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.

None

None

None

None

None

None

Modeling of the MAPK machinery activation in response to various abiotic and biotic stresses in plants by a system biology approach.

  • Rajesh Kumar Pathak
  • Gohar Taj
  • Dinesh Pandey
  • Sandeep Arora
  • Anil Kumar
Bioinformation 2013; 9 (9): 443-449
Abstract
Mitogen-Activated Protein Kinases (MAPKs) cascade plays an important role in regulating plant growth and development, generating cellular responses to the extracellular stimuli. MAPKs cascade mainly consist of three sub-families i.e. mitogen-activated protein kinase kinase kinase (MAPKKK), mitogen-activated protein kinase kinase (MAPKK) and mitogen activated protein kinase (MAPK), several cascades of which are activated by various abiotic and biotic stresses. In this work we have modeled the holistic molecular mechanisms essential to MAPKs activation in response to several abiotic and biotic stresses through a system biology approach and performed its simulation studies. As extent of abiotic and biotic stresses goes on increasing, the process of cell division, cell growth and cell differentiation slow down in time dependent manner. The models developed depict the combinatorial and multicomponent signaling triggered in response to several abiotic and biotic factors. These models can be used to predict behavior of cells in event of various stresses depending on their time and exposure through activation of complex signaling cascades.

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

Global parameters

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

Local parameters

Id Value Reaction

Assignment rules

Definition

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments