montagne1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000315) Biomodels notes: Time courses as in fig 2b of the article. Simulations were performed using Copasi 4.6.33 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 | |
|---|---|
| montagne2011_Fig2B |
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 | |
|---|---|---|
| — | 60.0 second | |
| — | 1e-09 mole | |
| — | 1e-09 mole litre^(-1.0) | |
| — | 16666666.666666666 mole^(-1.0) litre second^(-1.0) | |
| — | 0.016666666666666666 second^(-1.0) |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| sample | — | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| Inh | Inh | 0.0 | sample | ✘ | |
| Inh_T1 | Inh_T1 | 0.0 | sample | ✘ | |
| T1 | T1 | 38.5 | sample | ✘ | |
| T1_alpha | T1_alpha | 0.0 | sample | ✘ | |
| T2 | T2 | 3.89 | sample | ✘ | |
| T2_beta | T2_beta | 0.0 | sample | ✘ | |
| T3 | T3 | 38.5 | sample | ✘ | |
| T3_Inh | T3_Inh | 0.0 | sample | ✘ | |
| alpha | alpha | 10.0 | sample | ✘ | |
| alpha_T1 | alpha_T1 | 0.0 | sample | ✘ | |
| alpha_T1_alpha | alpha_T1_alpha | 0.0 | sample | ✘ | |
| alpha_T2 | alpha_T2 | 0.0 | sample | ✘ | |
| alpha_T2_beta | alpha_T2_beta | 0.0 | sample | ✘ | |
| alpha_alpha_T1 | alpha_alpha_T1 | 0.0 | sample | ✘ | |
| alpha_beta_T2 | alpha_beta_T2 | 0.0 | sample | ✘ | |
| beta | beta | 0.0 | sample | ✘ | |
| beta_Inh_T3 | beta_Inh_T3 | 0.0 | sample | ✘ | |
| beta_T3 | beta_T3 | 0.0 | sample | ✘ | |
| beta_T3_Inh | beta_T3_Inh | 0.0 | sample | ✘ | |
| empty | — | 0.0 | sample | ✔ |
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 | |
|---|---|---|---|---|---|
| ass_aa_l | — | T1 + alpha = alpha_T1 sample * (k0d * T1 * alpha - k0r * alpha_T1) | |||
| ass_ab_l | — | alpha + T2 = alpha_T2 sample * (k7d * alpha * T2 - k7r * alpha_T2) | |||
| ass_bc_l | — | beta + T3 = beta_T3 sample * (k14d * beta * T3 - k14r * beta_T3) | |||
| ass_bc_r | — | T3 + Inh = T3_Inh sample * (k16d * T3 * Inh - k16r * T3_Inh) | |||
| ass_bc_rl | — | beta + T3_Inh = beta_T3_Inh sample * (k17d * beta * T3_Inh - k17r * beta_T3_Inh) | |||
| dis_aa | — | alpha_T1_alpha > alpha + alpha_alpha_T1 sample * k5d * alpha_T1_alpha | |||
| dis_ab | — | alpha_T2_beta > beta + alpha_beta_T2 sample * k12d * alpha_T2_beta | |||
| dis_bc | — | beta_T3_Inh > Inh + beta_Inh_T3 sample * k19d * beta_T3_Inh | |||
| exo_a | — | alpha = empty sample * k24d * alpha | |||
| exo_b | — | beta = empty sample * k25d * beta | |||
| exo_c | — | Inh = empty sample * k26d * Inh | |||
| inh_ac | — | T1 + Inh = Inh_T1 sample * (k21d * T1 * Inh - k21r * Inh_T1) | |||
| inh_displ_ac | — | T1_alpha + Inh = alpha + Inh_T1 sample * (k22d * T1_alpha * Inh - k22r * alpha * Inh_T1) | |||
| m_ass_aa_lr | — | alpha_T1_alpha = alpha + alpha_T1 sample * (k1d * alpha_T1_alpha - k1r * alpha * alpha_T1) | |||
| m_ass_aa_r | — | T1_alpha = T1 + alpha sample * (k2d * T1_alpha - k2r * T1 * alpha) | |||
| m_ass_aa_rl | — | alpha_T1_alpha = alpha + T1_alpha sample * (k3d * alpha_T1_alpha - k3r * alpha * T1_alpha) | |||
| m_ass_ab_lr | — | alpha_T2_beta = alpha_T2 + beta sample * (k8d * alpha_T2_beta - k8r * alpha_T2 * beta) | |||
| m_ass_ab_r | — | T2_beta = T2 + beta sample * (k9d * T2_beta - k9r * T2 * beta) | |||
| m_ass_ab_rl | — | alpha_T2_beta = alpha + T2_beta sample * (k10d * alpha_T2_beta - k10r * alpha * T2_beta) | |||
| m_ass_bc_lr | — | beta_T3_Inh = beta_T3 + Inh sample * (k15d * beta_T3_Inh - k15r * beta_T3 * Inh) | |||
| m_inh_displ_ca | — | alpha + Inh_T1 = alpha_T1 + Inh sample * (k23d * alpha * Inh_T1 - k23r * alpha_T1 * Inh) | |||
| nick_aa | — | alpha_alpha_T1 > alpha_T1_alpha sample * k6d * alpha_alpha_T1 | |||
| nick_ab | — | alpha_beta_T2 > alpha_T2_beta sample * k13d * alpha_beta_T2 | |||
| nick_bc | — | beta_Inh_T3 > beta_T3_Inh sample * k20d * beta_Inh_T3 | |||
| pol_aa | — | alpha_T1 > alpha_alpha_T1 sample * k4d * alpha_T1 | |||
| pol_ab | — | alpha_T2 > alpha_beta_T2 sample * k11d * alpha_T2 | |||
| pol_bc | — | beta_T3 > beta_Inh_T3 sample * k18d * beta_T3 |
| Id | Value | |
|---|---|---|
| Bp_concentration | <assignment rule> nM | |
| Inh_total | <assignment rule> nM | |
| alpha_total | <assignment rule> nM | |
| beta_total | <assignment rule> nM | |
| fluorescence | 0.0 | |
| k0d | 0.0294 | |
| k0r | 3.43457943925 per_min | |
| k10d | 3.43457943925 per_min | |
| k10r | 0.0294 | |
| k11d | 11.8408 per_min | |
| k12d | 9.2239832 per_min | |
| k13d | 2.60186 per_min | |
| k14d | 0.0171 | |
| k14r | 0.610714285714 per_min | |
| k15d | 0.00186296832954 per_min | |
| k15r | 0.027 | |
| k16d | 0.027 | |
| k16r | 0.00186296832954 per_min | |
| k17d | 0.0171 | |
| k17r | 0.610714285714 per_min | |
| k18d | 17.024 per_min | |
| k19d | 5.566848 per_min | |
| k1d | 3.43457943925 per_min | |
| k1r | 0.0294 | |
| k20d | 3.2064 per_min | |
| k21d | 0.027 | |
| k21r | 0.00608108108108 per_min | |
| k22d | 0.021546 | |
| k22r | 0.0000415391351351 | |
| k23d | 0.0000415391351351 | |
| k23r | 0.021546 | |
| k24d | 0.411 per_min | |
| k25d | 0.485802 per_min | |
| k26d | 1.7262 per_min | |
| k2d | 3.43457943925 per_min | |
| k2r | 0.0294 | |
| k3d | 3.43457943925 per_min | |
| k3r | 0.0294 | |
| k4d | 15.2 per_min | |
| k5d | 11.8408 per_min | |
| k6d | 3.34 per_min | |
| k7d | 0.0294 | |
| k7r | 3.43457943925 per_min | |
| k8d | 0.610714285714 per_min | |
| k8r | 0.0171 | |
| k9d | 0.610714285714 per_min | |
| k9r | 0.0171 |
| Id | Value | Reaction |
|---|
| Definition | |
|---|---|
| alpha_total = alpha + alpha_T1 + T1_alpha + 2.0 * alpha_T1_alpha + alpha_T2 + alpha_T2_beta + alpha_T2 | |
| beta_total = beta + T2_beta + alpha_T2_beta + beta_T3 + beta_T3_Inh | |
| Inh_total = Inh + T3_Inh + beta_T3_Inh + Inh_T1 | |
| fluorescence = -0.38 + 0.00093 * (11.0 * (alpha_T1 + T1_alpha + alpha_T2 + T2_beta + beta_T3) + 16.0 * (T3_Inh + Inh_T1) + 22.0 * (alpha_T1_alpha + alpha_alpha_T1 + alpha_T2_beta + alpha_beta_T2) + 27.0 * (beta_T3_Inh + beta_Inh_T3)) | |
| Bp_concentration = 11.0 * (alpha_T1 + T1_alpha + alpha_T2 + T2_beta + beta_T3) + 16.0 * (T3_Inh + Inh_T1) + 22.0 * (alpha_T1_alpha + alpha_alpha_T1 + alpha_T2_beta + alpha_beta_T2) + 27.0 * (beta_T3_Inh + beta_Inh_T3) |
| Definition |
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| Definition |
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| Definition |
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| Trigger | Assignments |
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