marinhernandez3
hyper-glycemic
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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 | |
|---|---|---|
| — | 0.001 litre | |
| — | 60.0 second | |
| — | 0.001 mole |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| compartment | compartment | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| ADP | ADP | 2.1 | compartment (compartment) | ✘ | |
| AMP | AMP | 1.6 | compartment (compartment) | ✘ | |
| ATP | ATP | 11.0 | compartment (compartment) | ✘ | |
| Cit | Cit | 1.7 | compartment (compartment) | ✔ | |
| DHAP | DHAP | 0.8 | compartment (compartment) | ✘ | |
| Ery4P | Ery4P | 0.22 | compartment (compartment) | ✔ | |
| F26BP | F26BP | 0.0042 | compartment (compartment) | ✔ | |
| F6P | F6P | 2.7 | compartment (compartment) | ✘ | |
| FBP | FBP | 0.5 | compartment (compartment) | ✘ | |
| G3P | G3P | 0.5 | compartment (compartment) | ✘ | |
| G6P | G6P | 4.0 | compartment (compartment) | ✘ | |
| Gluin | Gluin | 0.001 | compartment (compartment) | ✘ | |
| Gluout | Gluout | 5.0 | compartment (compartment) | ✔ | |
| Lacin | Lacin | 33.0 | compartment (compartment) | ✘ | |
| Lacout | Lacout | 1.9 | compartment (compartment) | ✔ | |
| NAD | NAD | 1.3 | compartment (compartment) | ✘ | |
| NADH | NADH | 0.05 | compartment (compartment) | ✘ | |
| PEP | PEP | 0.5 | compartment (compartment) | ✘ | |
| Pi | Pi | 4.0 | compartment (compartment) | ✔ | |
| Pyr | Pyr | 2.7 | compartment (compartment) | ✘ | |
| Xy5P | Xy5P | 0.016 | compartment (compartment) | ✔ | |
| _13BPG | 13BPG | 0.001 | compartment (compartment) | ✘ | |
| _2PG | 2PG | 0.001 | compartment (compartment) | ✘ | |
| _3PG | 3PG | 0.001 | compartment (compartment) | ✘ | |
| _6PG | 6PG | 1.5 | compartment (compartment) | ✔ | |
| glycogen | glycogen | 57.0 | compartment (compartment) | ✔ |
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 | |
|---|---|---|---|---|---|
| AK | AK | ATP + AMP = {2.0}ADP compartment * (k1 * ATP * AMP - k2 * pow(ADP, 2)) | |||
| ALDO | ALDO | FBP = DHAP + G3P compartment * ALDO_rate_equation(FBP, DHAP, G3P, Vmf, Kfbp, Vmr, Kdhap, Kg3p) | |||
| ATPases | ATPases | ATP > ADP + Pi compartment * k1 * ATP | |||
| DHases | DHases | NADH = NAD compartment * (k1 * NADH - k2 * NAD) | |||
| ENO | ENO | _2PG = PEP compartment * Reversible_Michaelis_Menten(_2PG, PEP, Kms, Kmp, Vf, Vr) | |||
| GAPDH | GAPDH | NAD + G3P + Pi = _13BPG + NADH compartment * GAPDH_0(NAD, G3P, Pi, _13BPG, NADH, Vmf, Knad, Kg3p, Kp, Vmr, Kdpg, Knadh) | |||
| GLUT | GLUT | Gluout = Gluin compartment * GLUT_isoforms_rate_equation(Gluout, Gluin, Vmf, f1, Keq, Kgluout, Kgluin, f2, Keq1, Kgluout1, Kgluin1) | |||
| Glycogen_degradation | Glycogen degradation | glycogen + Pi > G6P compartment * Constant_flux__irreversible(v) | |||
| Glycogen_synthesis | Glycogen synthesis | G6P + ATP > glycogen + ADP + {2.0}Pi compartment * Constant_flux__irreversible(v) | |||
| HK | HK | Gluin + ATP = G6P + ADP compartment * HK_isoforms_rate_equation(Gluin, ATP, G6P, ADP, Vm, f1, Ka, Kb, Keq, Kp, Kq, f2, Ka2) | |||
| HPI | HPI | G6P = F6P compartment * HPI_rate_equation(G6P, F6P, Ery4P, FBP, _6PG, Vmf, Kg6p, Vmr, Kf6p, Kery4p, Kfbp, Kpg) | |||
| LDH | LDH | NADH + Pyr = Lacin + NAD compartment * Random_Bi_Bi_reversible_Michaelis_Menten(NADH, Pyr, Lacin, NAD, Vmf, alfa, Ka, Kb, Vmr, beta, Kp, Kq) | |||
| MCT1 | MCT1 | Lacin = Lacout compartment * MCT1_0(Lacin, Lacout, Vmf, Keq, Klacin, Klacout) | |||
| MPM | MPM | Pyr + {13.0}ADP + {13.0}Pi > {13.0}ATP compartment * Constant_flux__irreversible(v) | |||
| OxPhos | OxPhos | ADP + Pi > ATP compartment * Constant_flux__irreversible(v) | |||
| PFK1 | PFK1 | F6P + ATP = FBP + ADP compartment * PFK_1_rate_equation(F6P, ATP, FBP, ADP, F26BP, Cit, Vm, Katp, beta, alfa, Kf26bp, Kf6p, L, Kcit, Kiatp, Kadp, Kfbp, Keq) | |||
| PGAM | PGAM | _3PG = _2PG compartment * Reversible_Michaelis_Menten(_3PG, _2PG, Kms, Kmp, Vf, Vr) | |||
| PGK | PGK | _13BPG + ADP = _3PG + ATP compartment * Random_Bi_Bi_reversible_Michaelis_Menten(_13BPG, ADP, _3PG, ATP, Vmf, alfa, Ka, Kb, Vmr, beta, Kp, Kq) | |||
| PPP | PPP | G6P > _6PG compartment * Constant_flux__irreversible(v) | |||
| PYK | PYK | PEP + ADP = Pyr + ATP compartment * PYK_kinetics(PEP, ADP, Pyr, ATP, Vmax, Kpep, Kadp, Keq, Kpyr, Katp) | |||
| TK | TK | Xy5P + Ery4P > G3P + F6P compartment * Constant_flux__irreversible(v) | |||
| TPI | TPI | DHAP = G3P compartment * Reversible_Michaelis_Menten(DHAP, G3P, Kms, Kmp, Vf, Vr) |
| Id | Value |
|---|
| Id | Value | Reaction | |
|---|---|---|---|
| Vmf | 0.023 | GLUT (GLUT) | |
| f1 | 0.14 | GLUT (GLUT) | |
| Keq | 1.0 | GLUT (GLUT) | |
| Kgluout | 1.8 | GLUT (GLUT) | |
| Kgluin | 10.0 | GLUT (GLUT) | |
| f2 | 0.86 | GLUT (GLUT) | |
| Keq1 | 1.0 | GLUT (GLUT) | |
| Kgluout1 | 9.3 | GLUT (GLUT) | |
| Kgluin1 | 10.0 | GLUT (GLUT) | |
| Vm | 0.036 | HK (HK) | |
| f1 | 0.01 | HK (HK) | |
| Ka | 0.03 | HK (HK) | |
| Kb | 1.1 | HK (HK) | |
| Keq | 651.0 | HK (HK) | |
| Kp | 0.02 | HK (HK) | |
| Kq | 3.5 | HK (HK) | |
| f2 | 0.99 | HK (HK) | |
| Ka2 | 0.3 | HK (HK) | |
| Vmf | 0.24 | HPI (HPI) | |
| Kg6p | 0.4 | HPI (HPI) | |
| Vmr | 0.54 | HPI (HPI) | |
| Kf6p | 0.05 | HPI (HPI) | |
| Kery4p | 0.001 | HPI (HPI) | |
| Kfbp | 0.06 | HPI (HPI) | |
| Kpg | 0.015 | HPI (HPI) | |
| Vm | 0.022 | PFK1 (PFK1) | |
| Katp | 0.0292 | PFK1 (PFK1) | |
| beta | 1.18 | PFK1 (PFK1) | |
| alfa | 0.75 | PFK1 (PFK1) | |
| Kf26bp | 0.00099 | PFK1 (PFK1) | |
| Kf6p | 1.1 | PFK1 (PFK1) | |
| L | 6.6 | PFK1 (PFK1) | |
| Kcit | 6.7 | PFK1 (PFK1) | |
| Kiatp | 1.1 | PFK1 (PFK1) | |
| Kadp | 5.0 | PFK1 (PFK1) | |
| Kfbp | 5.0 | PFK1 (PFK1) | |
| Keq | 247.0 | PFK1 (PFK1) | |
| Vmf | 0.08 | ALDO (ALDO) | |
| Kfbp | 0.009 | ALDO (ALDO) | |
| Vmr | 0.063 | ALDO (ALDO) | |
| Kdhap | 0.08 | ALDO (ALDO) | |
| Kg3p | 0.16 | ALDO (ALDO) | |
| Kms | 1.6 | TPI (TPI) | |
| Kmp | 0.51 | TPI (TPI) | |
| Vf | 3.4 | TPI (TPI) | |
| Vr | 28.0 | TPI (TPI) | |
| Vmf | 0.28 | GAPDH (GAPDH) | |
| Knad | 0.09 | GAPDH (GAPDH) | |
| Kg3p | 0.19 | GAPDH (GAPDH) | |
| Kp | 11.0 | GAPDH (GAPDH) | |
| Vmr | 0.35 | GAPDH (GAPDH) | |
| Kdpg | 0.022 | GAPDH (GAPDH) | |
| Knadh | 0.01 | GAPDH (GAPDH) | |
| Vmf | 8.7 | PGK (PGK) | |
| alfa | 1.0 | PGK (PGK) | |
| Ka | 0.079 | PGK (PGK) | |
| Kb | 0.04 | PGK (PGK) | |
| Vmr | 2.5 | PGK (PGK) | |
| beta | 1.0 | PGK (PGK) | |
| Kp | 0.13 | PGK (PGK) | |
| Kq | 0.27 | PGK (PGK) | |
| Kms | 0.19 | PGAM (PGAM) | |
| Kmp | 0.12 | PGAM (PGAM) | |
| Vf | 0.94 | PGAM (PGAM) | |
| Vr | 0.36 | PGAM (PGAM) | |
| Kms | 0.038 | ENO (ENO) | |
| Kmp | 0.06 | ENO (ENO) | |
| Vf | 0.34 | ENO (ENO) | |
| Vr | 0.38 | ENO (ENO) | |
| Vmax | 0.072 | PYK (PYK) | |
| Kpep | 0.05 | PYK (PYK) | |
| Kadp | 0.4 | PYK (PYK) | |
| Keq | 195172.4 | PYK (PYK) | |
| Kpyr | 10.0 | PYK (PYK) | |
| Katp | 0.86 | PYK (PYK) | |
| Vmf | 0.44 | LDH (LDH) | |
| alfa | 1.0 | LDH (LDH) | |
| Ka | 0.002 | LDH (LDH) | |
| Kb | 0.3 | LDH (LDH) | |
| Vmr | 0.07 | LDH (LDH) | |
| beta | 1.0 | LDH (LDH) | |
| Kp | 4.7 | LDH (LDH) | |
| Kq | 0.07 | LDH (LDH) | |
| v | 0.0045 | Glycogen_degradation (Glycogen degradation) | |
| k1 | 0.00265 | ATPases (ATPases) | |
| k1 | 1.0 | AK (AK) | |
| k2 | 2.26 | AK (AK) | |
| k1 | 250.0 | DHases (DHases) | |
| k2 | 1.0 | DHases (DHases) | |
| v | 0.000095 | PPP (PPP) | |
| v | 0.001 | Glycogen_synthesis (Glycogen synthesis) | |
| v | 0.0001 | MPM (MPM) | |
| v | 0.000095 | TK (TK) | |
| Vmf | 0.03 | MCT1 (MCT1) | |
| Keq | 1.0 | MCT1 (MCT1) | |
| Klacin | 8.5 | MCT1 (MCT1) | |
| Klacout | 0.5 | MCT1 (MCT1) | |
| v | 0.01875 | OxPhos (OxPhos) |
| Definition |
|---|
| Definition |
|---|
| Definition |
|---|
| Definition | |
|---|---|
| MCT1_0(Lacin, Lacout, Vmf, Keq, Klacin, Klacout) = Vmf * (Lacin - Lacout / Keq) / (Klacin * (1 + Lacout / Klacout) + Lacin) | |
| GLUT_isoforms_rate_equation(Gluout, Gluin, Vmf, f1, Keq, Kgluout, Kgluin, f2, Keq1, Kgluout1, Kgluin1) = Vmf * (f1 * (Gluout - Gluin / Keq) / (Kgluout * (1 + Gluin / Kgluin) + Gluout) + f2 * (Gluout - Gluin / Keq1) / (Kgluout1 * (1 + Gluin / Kgluin1) + Gluout)) | |
| Random_Bi_Bi_reversible_Michaelis_Menten(A, B, P, Q, Vmf, alfa, Ka, Kb, Vmr, beta, Kp, Kq) = (Vmf * (A * B / (alfa * Ka * Kb)) - Vmr * (P * Q / (beta * Kp * Kq))) / (1 + A / Ka + B / Kb + A * B / (alfa * Ka * Kb) + P * Q / (beta * Kp * Kq) + P / Kp + Q / Kq) | |
| Reversible_Michaelis_Menten(substrate, product, Kms, Kmp, Vf, Vr) = (Vf * substrate / Kms - Vr * product / Kmp) / (1 + substrate / Kms + product / Kmp) | |
| Constant_flux__irreversible(v) = v | |
| PYK_kinetics(A, B, P, Q, Vmax, Kpep, Kadp, Keq, Kpyr, Katp) = Vmax * (A * B / (Kpep * Kadp) - P * Q / (Kpep * Kadp * Keq)) / ((1 + A / Kpep + P / Kpyr) * (1 + B / Kadp + Q / Katp)) | |
| HPI_rate_equation(G6P, F6P, ERY4P, FBP, PG, Vmf, Kg6p, Vmr, Kf6p, Kery4p, Kfbp, Kpg) = (Vmf * (G6P / Kg6p) - Vmr * (F6P / Kf6p)) / (1 + G6P / Kg6p + F6P / Kf6p + ERY4P / Kery4p + FBP / Kfbp + PG / Kpg) | |
| GAPDH_0(NAD, G3P, P, DPG, NADH, Vmf, Knad, Kg3p, Kp, Vmr, Kdpg, Knadh) = (Vmf * (NAD * G3P * P / (Knad * Kg3p * Kp)) - Vmr * (DPG * NADH / (Kdpg * Knadh))) / (1 + NAD / Knad + NAD * G3P / (Knad * Kg3p) + NAD * G3P * P / (Knad * Kg3p * Kp) + DPG * NADH / (Kdpg * Knadh) + NADH / Knadh) | |
| PFK_1_rate_equation(ATP, F6P, ADP, FBP, F26BP, CIT, Vm, Katp, beta, alfa, Kf26bp, Kf6p, L, Kcit, Kiatp, Kadp, Kfbp, Keq) = Vm * (ATP / Katp / (1 + ATP / Katp)) * ((1 + beta * F26BP / (alfa * Kf26bp)) / (1 + F26BP / (alfa * Kf26bp))) * (F6P * (1 + F26BP / (alfa * Kf26bp)) / (Kf6p * (1 + F26BP / Kf26bp)) * pow(1 + F6P * (1 + F26BP / (alfa * Kf26bp)) / (Kf6p * (1 + F26BP / Kf26bp)), 3) / (L * pow(1 + CIT / Kcit, 4) * pow(1 + ATP / Kiatp, 4) / pow(1 + F26BP / Kf26bp, 4) + pow(1 + F6P * (1 + F26BP / (alfa * Kf26bp)) / (Kf6p * (1 + F26BP / Kf26bp)), 4)) - ADP * FBP / (Kadp * Kfbp * Keq) / (ADP / Kadp + FBP / Kfbp + ADP * FBP / (Kadp * Kfbp) + 1)) | |
| ALDO_rate_equation(FBP, DHAP, G3P, Vmf, Kfbp, Vmr, Kdhap, Kg3p) = (Vmf * (FBP / Kfbp) - Vmr * (DHAP * G3P / (Kdhap * Kg3p))) / (1 + FBP / Kfbp + DHAP / Kdhap + G3P / Kg3p + DHAP * G3P / (Kdhap * Kg3p)) | |
| HK_isoforms_rate_equation(A, B, P, Q, Vm, f1, Ka, Kb, Keq, Kp, Kq, f2, Ka2) = Vm * (f1 / (Ka * Kb) * (A * B - P * Q / Keq) / (1 + A / Ka + B / Kb + A * B / (Ka * Kb) + P / Kp + Q / Kq + P * Q / (Kp * Kq) + A * Q / (Ka * Kq) + P * B / (Kp * Kb)) + f2 / (Ka2 * Kb) * (A * B - P * Q / Keq) / (1 + A / Ka2 + B / Kb + A * B / (Ka2 * Kb) + P / Kp + Q / Kq + P * Q / (Kp * Kq) + A * Q / (Ka2 * Kq) + P * B / (Kp * Kb))) |
| Trigger | Assignments |
|---|