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BIOMD0000000111 - Novak2001_FissionYeast_CellCycle

 

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Reference Publication
Publication ID: 12779461
Novak B, Pataki Z, Ciliberto A, Tyson JJ.
Mathematical model of the cell division cycle of fission yeast.
Chaos 2001 Mar; 11(1): 277-286
Department of Agricultural Chemical Technology, Budapest University of Technology and Economics, Szt Gellert ter 4, 1111 Budapest, Hungary.  [more]
Model
Original Model: BIOMD0000000111.xml.origin
Submitter: Harish Dharuri
Submission ID: MODEL6488296959
Submission Date: 20 Apr 2007 17:58:22 UTC
Last Modification Date: 05 Jul 2012 16:47:55 UTC
Creation Date: 13 Apr 2007 05:35:42 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:isVersionOf KEGG Pathway spo04111
Gene Ontology mitotic cell cycle
bqbiol:occursIn Taxonomy Schizosaccharomycetaceae
bqbiol:hasVersion Reactome REACT_152
Notes

The model reproduces the time evolution of several species as depicted in Fig 4 of the paper. Events have been used to reset cell mass when the value of M-phase promoting factor (MPF) decreases through 0.1. The model was successfully tested on Cell Designer.


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: 12779461 Submission Date: 20 Apr 2007 17:58:22 UTC Last Modification Date: 05 Jul 2012 16:47:55 UTC Creation Date: 13 Apr 2007 05:35:42 UTC
Mathematical expressions
Reactions
cdc13T synthesis Targeting cdc13T to APC core wee1 dependent MPF inactivation cdc25 dependent preMPF phosphorylation
preMPF inactivation slp1 dependent ste9 activation ste9 phosphorylation (inactivation) by starter kinase slp1T activation by MPF
slp1T inactivation slp1 activation by intermediary enzyme slp1 inactivation slp1 inactivation
Intermediary enzyme activation IEP inactivation rum1T activation SK dependent rum1T inactivation
SK synthesis SK degradation Cell growth  
Rules
Assignment Rule (variable: sigma) Assignment Rule (variable: Trimer) Assignment Rule (variable: M-phase promoting factor) Assignment Rule (variable: TF)
Assignment Rule (variable: kwee) Assignment Rule (variable: k25)    
Events
event_0000001 event_0000002    
Physical entities
Compartments Species
cell Total cdc13 preMPF ste9
slp1T slp1 IEP
rum1T SK Cell Mass
M-phase promoting factor    
Global parameters
flag_MPF sigma Kdiss Trimer
TF k15 J16 k16_prime
k16_double_prime J15 kwee kwee_prime
kwee_double_prime Vawee Jiwee Viwee
Jawee k25 k25_prime k25_double_prime
Va25 Ji25 Vi25 Ja25
k1 k2_prime k2_double_prime k2_triple_prime
k3_prime k3_double_prime J3 k4_prime
k4 J4 k5_prime k5_double_prime
J5 k6 k7 J7
k8 J8 k9 J9
k10 J10 k11 k12
k12_prime k12_double_prime k13 k14
mu      
Reactions (19)
 
 cdc13T synthesis  → [Total cdc13];   {Cell Mass}
 
 Targeting cdc13T to APC core [Total cdc13] → ;   {ste9} , {slp1}
 
 wee1 dependent MPF inactivation  → [preMPF];   {Total cdc13}
 
 cdc25 dependent preMPF phosphorylation [preMPF] → ;  
 
 preMPF inactivation [preMPF] → ;   {ste9} , {slp1}
 
 slp1 dependent ste9 activation  → [ste9];   {slp1}
 
 ste9 phosphorylation (inactivation) by starter kinase [ste9] → ;   {SK} , {M-phase promoting factor}
 
 slp1T activation by MPF  → [slp1T];   {M-phase promoting factor}
 
 slp1T inactivation [slp1T] → ;  
 
 slp1 activation by intermediary enzyme  → [slp1];   {IEP} , {slp1T}
 
 slp1 inactivation [slp1] → ;  
 
 slp1 inactivation [slp1] → ;  
 
 Intermediary enzyme activation  → [IEP];   {M-phase promoting factor}
 
 IEP inactivation [IEP] → ;  
 
 rum1T activation  → [rum1T];  
 
 SK dependent rum1T inactivation [rum1T] → ;   {SK} , {M-phase promoting factor}
 
 SK synthesis  → [SK];  
 
 SK degradation [SK] → ;  
 
 Cell growth  → [Cell Mass];  
 
Rules (6)
 
 Assignment Rule (name: sigma) sigma = cdc13T+rum1T+Kdiss
 
 Assignment Rule (name: Trimer) Trimer = 2*cdc13T*rum1T/(sigma+(sigma^2-4*cdc13T*rum1T)^0.5)
 
 Assignment Rule (name: MPF) M-phase promoting factor = (cdc13T-preMPF)*(cdc13T-Trimer)/cdc13T
 
 Assignment Rule (name: TF) TF = 2*k15*M*J16/(k16_prime+k16_double_prime*MPF-k15*M+(k16_prime+k16_double_prime*MPF)*J15+k15*M*J16+((k16_prime+k16_double_prime*MPF-k15*M+(k16_prime+k16_double_prime*MPF)*J15+k15*M*J16)^2-4*(k16_prime+k16_double_prime*MPF-k15*M)*k15*M*J16)^(0.5))
 
 Assignment Rule (name: kwee) kwee = kwee_prime+(kwee_double_prime-kwee_prime)*2*Vawee*Jiwee/(Viwee*MPF-Vawee+Viwee*MPF*Jawee+Vawee*Jiwee+((Viwee*MPF-Vawee+Viwee*MPF*Jawee+Vawee*Jiwee)^2-4*(Viwee*MPF-Vawee)*Vawee*Jiwee)^(0.5))
 
 Assignment Rule (name: k25) k25 = k25_prime+(k25_double_prime-k25_prime)*2*Va25*MPF*Ji25/(Vi25-Va25*MPF+Vi25*Ja25+Va25*MPF*Ji25+((Vi25-Va25*MPF+Vi25*Ja25+Va25*MPF*Ji25)^2-4*(Vi25-Va25*MPF)*Va25*MPF*Ji25)^(0.5))
 
Events (2)
 
 event_0000001
Cell Mass = M/2
flag_MPF = 0
 
 event_0000002
flag_MPF = 1
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 Total cdc13
Compartment: cell
Initial amount: 0.2
 
 preMPF
Compartment: cell
Initial amount: 0.0
 
 ste9
Compartment: cell
Initial amount: 1.0
 
 slp1T
Compartment: cell
Initial amount: 0.0
 
 slp1
Compartment: cell
Initial amount: 2.2
 
   IEP
Compartment: cell
Initial amount: 0.0
 
 rum1T
Compartment: cell
Initial amount: 0.0
 
 SK
Compartment: cell
Initial amount: 0.0
 
   Cell Mass
Compartment: cell
Initial amount: 1.0
 
  M-phase promoting factor
Compartment: cell
Initial amount: 0.0
 
Global Parameters (53)
 
   flag_MPF  
 
   sigma  
 
   Kdiss
Value: 0.0010   (Units: dimensionless)
Constant
 
   Trimer  
 
   TF  
 
   k15
Value: 1.5   (Units: min_inv)
Constant
 
   J16
Value: 0.01   (Units: dimensionless)
Constant
 
   k16_prime
Value: 1.0   (Units: min_inv)
Constant
 
   k16_double_prime
Value: 2.0   (Units: min_inv)
Constant
 
   J15
Value: 0.01   (Units: dimensionless)
Constant
 
   kwee  
 
   kwee_prime
Value: 0.15   (Units: min_inv)
Constant
 
   kwee_double_prime
Value: 1.3   (Units: min_inv)
Constant
 
   Vawee
Value: 0.25   (Units: min_inv)
Constant
 
   Jiwee
Value: 0.01   (Units: dimensionless)
Constant
 
   Viwee
Value: 1.0   (Units: min_inv)
Constant
 
   Jawee
Value: 0.01   (Units: dimensionless)
Constant
 
   k25  
 
   k25_prime
Value: 0.05   (Units: min_inv)
Constant
 
   k25_double_prime
Value: 5.0   (Units: min_inv)
Constant
 
   Va25
Value: 1.0   (Units: min_inv)
Constant
 
   Ji25
Value: 0.01   (Units: dimensionless)
Constant
 
   Vi25
Value: 0.25   (Units: min_inv)
Constant
 
   Ja25
Value: 0.01   (Units: dimensionless)
Constant
 
   k1
Value: 0.03   (Units: min_inv)
Constant
 
   k2_prime
Value: 0.03   (Units: min_inv)
Constant
 
   k2_double_prime
Value: 1.0   (Units: min_inv)
Constant
 
   k2_triple_prime
Value: 0.1   (Units: min_inv)
Constant
 
   k3_prime
Value: 1.0   (Units: min_inv)
Constant
 
   k3_double_prime
Value: 10.0   (Units: min_inv)
Constant
 
   J3
Value: 0.01   (Units: dimensionless)
Constant
 
   k4_prime
Value: 2.0   (Units: min_inv)
Constant
 
   k4
Value: 35.0   (Units: min_inv)
Constant
 
   J4
Value: 0.01   (Units: dimensionless)
Constant
 
   k5_prime
Value: 0.0050   (Units: min_inv)
Constant
 
   k5_double_prime
Value: 0.3   (Units: min_inv)
Constant
 
   J5
Value: 0.3   (Units: dimensionless)
Constant
 
   k6
Value: 0.1   (Units: min_inv)
Constant
 
   k7
Value: 1.0   (Units: min_inv)
Constant
 
   J7
Value: 0.0010   (Units: dimensionless)
Constant
 
   k8
Value: 0.25   (Units: min_inv)
Constant
 
   J8
Value: 0.0010   (Units: dimensionless)
Constant
 
   k9
Value: 0.1   (Units: min_inv)
Constant
 
   J9
Value: 0.01   (Units: dimensionless)
Constant
 
   k10
Value: 0.04   (Units: min_inv)
Constant
 
   J10
Value: 0.01   (Units: dimensionless)
Constant
 
   k11
Value: 0.1   (Units: min_inv)
Constant
 
   k12
Value: 0.01   (Units: min_inv)
Constant
 
   k12_prime
Value: 1.0   (Units: min_inv)
Constant
 
   k12_double_prime
Value: 3.0   (Units: min_inv)
Constant
 
   k13
Value: 0.1   (Units: min_inv)
Constant
 
   k14
Value: 0.1   (Units: min_inv)
Constant
 
   mu
Value: 0.0050   (Units: min_inv)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000111

Curator's comment: (updated: 07 Oct 2009 14:37:08 BST)

Reproduction of figure 4 from the original publication using SBW 2.7.10

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