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BIOMD0000000144 - Calzone2007_CellCycle

 

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Reference Publication
Publication ID: 17667953
Calzone L, Thieffry D, Tyson JJ, Novak B.
Dynamical modeling of syncytial mitotic cycles in Drosophila embryos.
Mol. Syst. Biol. 2007; 3: 131
Molecular Network Dynamics Research Group of Hungarian Academy of Sciences and Budapest University of Technology and Economics, Budapest, Gellért tér, Hungary.  [more]
Model
Original Model: BIOMD0000000144.origin
Submitter: Laurence Calzone
Submission ID: MODEL1509031628
Submission Date: 23 Aug 2007 16:12:45 UTC
Last Modification Date: 05 Jul 2012 16:48:32 UTC
Creation Date: 08 Jun 2007 08:29:58 UTC
Encoders:  Nicolas Le Novère
   Enuo He
   Laurence Calzone
set #1
bqbiol:isVersionOf Gene Ontology regulation of nuclear division
Gene Ontology mitotic cell cycle
bqbiol:occursIn Taxonomy Drosophila
Notes

This is the Dynamical model of nuclear division cycles during early embryogenesis of Drosophila, without StringT regulation. so ksstg=kdstg=0. Figure1B has been simulated by MathSBML. Curator changed model from only one compartment into two compartments according to the paper. Detail explaination of the models are in the supplement information of the paper.The author didn't specify which compartment Xm, Stgm, Xp are located, we assume that they locate in cytoplasm.

Some of the parameter values for the equations are dimensionless parameters.


To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.


To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 17667953 Submission Date: 23 Aug 2007 16:12:45 UTC Last Modification Date: 05 Jul 2012 16:48:32 UTC Creation Date: 08 Jun 2007 08:29:58 UTC
Mathematical expressions
Reactions
Synthesis of MPFc Activation of MPFc Inactivation of MPFc Degradation of cyclin
degradation of cyclin Inactivation of Wee1c Activation of Wee1c mRNA of Stg
Synthesis of Stg activation of Stgc inactivation of Stgc degradation of Stgc
degradation of active Stgc export of MPF from cytoplasm import of MPF into cytoplasm import of MPF into nucleus
export of MPF from nucleus import of preMPF into cytoplasm export of preMPF from cytoplasm import of preMPF into nucleus
export of preMPFn from nucleus export of Wee1P from nucleus import of Wee1P into cytoplasm export of Wee1P from cytoplasm
import of Wee1P into nucleus export of Wee1 from nucleus import of Wee1 into cytoplasm export of Wee1c from cytoplasm
import of Wee1 into nucleus export of StgP from nucleus import of StgP into cytoplasm export of StgP from cytoplasm
import of StgP into nucleus export of Stg from nucleus import of Stg into cytoplasm export of Stg from cytoplasm
import of Stg into nucleus activation of MPFn inactivation of MPFn degradation of preMPFn
degradation of MPFn activation of intermediary enzyme inactivation of intermediary enzyme activation of FZY
inactivation of FZY inactivation of Wee1n activation of Wee1n activation of StgPn
inactivation of StgPn degradation of Stgn degradation of StgPn Nuclei
Zygotic mRNA Zygotic proteins    
Rules
Assignment Rule (variable: CycBT) Assignment Rule (variable: StgPT) Assignment Rule (variable: Wee1Pc)  
Events
       
Physical entities
Compartments Species
nuclei MPFn preMPFn Wee1Pn
Wee1n StgPn Stgn
FZYa IEa_1 N
cytoplasm MPFc preMPFc StgPc
Wee1c Wee1Pc Stgm
Xp Stgc Xm
     
Global parameters
ksc kdcp kdnp kdnpp
kaie kiie kafzy kifzy
kweep kweepp kstgp kstgpp
ksstg kdstg kastgp kastgpp
kistg kawee kiweep kiweepp
kin Jaie Jiie Jafzy
Jifzy Jastg Jistg Jawee
Jiwee Jm kdmp kdmpp
koutw kinw kouts kins
kez factor E ksxp
ksxm kout CycBT StringT
Wee1T StgPT    
Reactions (54)
 
 Synthesis of MPFc  → [MPFc];  
 
 Activation of MPFc [preMPFc] → [MPFc];   {StgPc}
 
 Inactivation of MPFc [MPFc] → [preMPFc];   {Wee1c}
 
 Degradation of cyclin [preMPFc] → ;  
 
 degradation of cyclin [MPFc] → ;  
 
 Inactivation of Wee1c [Wee1c] → [Wee1Pc];   {MPFc}
 
 Activation of Wee1c [Wee1Pc] → [Wee1c];   {Wee1Pc}
 
 mRNA of Stg [Stgm] → ;   {Xp}
 
 Synthesis of Stg  → [Stgc];   {Stgm}
 
 activation of Stgc [Stgc] → [StgPc];   {MPFc}
 
 inactivation of Stgc [StgPc] → [Stgc];  
 
 degradation of Stgc [Stgc] → ;  
 
 degradation of active Stgc [StgPc] → ;  
 
 export of MPF from cytoplasm [MPFc] → ;   {N}
 
 import of MPF into cytoplasm  → [MPFc];   {N} , {MPFn}
 
 import of MPF into nucleus  → [MPFn];   {MPFc}
 
 export of MPF from nucleus [MPFn] → ;  
 
 import of preMPF into cytoplasm  → [preMPFc];   {preMPFn} , {N}
 
 export of preMPF from cytoplasm [preMPFc] → ;   {N}
 
 import of preMPF into nucleus  → [preMPFn];   {preMPFc}
 
 export of preMPFn from nucleus [preMPFn] → ;  
 
 export of Wee1P from nucleus [Wee1Pn] → ;  
 
 import of Wee1P into cytoplasm  → [Wee1Pc];   {Wee1Pn} , {N}
 
 export of Wee1P from cytoplasm [Wee1Pc] → ;   {N}
 
 import of Wee1P into nucleus  → [Wee1Pn];   {Wee1Pc}
 
 export of Wee1 from nucleus [Wee1n] → ;  
 
 import of Wee1 into cytoplasm  → [Wee1c];   {Wee1n} , {N}
 
 export of Wee1c from cytoplasm [Wee1c] → ;   {N}
 
 import of Wee1 into nucleus  → [Wee1n];   {Wee1c}
 
 export of StgP from nucleus [StgPn] → ;  
 
 import of StgP into cytoplasm  → [StgPc];   {StgPn} , {N}
 
 export of StgP from cytoplasm [StgPc] → ;   {N}
 
 import of StgP into nucleus  → [StgPn];   {StgPc}
 
 export of Stg from nucleus [Stgn] → ;  
 
 import of Stg into cytoplasm  → [Stgc];   {Stgn} , {N}
 
 export of Stg from cytoplasm [Stgc] → ;   {N}
 
 import of Stg into nucleus  → [Stgn];   {Stgc}
 
 activation of MPFn [preMPFn] → [MPFn];   {StgPn}
 
 inactivation of MPFn [MPFn] → [preMPFn];   {Wee1n}
 
 degradation of preMPFn [preMPFn] → ;   {FZYa}
 
 degradation of MPFn [MPFn] → ;   {FZYa}
 
 activation of intermediary enzyme [IEa_1] → ;  
 
 inactivation of intermediary enzyme  → [IEa_1];   {MPFn}
 
 activation of FZY  → [FZYa];   {IEa_1}
 
 inactivation of FZY [FZYa] → ;  
 
 inactivation of Wee1n [Wee1n] → [Wee1Pn];   {MPFn}
 
 activation of Wee1n [Wee1Pn] → [Wee1n];  
 
 activation of StgPn [Stgn] → [StgPn];   {MPFn}
 
 inactivation of StgPn [StgPn] → [Stgn];  
 
 degradation of Stgn [Stgn] → ;  
 
 degradation of StgPn [StgPn] → ;  
 
 Nuclei  → [N];  
 
 Zygotic mRNA  → [Xm];   {N}
 
 Zygotic proteins  → [Xp];   {Xm}
 
Rules (3)
 
 Assignment Rule (name: CycBT) CycBT = (1-N*E_1)*(MPFc+preMPFc)+N*E_1*(MPFn+preMPFn)
 
 Assignment Rule (name: StgPT) StgPT = (1-N*E_1)*StgPc+N*E_1*StgPn
 
 Assignment Rule (name: Wee1Pc) Wee1Pc = (Wee1T-N*E_1*(Wee1n+Wee1Pn))/(1-N*E_1)-Wee1c
 
Events (1)
 
  
N = factor_1*N
MPFn = MPFn/1.95
preMPFn = preMPFn/1.95
Wee1n = Wee1n/1.95
Wee1Pn = Wee1Pn/1.95
Wee1c = Wee1c*(1-N*E_1)/(1-1.95*N*E_1)
Stgn = Stgn/1.95
StgPc = StgPc*(1-N*E_1)/(1-1.95*N*E_1)
Stgc = Stgc*(1-N*E_1)/(1-1.95*N*E_1)
StgPn = StgPn/1.95
MPFc = MPFc*(1-N*E_1)/(1-1.95*N*E_1)
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 MPFn
Compartment: nuclei
Initial concentration: 0.0
 
 preMPFn
Compartment: nuclei
Initial concentration: 0.0
 
 Wee1Pn
Compartment: nuclei
Initial concentration: 0.0
 
 Wee1n
Compartment: nuclei
Initial concentration: 0.0
 
 StgPn
Compartment: nuclei
Initial concentration: 0.0
 
 Stgn
Compartment: nuclei
Initial concentration: 0.0
 
 FZYa
Compartment: nuclei
Initial concentration: 0.0
 
   IEa_1
Compartment: nuclei
Initial concentration: 0.0
 
   N
Compartment: nuclei
Initial concentration: 1.0
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 MPFc
Compartment: cytoplasm
Initial concentration: 1.0
 
 preMPFc
Compartment: cytoplasm
Initial concentration: 0.0
 
 StgPc
Compartment: cytoplasm
Initial concentration: 0.8
 
 Wee1c
Compartment: cytoplasm
Initial concentration: 0.0
 
  Wee1Pc
Compartment: cytoplasm
Initial concentration: 0.8
 
 Stgm
Compartment: cytoplasm
Initial concentration: 1.0
 
   Xp
Compartment: cytoplasm
Initial concentration: 0.0
 
 Stgc
Compartment: cytoplasm
Initial concentration: 0.0
 
 Xm
Compartment: cytoplasm
Initial concentration: 0.0
 
Global Parameters (46)
 
   ksc
Value: 0.01
Constant
 
   kdcp
Value: 0.01
Constant
 
   kdnp
Value: 0.01
Constant
 
   kdnpp
Value: 1.5
Constant
 
   kaie
Value: 1.0
Constant
 
   kiie
Value: 0.4
Constant
 
   kafzy
Value: 1.0
Constant
 
   kifzy
Value: 0.2
Constant
 
   kweep
Value: 0.0050
Constant
 
   kweepp
Value: 1.0
Constant
 
   kstgp
Value: 0.2
Constant
 
   kstgpp
Value: 2.0
Constant
 
 ksstg
Constant
 
 kdstg
Constant
 
   kastgp
Constant
 
   kastgpp
Value: 1.0
Constant
 
   kistg
Value: 0.3
Constant
 
   kawee
Value: 0.3
Constant
 
   kiweep
Value: 0.01
Constant
 
   kiweepp
Value: 1.0
Constant
 
   kin
Value: 0.15
Constant
 
   Jaie
Value: 0.01
Constant
 
   Jiie
Value: 0.01
Constant
 
   Jafzy
Value: 0.01
Constant
 
   Jifzy
Value: 0.01
Constant
 
   Jastg
Value: 0.05
Constant
 
   Jistg
Value: 0.05
Constant
 
   Jawee
Value: 0.05
Constant
 
   Jiwee
Value: 0.05
Constant
 
   Jm
Value: 0.05
Constant
 
   kdmp
Value: 0.0020
Constant
 
   kdmpp
Value: 0.2
Constant
 
   koutw
Value: 0.01
Constant
 
   kinw
Value: 0.04
Constant
 
   kouts
Value: 0.02
Constant
 
   kins
Value: 0.08
Constant
 
   kez
Value: 0.5
Constant
 
   factor
Value: 1.95
Constant
 
   E
Value: 7.0E-5
Constant
 
   ksxp
Value: 0.0010
Constant
 
   ksxm
Value: 5.0E-4
Constant
 
   kout
Constant
 
   CycBT
Value: NaN
 
 StringT
Value: 0.8
Constant
 
 Wee1T
Value: 0.8
Constant
 
   StgPT  
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000144

Curator's comment: (updated: 21 Aug 2007 20:11:55 BST)

Figure1B has been simulated by MathSBML.

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