |
| XSI_0 = XSI / 6.000000e-05 | |
| XI_0 = XI / 6.000000e-05 | |
| DIH_0 = DIH / 7.000000e-05 | |
| DIN_0 = DIN / 7.000000e-05 | |
| LAC_0 = LAC / 0.0012 | |
| PYR_0 = PYR / 0.002 | |
| PGA_0 = PGA / 0.0002 | |
| DGA_0 = DGA / 0.0002 | |
| PID_0 = PID / 0.005 | |
| DPH_0 = DPH / 0.0002 | |
| DPN_0 = DPN / 0.00025 | |
| DHA_0 = DHA / 0.0013 | |
| GAP_0 = GAP / 0.0002 |
| Definition |
|---|
| Definition |
|---|
| Definition |
|---|
| Trigger | Assignments | |
|---|---|---|
| geq(time, 64) | GLU = 0.003 | |
| geq(time, 119) | DBP = 0.025 |