pathak1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000491) Biomodels notes: Figure 3a of the reference publication has been reproduced here. The model was simulated using SBML odeSolver and the plot was generated using Gnuplot. Note: The model is not loading in Copasi (core dump error). 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 | |
|---|---|
| pathak2013_Fig3A |
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 | |
| — | 0.001 litre | |
| — | 1.0 metre^(2.0) | |
| — | 1.0 metre | |
| — | 1.0 second | |
| — | 1.0 second^(-1.0) |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| c1 | Cytosol | 3.0 | 1.0 volume | |
| c2 | Nucleus | 3.0 | 1.0 volume | |
| default | — | 3.0 | 1.0 volume |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| s1 | Cold | 0.5 substance | default | ✘ | |
| s10 | LecRK2 | 0.8 substance | c1 (Cytosol) | ✘ | |
| s11 | ETR1 | 0.8 substance | c1 (Cytosol) | ✘ | |
| s12 | ETR2 | 0.8 substance | c1 (Cytosol) | ✘ | |
| s13 | MAPKKK | 1.0 substance | c1 (Cytosol) | ✘ | |
| s14 | MAPKKK | 1.0 substance | c1 (Cytosol) | ✘ | |
| s15 | MAPKKK1 | 1.0 substance | c1 (Cytosol) | ✘ | |
| s16 | CTR1 | 1.0 substance | c1 (Cytosol) | ✘ | |
| s17 | MAPKK | 1.0 substance | c1 (Cytosol) | ✘ | |
| s18 | MAPKK | 1.0 substance | c1 (Cytosol) | ✘ | |
| s19 | MAPKK1 | 1.0 substance | c1 (Cytosol) | ✘ | |
| s2 | Salt | 0.5 substance | default | ✘ | |
| s20 | MAPKK2 | 1.0 substance | c1 (Cytosol) | ✘ | |
| s21 | MAPKK3 | 1.0 substance | c1 (Cytosol) | ✘ | |
| s22 | MAPKK4 | 1.0 substance | c1 (Cytosol) | ✘ | |
| s23 | MAPKK5 | 1.0 substance | c1 (Cytosol) | ✘ | |
| s24 | MAPKK6 | 1.0 substance | c1 (Cytosol) | ✘ | |
| s25 | MAPKK7 | 1.0 substance | c1 (Cytosol) | ✘ | |
| s26 | MAPKK9 | 1.0 substance | c1 (Cytosol) | ✘ | |
| s27 | MAPK | 1.0 substance | c1 (Cytosol) | ✘ | |
| s28 | MAPK | 1.0 substance | c1 (Cytosol) | ✘ | |
| s29 | MAPK2 | 1.0 substance | c1 (Cytosol) | ✘ | |
| s3 | Drought | 0.5 substance | default | ✘ | |
| s30 | MAPK3 | 1.0 substance | c1 (Cytosol) | ✘ | |
| s31 | MAPK4 | 1.0 substance | c1 (Cytosol) | ✘ | |
| s32 | MAPK6 | 1.0 substance | c1 (Cytosol) | ✘ | |
| s33 | WRKY1 | 1.2 substance | c2 (Nucleus) | ✘ | |
| s34 | WRKY1 | 1.2 substance | c2 (Nucleus) | ✘ | |
| s35 | WRKY12 | 1.2 substance | c2 (Nucleus) | ✘ | |
| s36 | WRKY12 | 1.2 substance | c2 (Nucleus) | ✘ | |
| s37 | WRKY8 | 1.2 substance | c2 (Nucleus) | ✘ | |
| s38 | WRKY8 | 1.2 substance | c2 (Nucleus) | ✘ | |
| s39 | WRKY25 | 1.2 substance | c2 (Nucleus) | ✘ | |
| s4 | H2O2 | 0.5 substance | default | ✘ | |
| s40 | WRKY25 | 1.2 substance | c2 (Nucleus) | ✘ | |
| s41 | WRKY22 | 1.2 substance | c2 (Nucleus) | ✘ | |
| s42 | WRKY22 | 1.2 substance | c2 (Nucleus) | ✘ | |
| s43 | WRKY29 | 1.2 substance | c2 (Nucleus) | ✘ | |
| s44 | WRKY29 | 1.2 substance | c2 (Nucleus) | ✘ | |
| s45 | WRKY33 | 1.2 substance | c2 (Nucleus) | ✘ | |
| s46 | WRKY33 | 1.2 substance | c2 (Nucleus) | ✘ | |
| s47 | WRKY28 | 1.2 substance | c2 (Nucleus) | ✘ | |
| s48 | WRKY28 | 1.2 substance | c2 (Nucleus) | ✘ | |
| s49 | MYB2 | 1.5 substance | c2 (Nucleus) | ✘ | |
| s5 | Heavy Metal | 0.5 substance | default | ✘ | |
| s50 | MYB2 | 1.5 substance | c2 (Nucleus) | ✘ | |
| s51 | MYB4 | 1.5 substance | c2 (Nucleus) | ✘ | |
| s52 | MYB4 | 1.5 substance | c2 (Nucleus) | ✘ | |
| s53 | MYB44 | 1.5 substance | c2 (Nucleus) | ✘ | |
| s54 | NAC | 1.8 substance | c2 (Nucleus) | ✘ | |
| s55 | bZIP | 2.0 substance | c2 (Nucleus) | ✘ | |
| s56 | AP2 | 2.2 substance | c2 (Nucleus) | ✘ | |
| s57 | Response | 2.5 substance | default | ✘ | |
| s6 | Ethylene | 0.5 substance | default | ✘ | |
| s7 | RLKs | 0.8 substance | c1 (Cytosol) | ✘ | |
| s8 | LRR | 0.8 substance | c1 (Cytosol) | ✘ | |
| s9 | CRKs | 0.8 substance | c1 (Cytosol) | ✘ |
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 | |
|---|---|---|---|---|---|
| re1 | — | s1 = s7 kass_re1 * s1 - kdiss_re1 * s7 | |||
| re10 | — | s4 = s7 kass_re10 * s4 - kdiss_re10 * s7 | |||
| re11 | — | s5 = s7 kass_re11 * s5 - kdiss_re11 * s7 | |||
| re12 | — | s13 = s14 kass_re12 * s13 - kdiss_re12 * s14 | |||
| re13 | — | s7 = s13 kass_re13 * s7 - kdiss_re13 * s13 | |||
| re14 | — | s8 = s13 kass_re14 * s8 - kdiss_re14 * s13 | |||
| re15 | — | s9 = s13 kass_re15 * s9 - kdiss_re15 * s13 | |||
| re16 | — | s10 = s13 kass_re16 * s10 - kdiss_re16 * s13 | |||
| re17 | — | s14 = s15 kass_re17 * s14 - kdiss_re17 * s15 | |||
| re18 | — | s7 = s15 kass_re18 * s7 - kdiss_re18 * s15 | |||
| re19 | — | s14 = s16 kass_re19 * s14 - kdiss_re19 * s16 | |||
| re2 | — | s2 = s7 kass_re2 * s2 - kdiss_re2 * s7 | |||
| re20 | — | s11 = s16 kass_re20 * s11 - kdiss_re20 * s16 | |||
| re21 | — | s12 = s16 kass_re21 * s12 - kdiss_re21 * s16 | |||
| re22 | — | s17 = s18 kass_re22 * s17 - kdiss_re22 * s18 | |||
| re23 | — | s14 = s17 kass_re23 * s14 - kdiss_re23 * s17 | |||
| re24 | — | s18 = s19 kass_re24 * s18 - kdiss_re24 * s19 | |||
| re25 | — | s18 = s20 kass_re25 * s18 - kdiss_re25 * s20 | |||
| re26 | — | s18 = s21 kass_re26 * s18 - kdiss_re26 * s21 | |||
| re27 | — | s18 = s22 kass_re27 * s18 - kdiss_re27 * s22 | |||
| re28 | — | s18 = s23 kass_re28 * s18 - kdiss_re28 * s23 | |||
| re29 | — | s18 = s24 kass_re29 * s18 - kdiss_re29 * s24 | |||
| re3 | — | s2 = s8 kass_re3 * s2 - kdiss_re3 * s8 | |||
| re30 | — | s18 = s25 kass_re30 * s18 - kdiss_re30 * s25 | |||
| re31 | — | s18 = s26 kass_re31 * s18 - kdiss_re31 * s26 | |||
| re32 | — | s27 = s28 kass_re32 * s27 - kdiss_re32 * s28 | |||
| re33 | — | s18 = s27 kass_re33 * s18 - kdiss_re33 * s27 | |||
| re34 | — | s15 = s19 kass_re34 * s15 - kdiss_re34 * s19 | |||
| re35 | — | s15 = s20 kass_re35 * s15 - kdiss_re35 * s20 | |||
| re36 | — | s16 = s26 kass_re36 * s16 - kdiss_re36 * s26 | |||
| re37 | — | s28 = s29 kass_re37 * s28 - kdiss_re37 * s29 | |||
| re38 | — | s28 = s30 kass_re38 * s28 - kdiss_re38 * s30 | |||
| re39 | — | s28 = s31 kass_re39 * s28 - kdiss_re39 * s31 | |||
| re4 | — | s2 = s9 kass_re4 * s2 - kdiss_re4 * s9 | |||
| re40 | — | s28 = s32 kass_re40 * s28 - kdiss_re40 * s32 | |||
| re41 | — | s20 = s30 kass_re41 * s20 - kdiss_re41 * s30 | |||
| re42 | — | s20 = s31 kass_re42 * s20 - kdiss_re42 * s31 | |||
| re43 | — | s20 = s32 kass_re43 * s20 - kdiss_re43 * s32 | |||
| re44 | — | s26 = s30 kass_re44 * s26 - kdiss_re44 * s30 | |||
| re45 | — | s33 = s34 kass_re45 * s33 - kdiss_re45 * s34 | |||
| re46 | — | s35 = s36 kass_re46 * s35 - kdiss_re46 * s36 | |||
| re47 | — | s37 = s38 kass_re47 * s37 - kdiss_re47 * s38 | |||
| re48 | — | s39 = s40 kass_re48 * s39 - kdiss_re48 * s40 | |||
| re49 | — | s41 = s42 kass_re49 * s41 - kdiss_re49 * s42 | |||
| re5 | — | s6 = s12 kass_re5 * s6 - kdiss_re5 * s12 | |||
| re50 | — | s43 = s44 kass_re50 * s43 - kdiss_re50 * s44 | |||
| re51 | — | s45 = s46 kass_re51 * s45 - kdiss_re51 * s46 | |||
| re52 | — | s47 = s48 kass_re52 * s47 - kdiss_re52 * s48 | |||
| re53 | — | s49 = s50 kass_re53 * s49 - kdiss_re53 * s50 | |||
| re54 | — | s51 = s52 kass_re54 * s51 - kdiss_re54 * s52 | |||
| re55 | — | s29 = s37 kass_re55 * s29 - kdiss_re55 * s37 | |||
| re56 | — | s29 = s33 kass_re56 * s29 - kdiss_re56 * s33 | |||
| re57 | — | s30 = s35 kass_re57 * s30 - kdiss_re57 * s35 | |||
| re58 | — | s30 = s41 kass_re58 * s30 - kdiss_re58 * s41 | |||
| re59 | — | s30 = s47 kass_re59 * s30 - kdiss_re59 * s47 | |||
| re6 | — | s6 = s11 kass_re6 * s6 - kdiss_re6 * s11 | |||
| re60 | — | s31 = s33 kass_re60 * s31 - kdiss_re60 * s33 | |||
| re61 | — | s31 = s45 kass_re61 * s31 - kdiss_re61 * s45 | |||
| re62 | — | s31 = s39 kass_re62 * s31 - kdiss_re62 * s39 | |||
| re63 | — | s32 = s47 kass_re63 * s32 - kdiss_re63 * s47 | |||
| re64 | — | s32 = s45 kass_re64 * s32 - kdiss_re64 * s45 | |||
| re65 | — | s32 = s35 kass_re65 * s32 - kdiss_re65 * s35 | |||
| re66 | — | s28 = s56 kass_re66 * s28 - kdiss_re66 * s56 | |||
| re67 | — | s28 = s49 kass_re67 * s28 - kdiss_re67 * s49 | |||
| re68 | — | s28 = s51 kass_re68 * s28 - kdiss_re68 * s51 | |||
| re69 | — | s28 = s53 kass_re69 * s28 - kdiss_re69 * s53 | |||
| re7 | — | s6 = s10 kass_re7 * s6 - kdiss_re7 * s10 | |||
| re70 | — | s28 = s54 kass_re70 * s28 - kdiss_re70 * s54 | |||
| re71 | — | s28 = s55 kass_re71 * s28 - kdiss_re71 * s55 | |||
| re72 | — | s40 = s57 kass_re72 * s40 - kdiss_re72 * s57 | |||
| re73 | — | s53 = s57 kass_re73 * s53 - kdiss_re73 * s57 | |||
| re74 | — | s54 = s57 kass_re74 * s54 - kdiss_re74 * s57 | |||
| re75 | — | s52 = s57 kass_re75 * s52 - kdiss_re75 * s57 | |||
| re76 | — | s50 = s57 kass_re76 * s50 - kdiss_re76 * s57 | |||
| re77 | — | s56 = s57 kass_re77 * s56 - kdiss_re77 * s57 | |||
| re78 | — | s48 = s57 kass_re78 * s48 - kdiss_re78 * s57 | |||
| re79 | — | s30 = s43 kass_re79 * s30 - kdiss_re79 * s43 | |||
| re8 | — | s3 = s9 kass_re8 * s3 - kdiss_re8 * s9 | |||
| re80 | — | s55 = s57 kass_re80 * s55 - kdiss_re80 * s57 | |||
| re81 | — | s42 = s57 kass_re81 * s42 - kdiss_re81 * s57 | |||
| re82 | — | s44 = s57 kass_re82 * s44 - kdiss_re82 * s57 | |||
| re83 | — | s38 = s57 kass_re83 * s38 - kdiss_re83 * s57 | |||
| re84 | — | s36 = s57 kass_re84 * s36 - kdiss_re84 * s57 | |||
| re85 | — | s34 = s57 kass_re85 * s34 - kdiss_re85 * s57 | |||
| re86 | — | s46 = s57 kass_re86 * s46 - kdiss_re86 * s57 | |||
| re9 | — | s3 = s7 kass_re9 * s3 - kdiss_re9 * s7 |
| Id | Value | |
|---|---|---|
| kass_re1 | 1.0 per_second | |
| kass_re10 | 1.0 per_second | |
| kass_re11 | 1.0 per_second | |
| kass_re12 | 1.0 per_second | |
| kass_re13 | 1.0 per_second | |
| kass_re14 | 1.0 per_second | |
| kass_re15 | 1.0 per_second | |
| kass_re16 | 1.0 per_second | |
| kass_re17 | 1.0 per_second | |
| kass_re18 | 1.0 per_second | |
| kass_re19 | 1.0 per_second | |
| kass_re2 | 1.0 per_second | |
| kass_re20 | 1.0 per_second | |
| kass_re21 | 1.0 per_second | |
| kass_re22 | 1.0 per_second | |
| kass_re23 | 1.0 per_second | |
| kass_re24 | 1.0 per_second | |
| kass_re25 | 1.0 per_second | |
| kass_re26 | 1.0 per_second | |
| kass_re27 | 1.0 per_second | |
| kass_re28 | 1.0 per_second | |
| kass_re29 | 1.0 per_second | |
| kass_re3 | 1.0 per_second | |
| kass_re30 | 1.0 per_second | |
| kass_re31 | 1.0 per_second | |
| kass_re32 | 1.0 per_second | |
| kass_re33 | 1.0 per_second | |
| kass_re34 | 1.0 per_second | |
| kass_re35 | 1.0 per_second | |
| kass_re36 | 1.0 per_second | |
| kass_re37 | 1.0 per_second | |
| kass_re38 | 1.0 per_second | |
| kass_re39 | 1.0 per_second | |
| kass_re4 | 1.0 per_second | |
| kass_re40 | 1.0 per_second | |
| kass_re41 | 1.0 per_second | |
| kass_re42 | 1.0 per_second | |
| kass_re43 | 1.0 per_second | |
| kass_re44 | 1.0 per_second | |
| kass_re45 | 1.0 per_second | |
| kass_re46 | 1.0 per_second | |
| kass_re47 | 1.0 per_second | |
| kass_re48 | 1.0 per_second | |
| kass_re49 | 1.0 per_second | |
| kass_re5 | 1.0 per_second | |
| kass_re50 | 1.0 per_second | |
| kass_re51 | 1.0 per_second | |
| kass_re52 | 1.0 per_second | |
| kass_re53 | 1.0 per_second | |
| kass_re54 | 1.0 per_second | |
| kass_re55 | 1.0 per_second | |
| kass_re56 | 1.0 per_second | |
| kass_re57 | 1.0 per_second | |
| kass_re58 | 1.0 per_second | |
| kass_re59 | 1.0 per_second | |
| kass_re6 | 1.0 per_second | |
| kass_re60 | 1.0 per_second | |
| kass_re61 | 1.0 per_second | |
| kass_re62 | 1.0 per_second | |
| kass_re63 | 1.0 per_second | |
| kass_re64 | 1.0 per_second | |
| kass_re65 | 1.0 per_second | |
| kass_re66 | 1.0 per_second | |
| kass_re67 | 1.0 per_second | |
| kass_re68 | 1.0 per_second | |
| kass_re69 | 1.0 per_second | |
| kass_re7 | 1.0 per_second | |
| kass_re70 | 1.0 per_second | |
| kass_re71 | 1.0 per_second | |
| kass_re72 | 1.0 per_second | |
| kass_re73 | 1.0 per_second | |
| kass_re74 | 1.0 per_second | |
| kass_re75 | 1.0 per_second | |
| kass_re76 | 1.0 per_second | |
| kass_re77 | 1.0 per_second | |
| kass_re78 | 1.0 per_second | |
| kass_re79 | 1.0 per_second | |
| kass_re8 | 1.0 per_second | |
| kass_re80 | 1.0 per_second | |
| kass_re81 | 1.0 per_second | |
| kass_re82 | 1.0 per_second | |
| kass_re83 | 1.0 per_second | |
| kass_re84 | 1.0 per_second | |
| kass_re85 | 1.0 per_second | |
| kass_re86 | 1.0 per_second | |
| kass_re9 | 1.0 per_second | |
| kdiss_re1 | 1.0 per_second | |
| kdiss_re10 | 1.0 per_second | |
| kdiss_re11 | 1.0 per_second | |
| kdiss_re12 | 1.0 per_second | |
| kdiss_re13 | 1.0 per_second | |
| kdiss_re14 | 1.0 per_second | |
| kdiss_re15 | 1.0 per_second | |
| kdiss_re16 | 1.0 per_second | |
| kdiss_re17 | 1.0 per_second | |
| kdiss_re18 | 1.0 per_second | |
| kdiss_re19 | 1.0 per_second | |
| kdiss_re2 | 1.0 per_second | |
| kdiss_re20 | 1.0 per_second | |
| kdiss_re21 | 1.0 per_second | |
| kdiss_re22 | 1.0 per_second | |
| kdiss_re23 | 1.0 per_second | |
| kdiss_re24 | 1.0 per_second | |
| kdiss_re25 | 1.0 per_second | |
| kdiss_re26 | 1.0 per_second | |
| kdiss_re27 | 1.0 per_second | |
| kdiss_re28 | 1.0 per_second | |
| kdiss_re29 | 1.0 per_second | |
| kdiss_re3 | 1.0 per_second | |
| kdiss_re30 | 1.0 per_second | |
| kdiss_re31 | 1.0 per_second | |
| kdiss_re32 | 1.0 per_second | |
| kdiss_re33 | 1.0 per_second | |
| kdiss_re34 | 1.0 per_second | |
| kdiss_re35 | 1.0 per_second | |
| kdiss_re36 | 1.0 per_second | |
| kdiss_re37 | 1.0 per_second | |
| kdiss_re38 | 1.0 per_second | |
| kdiss_re39 | 1.0 per_second | |
| kdiss_re4 | 1.0 per_second | |
| kdiss_re40 | 1.0 per_second | |
| kdiss_re41 | 1.0 per_second | |
| kdiss_re42 | 1.0 per_second | |
| kdiss_re43 | 1.0 per_second | |
| kdiss_re44 | 1.0 per_second | |
| kdiss_re45 | 1.0 per_second | |
| kdiss_re46 | 1.0 per_second | |
| kdiss_re47 | 1.0 per_second | |
| kdiss_re48 | 1.0 per_second | |
| kdiss_re49 | 1.0 per_second | |
| kdiss_re5 | 1.0 per_second | |
| kdiss_re50 | 1.0 per_second | |
| kdiss_re51 | 1.0 per_second | |
| kdiss_re52 | 1.0 per_second | |
| kdiss_re53 | 1.0 per_second | |
| kdiss_re54 | 1.0 per_second | |
| kdiss_re55 | 1.0 per_second | |
| kdiss_re56 | 1.0 per_second | |
| kdiss_re57 | 1.0 per_second | |
| kdiss_re58 | 1.0 per_second | |
| kdiss_re59 | 1.0 per_second | |
| kdiss_re6 | 1.0 per_second | |
| kdiss_re60 | 1.0 per_second | |
| kdiss_re61 | 1.0 per_second | |
| kdiss_re62 | 1.0 per_second | |
| kdiss_re63 | 1.0 per_second | |
| kdiss_re64 | 1.0 per_second | |
| kdiss_re65 | 1.0 per_second | |
| kdiss_re66 | 1.0 per_second | |
| kdiss_re67 | 1.0 per_second | |
| kdiss_re68 | 1.0 per_second | |
| kdiss_re69 | 1.0 per_second | |
| kdiss_re7 | 1.0 per_second | |
| kdiss_re70 | 1.0 per_second | |
| kdiss_re71 | 1.0 per_second | |
| kdiss_re72 | 1.0 per_second | |
| kdiss_re73 | 1.0 per_second | |
| kdiss_re74 | 1.0 per_second | |
| kdiss_re75 | 1.0 per_second | |
| kdiss_re76 | 1.0 per_second | |
| kdiss_re77 | 1.0 per_second | |
| kdiss_re78 | 1.0 per_second | |
| kdiss_re79 | 1.0 per_second | |
| kdiss_re8 | 1.0 per_second | |
| kdiss_re80 | 1.0 per_second | |
| kdiss_re81 | 1.0 per_second | |
| kdiss_re82 | 1.0 per_second | |
| kdiss_re83 | 1.0 per_second | |
| kdiss_re84 | 1.0 per_second | |
| kdiss_re85 | 1.0 per_second | |
| kdiss_re86 | 1.0 per_second | |
| kdiss_re9 | 1.0 per_second |
| Id | Value | Reaction |
|---|
| Definition |
|---|
| Definition |
|---|
| Definition |
|---|
| Definition |
|---|
| Trigger | Assignments |
|---|