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BIOMD0000000181 - Sriram2007_CellCycle

 

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Reference Publication
Publication ID: 18203579
Sriram K, Bernot G, Képès F.
A minimal mathematical model combining several regulatory cycles from the budding yeast cell cycle.
IET Syst Biol 2007 Nov; 1(6): 326-341
Epigenomics Project, 523, Place des Terrasses de 1' Agora, Tour Evry 2, Genopole, Evry, 91000 France. sridelin@yahoo.co.in  [more]
Model
Original Model: BIOMD0000000181.origin
Submitter: Harish Dharuri
Submission ID: MODEL8610478473
Submission Date: 14 Aug 2008 12:44:57 UTC
Last Modification Date: 27 May 2014 22:47:25 UTC
Creation Date: 12 Aug 2008 21:04:02 UTC
Encoders:  Harish Dharuri
set #1
bqmodel:isDerivedFrom BioModels Database Tyson2001_Cell_Cycle_Regulation
set #2
bqbiol:isHomologTo Reactome REACT_152
set #3
bqbiol:isPartOf KEGG Pathway sce04111
Gene Ontology mitotic cell cycle
set #4
bqbiol:hasTaxon Taxonomy Opisthokonta
Notes

The model reproduces the time profile of species depicted in Figure 12a and 12 b. The authors communicated to the curator that there is a typo in the paper, the values of kd1 and kd2 are reversed. Model successfully reproduced using MathSBML.

Model
Publication ID: 18203579 Submission Date: 14 Aug 2008 12:44:57 UTC Last Modification Date: 27 May 2014 22:47:25 UTC Creation Date: 12 Aug 2008 21:04:02 UTC
Mathematical expressions
Reactions
R1 R2 R3 R4
R5 R6 R7 R8
R9 R10 R11 R12
R13 R14 R15 R16
R17 R18    
Physical entities
Compartments Species
compartment T1 T2 T3
C1 C2 C3
Global parameters
j1 vd1 n km1
kc1 kd1 j2 vd2
km2 kc2 kd2 j3
vd3 km3 kc3 kd3
v12 k120 kd4 v11
k110 kd5 v10 k100
kd6      
Reactions (18)
 
 R1  → [T1];  
 
 R2  → [T1];   {T3}
 
 R3  → [T1];   {C1}
 
 R4 [T1] → ;  
 
 R5  → [T2];  
 
 R6  → [T2];   {T1}
 
 R7  → [T2];   {C2}
 
 R8 [T2] → ;  
 
 R9  → [T3];  
 
 R10  → [T3];   {T2}
 
 R11  → [T3];   {C3}
 
 R12 [T3] → ;  
 
 R13  → [C1];   {T1} , {C2}
 
 R14 [C1] → ;  
 
 R15  → [C2];   {T2} , {C3}
 
 R16 [C2] → ;  
 
 R17  → [C3];   {T3} , {C1}
 
 R18 [C3] → ;  
 
   Spatial dimensions: 3.0  Compartment size: 1.0
 
 T1
Compartment: compartment
Initial concentration: 6.0
 
 T2
Compartment: compartment
Initial concentration: 5.0
 
 T3
Compartment: compartment
Initial concentration: 1.0
 
 C1
Compartment: compartment
Initial concentration: 0.0
 
 C2
Compartment: compartment
Initial concentration: 0.0
 
 C3
Compartment: compartment
Initial concentration: 0.0
 
Global Parameters (25)
 
   j1
Value: 0.9   (Units: nM_min_1)
Constant
 
   vd1
Value: 6.0   (Units: nM_min_1)
Constant
 
   n
Value: 2.0   (Units: dimensionless)
Constant
 
   km1
Value: 5.0   (Units: nM)
Constant
 
   kc1
Value: 0.2   (Units: min_1)
Constant
 
   kd1
Value: 0.8   (Units: min_1)
Constant
 
   j2
Value: 0.5   (Units: nM_min_1)
Constant
 
   vd2
Value: 1.052   (Units: nM_min_1)
Constant
 
   km2
Value: 5.0   (Units: nM)
Constant
 
   kc2
Value: 0.22   (Units: min_1)
Constant
 
   kd2
Value: 0.9   (Units: min_1)
Constant
 
   j3
Value: 0.2   (Units: nM_min_1)
Constant
 
   vd3
Value: 3.0   (Units: nM_min_1)
Constant
 
   km3
Value: 5.0   (Units: nM)
Constant
 
   kc3
Value: 0.6   (Units: min_1)
Constant
 
   kd3
Value: 0.8   (Units: min_1)
Constant
 
   v12
Value: 15.0   (Units: nM_min_1)
Constant
 
   k120
Value: 10.0   (Units: nM)
Constant
 
   kd4
Value: 0.16   (Units: min_1)
Constant
 
   v11
Value: 15.0   (Units: nM_min_1)
Constant
 
   k110
Value: 10.0   (Units: nM)
Constant
 
   kd5
Value: 0.16   (Units: min_1)
Constant
 
   v10
Value: 15.0   (Units: nM_min_1)
Constant
 
   k100
Value: 10.0   (Units: nM)
Constant
 
   kd6
Value: 0.16   (Units: min_1)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000181

Curator's comment: (updated: 14 Aug 2008 13:37:52 BST)

The plots correspond to Fig 12a and 12b of the paper. Simulation result obtained using MathSBML.

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