smallbone19
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000380) Biomodels notes: The steady state concentration in Figure 18.4 of the reference publication has been reproduced here. The steady state concentration of the metabolites for 1) heat shock can be obtained by setting “heat=1” and 2) TPS1 mutant can be obtained by setting “heat=0” and by setting “activity=0.01” in the reaction T6P synthase. The model was simulated using Copasi v4.7 (Build 34). JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.
None
None
None
None
None
None
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 mole | |
| — | 60.0 second | |
| — | 0.001 mole litre^(-1.0) | |
| — | 0.016666666666666666 second^(-1.0) | |
| — | 1.6666666666666667e-05 mole litre^(-1.0) second^(-1.0) | |
| — | 1.0 dimensionless |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| cell | cell | 3.0 | 1.0 | |
| medium | medium | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| adp | ADP | 1.282 | cell (cell) | ✔ | |
| atp | ATP | 2.525 | cell (cell) | ✔ | |
| f6p | fructose 6-phosphate | 0.625 | cell (cell) | ✔ | |
| g1p | glucose 1-phosphate | 0.1 | cell (cell) | ✘ | |
| g6p | glucose 6-phosphate | 2.675 | cell (cell) | ✘ | |
| glc | glucose | 0.09675 | cell (cell) | ✘ | |
| glx | glucose | 100.0 | medium (medium) | ✔ | |
| h | H+ | 0.0 | cell (cell) | ✔ | |
| h2o | water | 0.0 | cell (cell) | ✔ | |
| pho | phosphate | 0.0 | cell (cell) | ✔ | |
| ppi | diphosphate | 0.0 | cell (cell) | ✔ | |
| t6p | trehalose 6-phosphate | 0.02 | cell (cell) | ✘ | |
| trh | trehalose | 0.05 | cell (cell) | ✘ | |
| udg | UDP glucose | 0.7 | cell (cell) | ✘ | |
| udp | UDP | 0.2815 | cell (cell) | ✔ | |
| utp | UTP | 0.6491 | 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 | |
|---|---|
| glc = glc_0 | |
| g1p = g1p_0 | |
| g6p = g6p_0 | |
| trh = trh_0 | |
| t6p = t6p_0 | |
| udg = udg_0 |
| Id | Name | Objective coefficient | Reaction Equation and Kinetic Law | Flux bounds | |
|---|---|---|---|---|---|
| hxk | hexokinase | glc + atp > g6p + adp + h cell * pow(shock, heat) * Vmax / (Kglc * Katp) * (glc * atp - g6p * adp / Keq) / ((1 + glc / Kglc + g6p / Kg6p + t6p / Kit6p) * (1 + atp / Katp + adp / Kadp)) | |||
| hxt | glucose transport | glx = glc cell * pow(shock, heat) * Vmax * (glx - glc) / Kglc / (1 + (glx + glc) / Kglc + Ki * glx * glc / pow(Kglc, 2)) | |||
| nth | trehalase | trh + h2o > {2.0}glc cell * pow(shock, heat) * Vmax * trh / Ktrh / (1 + trh / Ktrh) | |||
| pgi | G6P isomerase | g6p = f6p cell * pow(shock, heat) * Vmax / Kg6p * (g6p - f6p / Keq) / (1 + g6p / Kg6p + f6p / Kf6p) | |||
| pgm | phosphoglucomutase | g6p = g1p cell * pow(shock, heat) * Vmax / Kg6p * (g6p - g1p / Keq) / (1 + g6p / Kg6p + g1p / Kg1p) | |||
| tpp | T6P phosphatase | t6p + h2o > trh + pho cell * pow(shock, heat) * Vmax * t6p / Kt6p / (1 + t6p / Kt6p) | |||
| tps | T6P synthase | g6p + udg > t6p + udp + h cell * activity * pow(shock, heat) * Vmax * g6p * udg / (Kg6p * Kudg) / ((1 + g6p / Kg6p) * (1 + udg / Kudg)) | |||
| ugp | UDP glucose phosphorylase | g1p + utp + h > udg + ppi cell * pow(shock, heat) * Vmax * utp * g1p / (Kutp * Kg1p) / (Kiutp / Kutp + utp / Kutp + g1p / Kg1p + utp * g1p / (Kutp * Kg1p) + Kiutp / Kutp * udg / Kiudg + g1p * udg / (Kg1p * Kiudg)) |
| Id | Value | |
|---|---|---|
| g1p_0 | 0.1 mM | |
| g1p_change | <assignment rule> dimensionless | |
| g6p_0 | 2.675 mM | |
| g6p_change | <assignment rule> dimensionless | |
| glc_0 | 0.09765 mM | |
| glc_change | <assignment rule> dimensionless | |
| heat | 0.0 dimensionless | |
| t6p_0 | 0.02 mM | |
| t6p_change | <assignment rule> dimensionless | |
| trh_0 | 0.05 mM | |
| trh_change | <assignment rule> dimensionless | |
| udg_0 | 0.7 mM | |
| udg_change | <assignment rule> dimensionless |
| Id | Value | Reaction | |
|---|---|---|---|
| Vmax | 1071.0 mM per min | pgi (G6P isomerase) | |
| Kg6p | 1.4 mM | pgi (G6P isomerase) | |
| Kf6p | 0.29 mM | pgi (G6P isomerase) | |
| Keq | 0.3 dimensionless | pgi (G6P isomerase) | |
| shock | 1.0 dimensionless | pgi (G6P isomerase) | |
| Vmax | 97.24 mM per min | hxt (glucose transport) | |
| Kglc | 1.1918 mM | hxt (glucose transport) | |
| Ki | 0.91 dimensionless | hxt (glucose transport) | |
| shock | 8.0 dimensionless | hxt (glucose transport) | |
| Vmax | 289.6 mM per min | hxk (hexokinase) | |
| Kglc | 0.08 mM | hxk (hexokinase) | |
| Katp | 0.15 mM | hxk (hexokinase) | |
| Kg6p | 30.0 mM | hxk (hexokinase) | |
| Kadp | 0.23 mM | hxk (hexokinase) | |
| Keq | 2000.0 dimensionless | hxk (hexokinase) | |
| Kit6p | 0.04 mM | hxk (hexokinase) | |
| shock | 8.0 dimensionless | hxk (hexokinase) | |
| Vmax | 0.3545 mM per min | pgm (phosphoglucomutase) | |
| Kg6p | 0.05 mM | pgm (phosphoglucomutase) | |
| Kg1p | 0.023 mM | pgm (phosphoglucomutase) | |
| Keq | 0.1667 dimensionless | pgm (phosphoglucomutase) | |
| shock | 16.0 dimensionless | pgm (phosphoglucomutase) | |
| Vmax | 6.5 mM per min | tpp (T6P phosphatase) | |
| Kt6p | 0.5 mM | tpp (T6P phosphatase) | |
| shock | 18.0 dimensionless | tpp (T6P phosphatase) | |
| Vmax | 1.371 mM per min | tps (T6P synthase) | |
| Kg6p | 3.8 mM | tps (T6P synthase) | |
| Kudg | 0.886 mM | tps (T6P synthase) | |
| shock | 12.0 dimensionless | tps (T6P synthase) | |
| activity | 1.0 dimensionless | tps (T6P synthase) | |
| Vmax | 15.2 mM per min | nth (trehalase) | |
| Ktrh | 2.99 mM | nth (trehalase) | |
| shock | 6.0 dimensionless | nth (trehalase) | |
| Vmax | 36.82 mM per min | ugp (UDP glucose phosphorylase) | |
| Kutp | 0.11 mM | ugp (UDP glucose phosphorylase) | |
| Kiutp | 0.11 mM | ugp (UDP glucose phosphorylase) | |
| Kg1p | 0.32 mM | ugp (UDP glucose phosphorylase) | |
| Kiudg | 0.0035 mM | ugp (UDP glucose phosphorylase) | |
| shock | 16.0 dimensionless | ugp (UDP glucose phosphorylase) |
| Definition | |
|---|---|
| udg_change = log10(udg / udg_0) | |
| t6p_change = log10(t6p / t6p_0) | |
| trh_change = log10(trh / trh_0) | |
| g6p_change = log10(g6p / g6p_0) | |
| g1p_change = log10(g1p / g1p_0) | |
| glc_change = log10(glc / glc_0) |
| Definition |
|---|
| Definition |
|---|
| Definition |
|---|
| Trigger | Assignments |
|---|