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 | |
|---|---|---|
| — | 1e-06 litre | |
| — | 1e-12 mole |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| EL | EL | 3.0 | 0.00000259 | |
| LSEC | LSEC | 3.0 | 0.00000047 | |
| MC | MC | 3.0 | 0.00000035 | |
| c1 | nucleus | 3.0 | 0.0000008 | |
| default | cytoplasm | 3.0 | 0.000013 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| IkBa_cytoplasm | IkBa | 0.24615354235788 | default (cytoplasm) | ✘ | |
| IkBa_mRNA_cytoplasm | IkBa_mRNA | 6.25168191520823 | default (cytoplasm) | ✘ | |
| IkBa_mRNA_nucleus | IkBa_mRNA | 0.000170870057152887 | c1 (nucleus) | ✘ | |
| IkBa_pre_mRNA_1 | IkBa_pre_mRNA_1 | 8.4396878325918 | c1 (nucleus) | ✘ | |
| IkBa_pre_mRNA_2 | IkBa_pre_mRNA_2 | 8.4396878325918 | c1 (nucleus) | ✘ | |
| JNK | JNK | 0.982009456703999 | default (cytoplasm) | ✘ | |
| JNK_P | JNK_P | 0.0179905432960006 | default (cytoplasm) | ✘ | |
| LPS | LPS | 5.0 | EL (EL) | ✘ | |
| MSK1 | MSK1 | 14.9998313157222 | c1 (nucleus) | ✘ | |
| MSK1_P | MSK1_P | 0.000168684277806875 | c1 (nucleus) | ✘ | |
| TNFR1_EL | TNFR1 | 0.00122834645669284 | EL (EL) | ✘ | |
| TNFR1_cytoplasm | TNFR1 | 0.0000552755905511779 | default (cytoplasm) | ✘ | |
| TNFa_TNFR1_EL | TNFa:TNFR1 | 0.0 | EL (EL) | ✘ | |
| TNFa_TNFR1_cytoplasm | TNFa:TNFR1 | 0.0 | default (cytoplasm) | ✘ | |
| TNFa_mRNA_LSEC | TNFa_mRNA | 0.0 | LSEC (LSEC) | ✘ | |
| TNFa_mRNA_MC | TNFa_mRNA | 0.0 | MC (MC) | ✘ | |
| TNFa_pre_mRNA_LSEC | TNFa_pre_mRNA | 0.0 | LSEC (LSEC) | ✘ | |
| TNFa_pre_mRNA_MC | TNFa_pre_mRNA | 0.0 | MC (MC) | ✘ | |
| p38 | p38 | 0.829034372153804 | default (cytoplasm) | ✘ | |
| p38_P | p38_P | 0.170965627846196 | default (cytoplasm) | ✘ | |
| p65_2P | p65_2P | 0.000000397559152543905 | c1 (nucleus) | ✘ | |
| p65_IkBa_nucleus | p65-IkBa | 0.000570886877218979 | c1 (nucleus) | ✘ | |
| p65_cytoplasm | p65 | 0.000696598456889738 | default (cytoplasm) | ✘ | |
| p65_mRNA | p65_mRNA | 1.0 | default (cytoplasm) | ✔ | |
| p65_nucleus | p65 | 0.0347787246987784 | c1 (nucleus) | ✘ | |
| s11 | IkBa | 0.492306535300222 | c1 (nucleus) | ✘ | |
| s14 | IKKb | 0.299986251897689 | default (cytoplasm) | ✘ | |
| s15 | IKKb_p | 0.0000137481023113396 | default (cytoplasm) | ✘ | |
| s16 | TNFa | 0.0 | EL (EL) | ✘ | |
| s19 | p65-IkBa | 0.107747249215877 | default (cytoplasm) | ✘ | |
| s3 | p65_P | 0.0045725866204645 | default (cytoplasm) | ✘ | |
| s5 | IkBa_p | 0.0143429657251615 | default (cytoplasm) | ✘ | |
| s8 | p65_P | 0.228543326011228 | c1 (nucleus) | ✘ |
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 | |
|---|---|---|---|---|---|
| Complex_association_c | Complex_association_c | p65_cytoplasm + IkBa_cytoplasm = s19 default * (IkBa_p65_association_k * IkBa_cytoplasm * p65_cytoplasm - IkBa_p65_dissociation_k * s19) | |||
| Complex_degradation_IkBa_c | Complex_degradation_IkBa_c | s19 > p65_cytoplasm default * IkBa_deg_complex_cyt_k * s19 | |||
| Complex_degradation_IkBa_n | Complex_degradation_IkBa_n | p65_IkBa_nucleus > p65_nucleus c1 * IkBa_deg_complex_nuc_k * p65_IkBa_nucleus | |||
| Complex_degradation_p65_c | Complex_degradation_p65_c | s19 > IkBa_cytoplasm default * p65_degradation_k * s19 | |||
| Complex_degradation_p65_n | Complex_degradation_p65_n | p65_IkBa_nucleus > s11 c1 * p65_degradation_k * p65_IkBa_nucleus | |||
| Complex_nuclear_shuttle | Complex_nuclear_shuttle | p65_IkBa_nucleus = s19 IkBa_p65_nuclear_export_k * p65_IkBa_nucleus - IkBa_p65_nuclear_import_k * s19 | |||
| IKK_phosphorylation | IKK_phosphorylation | s14 > s15 default * Catalytic_activation__irrev(s14, TNFa_TNFR1_EL, IKKb_active_phosphorylation_kM, IKKb_active_phosphorylation_vmax, IKKb_active_phosphorylation_kA) | |||
| IkBa_degradation_c | IkBa_degradation_c | IkBa_cytoplasm > ∅ default * IkBa_deg_cyt_k * IkBa_cytoplasm | |||
| IkBa_degradation_n | IkBa_degradation_n | s11 > ∅ c1 * IkBa_deg_nuc_k * s11 | |||
| IkBa_mRNA_degradation_c | IkBa_mRNA_degradation_c | IkBa_mRNA_cytoplasm > ∅ default * IkBa_mRNA_deg_cyt_k * IkBa_mRNA_cytoplasm | |||
| IkBa_mRNA_degradation_n | IkBa_mRNA_degradation_n | IkBa_mRNA_nucleus > ∅ c1 * IkBa_mRNA_deg_nuc_k * IkBa_mRNA_nucleus | |||
| IkBa_mRNA_transport | IkBa_mRNA_transport | IkBa_mRNA_nucleus > IkBa_mRNA_cytoplasm IkBa_mRNA_transport_k * IkBa_mRNA_nucleus | |||
| IkBa_nuclear_shuttle | IkBa_nuclear_shuttle | IkBa_cytoplasm = s11 IkBa_nuclear_import_k * IkBa_cytoplasm - IkBa_nuclear_export_k * s11 | |||
| IkBa_phosphorylation | IkBa_phosphorylation | IkBa_cytoplasm > s5 default * Henri_Michaelis_Menten__irreversible(IkBa_cytoplasm, IkBa_phosphorylation_kM, IkBa_phosphorylation_vmax) | |||
| IkBa_transcription_elongation_1 | IkBa_transcription_elongation_1 | IkBa_pre_mRNA_1 > IkBa_pre_mRNA_2 c1 * IkBa_transcription_elongation_kbasal * IkBa_pre_mRNA_1 | |||
| IkBa_transcription_elongation_2 | IkBa_transcription_elongation_2 | IkBa_pre_mRNA_2 > IkBa_mRNA_nucleus c1 * IkBa_transcription_elongation_kbasal * IkBa_pre_mRNA_2 | |||
| IkBa_translation | IkBa_translation | IkBa_mRNA_cytoplasm > IkBa_mRNA_cytoplasm + IkBa_cytoplasm default * Henri_Michaelis_Menten__irreversible(IkBa_mRNA_cytoplasm, IkBa_translation_Km, IkBa_translation_vmax) | |||
| JNK_active_phosphorylation | JNK_active_phosphorylation | JNK > JNK_P default * Henri_Michaelis_Menten__irreversible(JNK, JNK_active_phoshorylation_Km, JNK_active_phosphorylation_vmax) | |||
| JNK_basal_phosphorylation | JNK_basal_phosphorylation | JNK > JNK_P default * JNK_basal_phosphorylation_k * JNK | |||
| JNK_dephosphorylation | JNK_dephosphorylation | JNK_P > JNK default * JNK_dephosphorylation_k * JNK_P | |||
| LPS_LSEC_degradation | LPS_LSEC_degradation | LPS > ∅ EL * LPS_LSEC_degradation_k * LPS | |||
| LPS_MC_degradation | LPS_MC_degradation | LPS > ∅ EL * LPS_MC_degradation_k * LPS | |||
| MSK1_activation | MSK1_activation | MSK1 > MSK1_P c1 * Henri_Michaelis_Menten__irreversible(MSK1, MSK1_activation_kM, MSK1_activation_vmax) | |||
| MSK1_deactivation | MSK1_deactivation | MSK1_P > MSK1 c1 * MSK1_dephosphorylation_k * MSK1_P | |||
| TNFR1_shuttle | TNFR1_shuttle | TNFR1_cytoplasm = TNFR1_EL k_TNFR1_vessicle2outer_membrane_shuttle * TNFR1_cytoplasm - k_TNFR1_outer_membrane2vessicle_shuttle * TNFR1_EL | |||
| TNFa_LSEC_transcription_elongation | TNFa_LSEC_transcription_elongation | TNFa_pre_mRNA_LSEC > TNFa_mRNA_LSEC LSEC * TNFa_LSEC_transcription_elongation_k * TNFa_pre_mRNA_LSEC | |||
| TNFa_LSEC_transcription_initiation | TNFa_LSEC_transcription_initiation | ∅ > {2.0}TNFa_pre_mRNA_LSEC LSEC * TNFa_transcription_initiation(TNFa_LSEC_transcription_initiation_kbasal, TNFa_LSEC_transcription_initiation_vA_LPS, LPS, TNFa_LSEC_transcription_initiation_kA_LPS) | |||
| TNFa_LSEC_translation | TNFa_LSEC_translation | TNFa_mRNA_LSEC > TNFa_mRNA_LSEC + s16 TNFa_LSEC_translation_k * TNFa_mRNA_LSEC | |||
| TNFa_MC_transcription_elongation | TNFa_MC_transcription_elongation | TNFa_pre_mRNA_MC > TNFa_mRNA_MC MC * TNFa_MC_transcription_elongation_k * TNFa_pre_mRNA_MC | |||
| TNFa_MC_transcription_initiation | TNFa_MC_transcription_initiation | ∅ > {2.0}TNFa_pre_mRNA_MC MC * TNFa_transcription_initiation(TNFa_MC_transcription_initiation_kbasal, TNFa_MC_transcription_initiation_vA_LPS, LPS, TNFa_MC_transcription_initiation_kA_LPS) | |||
| TNFa_MC_translation | TNFa_MC_translation | TNFa_mRNA_MC > TNFa_mRNA_MC + s16 TNFa_MC_translation_k * TNFa_mRNA_MC | |||
| TNFa_TNFR1_association | TNFa:TNFR1_association | TNFR1_EL + s16 = TNFa_TNFR1_EL EL * (k_TNFa_TNFR1_association * TNFR1_EL * s16 - k_TNFa_TNFR1_dissociation * TNFa_TNFR1_EL) | |||
| TNFa_TNFR1_internalisation | TNFa:TNFR1_internalisation | TNFa_TNFR1_EL > TNFa_TNFR1_cytoplasm k_TNFa_TNFR1_internalisation * TNFa_TNFR1_EL | |||
| TNFa_degradation | TNFa degradation | s16 > ∅ EL * TNFa_degradation_k * s16 | |||
| TNFa_internal_degradation | TNFa_internal_degradation | TNFa_TNFR1_cytoplasm > TNFR1_cytoplasm default * k_TNFa_internal_degradation * TNFa_TNFR1_cytoplasm | |||
| TNFa_mRNA_LSEC_degradation | TNFa_mRNA_LSEC_degradation | TNFa_mRNA_LSEC > ∅ LSEC * TNFa_mRNA_LSEC_degradation_k * TNFa_mRNA_LSEC | |||
| TNFa_mRNA_MC_degradation | TNFa_mRNA_MC_degradation | TNFa_mRNA_MC > ∅ MC * TNFa_mRNA_MC_degradation_k * TNFa_mRNA_MC | |||
| basal_IKKb_phosphorylation | basal_IKKb_phosphorylation | s14 > s15 default * IKKb_basal_phosphoylation_k * s14 | |||
| p38_active_phosphorylation | p38_active_phosphorylation | p38 > p38_P default * Henri_Michaelis_Menten__irreversible(p38, p38_active_phoshorylation_Km, p38_active_phosphorylation_vmax) | |||
| p38_basal_phosphorylation | p38_basal_phosphorylation | p38 > p38_P default * p38_basal_phosphorylation_k * p38 | |||
| p38_dephosphorylation | p38_dephosphorylation | p38_P > p38 default * p38_dephosphorylation_k * p38_P | |||
| p65_2P_degradation | p65_2P_degradation | p65_2P > ∅ c1 * p65_degradation_k * p65_2P | |||
| p65_2P_dephosphorylation_0 | p65_2P_dephosphorylation | p65_2P > p65_nucleus c1 * p65_2P_dephosphorylation * p65_2P | |||
| p65_P_degradation_c | p65_P_degradation_c | s3 > ∅ default * p65_degradation_k * s3 | |||
| p65_P_degradation_n | p65_P_degradation_n | s8 > ∅ c1 * p65_degradation_k * s8 | |||
| p65_P_dephosphorylation_c | p65_P_dephosphorylation_c | s8 > p65_nucleus c1 * p65_P_dephosphorylation_k * s8 | |||
| p65_P_dephosphorylation_n | p65_P_dephosphorylation_n | s3 > p65_cytoplasm default * p65_P_dephosphorylation_k * s3 | |||
| p65_P_phosphorylation_MSK1 | p65_P_phosphorylation_MSK1 | s8 > p65_2P c1 * Henri_Michaelis_Menten__irreversible(s8, p65_P_MSK1_phosphrylation_kM, p65_P_MSK1_phosphrylation_vmax) | |||
| p65_nuclear_shuttle | p65_nuclear_shuttle | p65_cytoplasm = p65_nucleus p65_nuclear_import_k * p65_cytoplasm - p65_nuclear_export_k * p65_nucleus | |||
| p65_phosphorylation_MSK1 | p65_phosphorylation_MSK1 | p65_nucleus > p65_2P c1 * Henri_Michaelis_Menten__irreversible(p65_nucleus, p65_MSK1_phosphorylation_kM, p65_MSK1_phosphrylation_vmax) | |||
| p65_translation | p65_translation | p65_mRNA > p65_mRNA + p65_cytoplasm default * p65_translation_k * p65_mRNA | |||
| re10 | IkBa_transcription_initiation | ∅ > IkBa_pre_mRNA_1 c1 * activated_Transcription__1(IkBa_transcription_initiation_kbasal, IkBa_transcription_kA2_p65_P, s8, IkBa_transcription_kA_p65, p65_nucleus, p65_2P, IkBa_transcription_kA3_p65_2P) | |||
| re14 | IkBa_p_active_degradation | s5 > ∅ default * IkBa_p_active_degradation_k * s5 | |||
| re15 | Complex_phosphorylation | s19 > s3 + s5 default * Henri_Michaelis_Menten__irreversible(s19, IkBa_p65_phosphorylation_kM, IkBa_p65_phosphorylation_vmax) | |||
| re17 | dephosphorylation IKK | s15 > s14 default * IKKb_dephopshorylation_k * s15 | |||
| re19 | Complex_association_n | p65_nucleus + s11 = p65_IkBa_nucleus c1 * (IkBa_p65_association_k * p65_nucleus * s11 - IkBa_p65_dissociation_k * p65_IkBa_nucleus) | |||
| re3 | p65_P_nuclear_shuttle | s3 = s8 p65_nuclear_import_k * s3 - p65_nuclear_export_k * s8 |
| Id | Value | |
|---|---|---|
| IKKb_active_phosphorylation_kA | 1.12012501519371 | |
| IKKb_active_phosphorylation_kM | 5.0 | |
| IKKb_active_phosphorylation_vmax | 999.999747666759 | |
| IKKb_basal_phosphoylation_k | 0.000000100000000221985 | |
| IKKb_dephopshorylation_k | 0.00218201934907053 | |
| IkBa_deg_complex_cyt_k | 0.00001 | |
| IkBa_deg_complex_nuc_k | 0.0000100784831509279 | |
| IkBa_deg_cyt_k | 0.0000263184315126283 | |
| IkBa_deg_nuc_k | 0.00001 | |
| IkBa_mRNA_deg_cyt_k | 0.000210245030513269 | |
| IkBa_mRNA_deg_nuc_k | 0.00005 | |
| IkBa_mRNA_transport_k | 0.0001 | |
| IkBa_nuclear_export_k | 0.0025 | |
| IkBa_nuclear_import_k | 0.005 | |
| IkBa_p65_association_k | 0.0999999999999998 | |
| IkBa_p65_dissociation_k | 0.000299999999999999 | |
| IkBa_p65_nuclear_export_k | 0.00199999999048107 | |
| IkBa_p65_nuclear_import_k | 0.0000105840674496221 | |
| IkBa_p65_phosphorylation_kM | 0.1 | |
| IkBa_p65_phosphorylation_kcat | 12.2948323895773 | |
| IkBa_p65_phosphorylation_vmax | 0.000169030613592681 | |
| IkBa_p_active_degradation_k | 0.00999999999999978 | |
| IkBa_phosphorylation_kM | 0.5 | |
| IkBa_phosphorylation_kcat | 12.2948323895773 | |
| IkBa_phosphorylation_vmax | 0.000169030613592681 | |
| IkBa_transcription_elongation_kbasal | 0.00253075304576218 | |
| IkBa_transcription_initiation_kbasal | 0.000001 | |
| IkBa_transcription_kA2_p65_P | 0.000100000000000222 | |
| IkBa_transcription_kA3_p65_2P | 0.000129463705141222 | |
| IkBa_transcription_kA_p65 | 0.61344720050337 | |
| IkBa_translation_Km | 9.86262014219756 | |
| IkBa_translation_vmax | 0.000389961249687994 | |
| JNK_active_phoshorylation_Km | 1.40482967455377 | |
| JNK_active_phosphorylation_kcat | 14242.2772650189 | |
| JNK_active_phosphorylation_vmax | 0.0 | |
| JNK_basal_phosphorylation_k | 0.0000129042787872645 | |
| JNK_dephosphorylation_k | 0.000704376938069221 | |
| LPS_LSEC_degradation_k | 0.000333538717101295 | |
| LPS_MC_degradation_k | 0.000144691531716043 | |
| MSK1_activation_kM | 0.332175 | |
| MSK1_activation_vmax | 0.00000172419833147535 | |
| MSK1_dephosphorylation_k | 0.00999999999999978 | |
| MSK1_phosphorylation_kcat | 0.0000100850583429932 | |
| TNFa_LSEC_transcription_elongation_k | 0.00000100000000022204 | |
| TNFa_LSEC_transcription_initiation_kA_LPS | 0.978126286843748 | |
| TNFa_LSEC_transcription_initiation_kbasal | 0.0 | |
| TNFa_LSEC_transcription_initiation_vA_LPS | 0.000012024024024793 | |
| TNFa_LSEC_translation_k | 0.0000213500321684928 | |
| TNFa_MC_transcription_elongation_k | 0.00000100000000022204 | |
| TNFa_MC_transcription_initiation_kA_LPS | 0.754012694494756 | |
| TNFa_MC_transcription_initiation_kbasal | 0.0 | |
| TNFa_MC_transcription_initiation_vA_LPS | 0.00000546584093798564 | |
| TNFa_MC_translation_k | 0.00000200280657450139 | |
| TNFa_degradation_k | 0.000107644105772485 | |
| TNFa_mRNA_LSEC_degradation_k | 0.608933606390876 | |
| TNFa_mRNA_MC_degradation_k | 0.0555247609448968 | |
| k_IkBa | 248129.354373767 | |
| k_IkBa_P | 2634581.18888326 | |
| k_IkBa_mRNA | 4483.90580831975 | |
| k_JNK_P | 2915421.59670066 | |
| k_MSK_P | 4826667313.54863 | |
| k_TNFR1_outer_membrane2vessicle_shuttle | 0.000018 | |
| k_TNFR1_vessicle2outer_membrane_shuttle | 0.0004 | |
| k_TNFa_TNFR1_association | 16.833 | |
| k_TNFa_TNFR1_dissociation | 0.000319827 | |
| k_TNFa_TNFR1_internalisation | 0.00077 | |
| k_TNFa_internal_degradation | 0.0000679015845264866 | |
| k_p38_P | 370308.147436699 | |
| k_p65 | 0.102372088824604 | |
| k_p65_P | 2310916.12550826 | |
| p38_active_phoshorylation_Km | 1.0884807748579 | |
| p38_active_phosphorylation_kcat | 139948.704840381 | |
| p38_active_phosphorylation_vmax | 0.0 | |
| p38_basal_phosphorylation_k | 0.00019306790829154 | |
| p38_dephosphorylation_k | 0.000936211179697006 | |
| p65_2P_dephosphorylation | 0.00469068413708133 | |
| p65_MSK1_phosphorylation_kM | 0.00190442700767811 | |
| p65_MSK1_phosphrylation_kcat | 0.00000571518737470576 | |
| p65_MSK1_phosphrylation_vmax | 0.000000000964062254833211 | |
| p65_P_MSK1_phosphrylation_kM | 0.00190442700767811 | |
| p65_P_MSK1_phosphrylation_kcat | 0.00000571518737470576 | |
| p65_P_MSK1_phosphrylation_vmax | 0.000000000964062254833211 | |
| p65_P_dephosphorylation_k | 0.00469068413708133 | |
| p65_degradation_k | 0.00001328912101 | |
| p65_nuclear_export_k | 0.00001 | |
| p65_nuclear_import_k | 0.0005 | |
| p65_translation_k | 0.00000168 | |
| scaled_IkBa | 1.285675 | |
| scaled_IkBa_P | 0.491240200000003 | |
| scaled_IkBa_mRNA | 0.364416 | |
| scaled_JNK_P | 0.68185024 | |
| scaled_MSK_P | 0.651346312 | |
| scaled_p38_P | 0.823029544 | |
| scaled_p65 | 0.000000172018719408048 | |
| scaled_p65_P | 0.559884800000002 | |
| unscaled_IkBa | 0.0000051814707826279 | |
| unscaled_IkBa_P | 0.0000001864585544271 | |
| unscaled_IkBa_mRNA | 0.0000812720015937527 | |
| unscaled_JNK_P | 0.000000233877062848008 | |
| unscaled_MSK_P | 0.0000000001349474222455 | |
| unscaled_p38_P | 0.00000222255316200055 | |
| unscaled_p65 | 0.00000168032831392911 | |
| unscaled_p65_P | 0.000000242278286875021 |
| Id | Value | Reaction |
|---|
| Definition | |
|---|---|
| unscaled_JNK_P = default * JNK_P | |
| IkBa_phosphorylation_kcat = IkBa_p65_phosphorylation_kcat | |
| p65_MSK1_phosphrylation_vmax = p65_MSK1_phosphrylation_kcat * MSK1_P | |
| k_TNFa_TNFR1_dissociation = k_TNFa_TNFR1_association * 1.9e-5 | |
| unscaled_MSK_P = c1 * MSK1_P | |
| scaled_MSK_P = k_MSK_P * unscaled_MSK_P | |
| IkBa_nuclear_export_k = IkBa_nuclear_import_k * 0.5 | |
| scaled_p65 = k_p65 * unscaled_p65 | |
| IkBa_phosphorylation_vmax = IkBa_phosphorylation_kcat * s15 | |
| unscaled_IkBa_P = s5 * default | |
| scaled_IkBa_P = k_IkBa_P * unscaled_IkBa_P | |
| p65_P_MSK1_phosphrylation_vmax = p65_P_MSK1_phosphrylation_kcat * MSK1_P | |
| p65_2P_dephosphorylation = p65_P_dephosphorylation_k * 1.0 | |
| unscaled_p38_P = default * p38_P | |
| scaled_p38_P = k_p38_P * unscaled_p38_P | |
| p65_nuclear_export_k = p65_nuclear_import_k * 0.02 | |
| scaled_p65_P = k_p65_P * unscaled_p65_P | |
| IkBa_p65_phosphorylation_vmax = IkBa_p65_phosphorylation_kcat * s15 | |
| IkBa_p65_dissociation_k = IkBa_p65_association_k * 0.003 | |
| unscaled_p65_P = c1 * s8 + default * s3 | |
| scaled_IkBa_mRNA = k_IkBa_mRNA * unscaled_IkBa_mRNA | |
| unscaled_IkBa_mRNA = IkBa_mRNA_cytoplasm * default + c1 * IkBa_mRNA_nucleus | |
| MSK1_activation_vmax = MSK1_phosphorylation_kcat * p38_P | |
| p65_P_MSK1_phosphrylation_kcat = p65_MSK1_phosphrylation_kcat * 1.0 | |
| scaled_IkBa = k_IkBa * unscaled_IkBa | |
| unscaled_IkBa = (s11 + p65_IkBa_nucleus) * c1 + (s5 + s19 + IkBa_cytoplasm) * default | |
| unscaled_p65 = (s3 + s19 + p65_cytoplasm) * default + c1 * (s8 + p65_IkBa_nucleus + p65_nucleus + p65_2P) | |
| JNK_active_phosphorylation_vmax = JNK_active_phosphorylation_kcat * TNFa_TNFR1_EL | |
| p65_P_MSK1_phosphrylation_kM = p65_MSK1_phosphorylation_kM * 1.0 | |
| scaled_JNK_P = k_JNK_P * unscaled_JNK_P | |
| p38_active_phosphorylation_vmax = p38_active_phosphorylation_kcat * TNFa_TNFR1_EL |
| Definition |
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| Definition |
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| Definition | |
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| Catalytic_activation__irrev(substrate, Activator, Kms, V, Ka) = V * substrate * Activator / ((Kms + substrate) * (Ka + Activator)) | |
| Henri_Michaelis_Menten__irreversible(substrate, Km, V) = V * substrate / (Km + substrate) | |
| activated_Transcription__1(k1, k2, Modifier, k3, Modifier2, Modifier3, k4) = k1 + k2 * Modifier + k3 * Modifier2 + k4 * Modifier3 | |
| TNFa_transcription_initiation(kbasal, vA, A, kA) = kbasal + vA * A / (A + kA) |
| Trigger | Assignments |
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