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BIOMD0000000481 - Stötzel2012 - Bovine estrous cycle, synchronization with prostaglandin F2α

 

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Reference Publication
Publication ID: 22980082
Stötzel C, Plöntzke J, Heuwieser W, Röblitz S.
Advances in modeling of the bovine estrous cycle: synchronization with PGF2?.
Theriogenology 2012 Oct; 78(7): 1415-1428
Computational Systems Biology Group, Numerical Analysis and Modeling, Zuse Institute Berlin, Takustr. 7, 14195 Berlin, Germany. stoetzel@zib.de  [more]
Model
Original Model: BIOMD0000000481.xml.origin
Submitter: Claudia Stötzel
Submission ID: MODEL1308100000
Submission Date: 10 Aug 2013 09:51:22 UTC
Last Modification Date: 02 Apr 2014 00:12:26 UTC
Creation Date: 23 Sep 2013 10:44:31 UTC
Encoders:  Vijayalakshmi Chelliah
   Claudia Stötzel
set #1
bqmodel:isDerivedFrom PubMed 22118087
PubMed 21377476
set #2
bqbiol:isVersionOf Gene Ontology ovulation cycle
Gene Ontology response to prostaglandin F
set #3
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
set #4
bqbiol:hasTaxon Taxonomy Bos taurus
Notes
Model
Publication ID: 22980082 Submission Date: 10 Aug 2013 09:51:22 UTC Last Modification Date: 02 Apr 2014 00:12:26 UTC Creation Date: 23 Sep 2013 10:44:31 UTC
Mathematical expressions
Reactions
re1 re2 re3 re4
re5 re6 re7 re8
re9 re10 re11 re12
re13 re14 re15 re16
re17 re18 re19 re20
re21 l re23 re24
re25 re26 re27 re28
Rules
Assignment Rule (variable: t_mod) Assignment Rule (variable: Total_PGF_2alpha) Rate Rule (variable: PGF_syn)  
Physical entities
Compartments Species
default GnRH_Pit LH_Pit LH_Bld
GnRH_Hyp FSH_Pit FSH_Bld
Foll CL E2
P4 Inh OT
Enz PGF IOF
src_GnRH src_E2 src_P4
src_Inh src_OT src_Enz
src_PGF src_LH src_FSH
snk_GnRH_Hyp src_GnRH_Pit src_Foll
src_IOF src_CL snk_Inh
snk_P4 snk_E2 snk_GnRH_Pit
snk_LH snk_FSH snk_IOF
snk_CL snk_Enz snk_OT
snk_PGF snk_Foll PGF_syn
Global parameters
k_G GnRH_max h_P4&E2_G T_E2_G1
T_p4_G1 h_p4_G2 T_p4_G2 h_e2_g2
T_e2_g2 cl_G h_inh_fsh T_inh_fsh
h_p4_fsh T_p4_fsh h_e2_fsh T_e2_fsh
h_gnrh_fsh T_gnrh_fsh cl_fsh b_fsh
h_e2_lh T_e2_lh h_p4_lh T_p4_lh
h_gnrh_lh T_gnrh_lh b_lh cl_lh
h_fsh_foll T_fsh_foll T_foll_fsh h_p4_fsh_2
T_p4_foll h_lh_foll T_lh_Foll h_enz_pgf
T_enz_pgf T_ot_pgf cl_pgf SF_CL
h_cl_cl T_cl_cl h_iof_cl T_iof_cl
k_cl_p4 cl_p4 k_foll_e2 cl_e2
k_foll_inh cl_inh h_p4_enz T_p4_enz
cl_enz h_e2cl_ot T_e2_ot cl_ot
h_pg_iof T_pg_ot T_cl_iof cl_iof
D beta c_PGF_syn t_mod
t_D Total_PGF_2alpha quantity_1 Initial for D
Initial for beta      
Reactions (28)
 
 re1 [LH_Pit] → [LH_Bld];   {GnRH_Pit} , {GnRH_Pit} , {LH_Pit}
 
 re2 [FSH_Pit] → [FSH_Bld];   {E2} , {P4} , {GnRH_Pit} , {E2} , {FSH_Pit} , {GnRH_Pit} , {P4}
 
 re3 [GnRH_Hyp] → [snk_GnRH_Hyp];   {E2} , {P4} , {E2} , {GnRH_Hyp} , {P4}
 
 re4 [src_CL] → [CL];   {Foll} , {CL} , {LH_Bld} , {CL} , {Foll} , {LH_Bld}
 
 re5 [src_GnRH] → [GnRH_Hyp];   {GnRH_Hyp} , {GnRH_Hyp}
 
 re6 [src_E2] → [E2];   {Foll} , {Foll}
 
 re7 [src_P4] → [P4];   {CL} , {CL}
 
 re8 [src_Inh] → [Inh];   {Foll} , {Foll}
 
 re9 [src_OT] → [OT];   {E2} , {CL} , {CL} , {E2}
 
 re10 [src_Enz] → [Enz];   {P4} , {P4}
 
 re11 [src_PGF] → [PGF];   {OT} , {Enz} , {Enz} , {OT}
 
 re12 [GnRH_Pit] → [snk_GnRH_Pit];   {GnRH_Pit}
 
 re13 [LH_Bld] → [snk_LH];   {LH_Bld}
 
 re14 [FSH_Bld] → [snk_FSH];   {FSH_Bld}
 
 re15 [P4] → [snk_P4];   {P4}
 
 re16 [E2] → [snk_E2];   {E2}
 
 re17 [Inh] → [snk_Inh];   {Inh}
 
 re18 [OT] → [snk_OT];   {OT}
 
 re19 [Enz] → [snk_Enz];   {Enz}
 
 re20 [PGF] → [snk_PGF];   {PGF}
 
 re21 [IOF] → [snk_IOF];   {IOF}
 
 l [Foll] → [snk_Foll];   {P4} , {LH_Bld} , {Foll} , {LH_Bld} , {P4}
 
 re23 [CL] → [snk_CL];   {IOF} , {CL} , {IOF}
 
 re24 [src_LH] → [LH_Pit];   {E2} , {P4} , {E2} , {P4}
 
 re25 [src_FSH] → [FSH_Pit];   {Inh} , {Inh}
 
 re26 [src_GnRH_Pit] → [GnRH_Pit];   {GnRH_Hyp} , {E2} , {P4} , {E2} , {GnRH_Hyp} , {P4}
 
 re27 [src_Foll] → [Foll];   {FSH_Bld} , {Foll} , {FSH_Bld} , {Foll}
 
 re28 [src_IOF] → [IOF];   {CL} , {PGF} , {CL} , {PGF}
 
Rules (3)
 
 Assignment Rule (name: parameter_4) t_mod = piecewise(time-parameter_5, time > parameter_5, 0)
 
 Assignment Rule (name: parameter_6) Total_PGF_2alpha = PGF+species_1
 
 Rate Rule (name: species_1) d [ PGF_syn] / d t= ModelValue_60*ModelValue_61*ModelValue_61*parameter_4*exp((-ModelValue_61)*parameter_4)-parameter_3*species_1
 
Functions (28)
 
 Function for re1 lambda(GnRH_Pit, LH_Pit, default, par35, par36, par37, (par37+par35*(GnRH_Pit*default)^5/((GnRH_Pit*default)^5+par36^5))*LH_Pit*default/default)
 
 Function for re2 lambda(E2, FSH_Pit, GnRH_Pit, P4, default, par23, par24, par25, par26, par27, par28, par30, (par30+par23*(P4*default)^2/((P4*default)^2+par24^2)+par25*par26^2/((E2*default)^2+par26^2)+par27*GnRH_Pit*default/(par28+GnRH_Pit*default))*FSH_Pit*default/default)
 
 Function for re3 lambda(E2, GnRH_Hyp, P4, default, par3, par4, par5, par6, par7, (par3*(par5^2/(par5^2+(P4*default)^2)+par4^2/(par4^2+(E2*default)^2)-par5^2/(par5^2+(P4*default)^2)*par4^2/(par4^2+(E2*default)^2))+par6*par7^2/((P4*default)^2+par7^2))*GnRH_Hyp*default/default)
 
 Function for re4 lambda(CL, Foll, LH_Bld, default, par47, par48, par62, par63, par64, (par62*par47*(LH_Bld*default)^2/((LH_Bld*default)^2+par48^2)*Foll*default+par63*(CL*default)^2/((CL*default)^2+par64^2))/default)
 
 Function for re5 lambda(GnRH_Hyp, default, par1, par2, par2*(1-GnRH_Hyp*default/par1)/default)
 
 Function for re6 lambda(Foll, default, par76, par76*(Foll*default)^2/default)
 
 Function for re7 lambda(CL, default, par71, par71*(CL*default)^2/default)
 
 Function for re8 lambda(Foll, default, par81, par81*(Foll*default)^2/default)
 
 Function for re9 lambda(CL, E2, default, par91, par92, par91*(E2*default)^2/((E2*default)^2+par92^2)*(CL*default)^2/default)
 
 Function for re10 lambda(P4, default, par86, par87, par86*(P4*default)^5/((P4*default)^5+par87^5)/default)
 
 Function for re11 lambda(Enz, OT, default, par56, par57, par58, par56*Enz^5/(Enz^5+par57^5)*(OT*default)^2/((OT*default)^2+par58^2)/default)
 
 Function for re12 lambda(GnRH_Pit, default, par10, par10*GnRH_Pit*default/default)
 
 Function for re13 lambda(LH_Bld, default, par38, par38*LH_Bld*default/default)
 
 Function for re14 lambda(FSH_Bld, default, par29, par29*FSH_Bld*default/default)
 
 Function for re15 lambda(P4, default, par72, par72*P4*default/default)
 
 Function for re16 lambda(E2, default, par77, par77*E2*default/default)
 
 Function for re17 lambda(Inh, default, par82, par82*Inh*default/default)
 
 Function for re18 lambda(OT, default, par94, par94*OT*default/default)
 
 Function for re19 lambda(Enz, default, par89, par89*Enz/default)
 
 Function for re20 lambda(PGF, default, par59, par59*PGF*default/default)
 
 Function for re21 lambda(IOF, default, par98, par98*IOF*default/default)
 
 Function for l lambda(Foll, LH_Bld, P4, default, par45, par46, par47, par48, (par45*(P4*default)^5/((P4*default)^5+par46^5)+par47*(LH_Bld*default)^2/((LH_Bld*default)^2+par48^2))*Foll*default/default)
 
 Function for re23 lambda(CL, IOF, default, par65, par66, par65*(IOF*default)^5/((IOF*default)^5+par66^5)*CL*default/default)
 
 Function for re24 lambda(E2, P4, default, par31, par32, par33, par34, (par31*(E2*default)^2/((E2*default)^2+par32^2)+par33*par34^2/(par34^2+(P4*default)^2))/default)
 
 Function for re25 lambda(Inh, default, par21, par22, par21*par22^5/(par22^5+(Inh*default)^5)/default)
 
 Function for re26 lambda(E2, GnRH_Hyp, P4, default, par3, par4, par5, par6, par7, par8, par9, par8*(E2*default)^5/((E2*default)^5+par9^5)*(par3*(par5^2/(par5^2+(P4*default)^2)+par4^2/(par4^2+(E2*default)^2)-par5^2/(par5^2+(P4*default)^2)*par4^2/(par4^2+(E2*default)^2))+par6*par7^2/((P4*default)^2+par7^2))*GnRH_Hyp*default/default)
 
 Function for re27 lambda(FSH_Bld, Foll, default, par41, par42, par43, par41*(FSH_Bld*default)^2/((par42*par43^2/(par43^2+(Foll*default)^2))^2+(FSH_Bld*default)^2)/default)
 
 Function for re28 lambda(CL, PGF, default, par95, par96, par97, par95*(PGF*default)^5/((PGF*default)^5+par96^5)*(CL*default)^10/((CL*default)^10+par97^10)/default)
 
 default Spatial dimensions: 3.0  Compartment size: 1.0  (Units: volume)
 
 GnRH_Pit
Compartment: default
Initial amount: 0.219992404098564
 
 LH_Pit
Compartment: default
Initial amount: 2.25000957482152
 
 LH_Bld
Compartment: default
Initial amount: 0.00633682772990623
 
 GnRH_Hyp
Compartment: default
Initial amount: 0.740638780629751
 
 FSH_Pit
Compartment: default
Initial amount: 0.00579108659591004
 
 FSH_Bld
Compartment: default
Initial amount: 0.0168604631992291
 
 Foll
Compartment: default
Initial amount: 0.0286570978235457
 
 CL
Compartment: default
Initial amount: 0.314393628471893
 
 E2
Compartment: default
Initial amount: 0.163690728507925
 
 P4
Compartment: default
Initial amount: 0.120192549532403
 
 Inh
Compartment: default
Initial amount: 0.493710210684922
 
 OT
Compartment: default
Initial amount: 0.111730059223483
 
 Enz
Compartment: default
Initial amount: 5.83626691122778E-5
 
 PGF
Compartment: default
Initial amount: 3.62064120302475E-4
 
 IOF
Compartment: default
Initial amount: 0.133415086647186
 
 src_GnRH
Compartment: default
Initial amount: 0.0
Constant
 
 src_E2
Compartment: default
Initial amount: 0.0
Constant
 
 src_P4
Compartment: default
Initial amount: 0.0
Constant
 
 src_Inh
Compartment: default
Initial amount: 0.0
Constant
 
 src_OT
Compartment: default
Initial amount: 0.0
Constant
 
 src_Enz
Compartment: default
Initial amount: 0.0
Constant
 
 src_PGF
Compartment: default
Initial amount: 0.0
Constant
 
 src_LH
Compartment: default
Initial amount: 0.0
Constant
 
 src_FSH
Compartment: default
Initial amount: 0.0
Constant
 
 snk_GnRH_Hyp
Compartment: default
Initial amount: 0.0
Constant
 
 src_GnRH_Pit
Compartment: default
Initial amount: 0.0
Constant
 
 src_Foll
Compartment: default
Initial amount: 0.0
Constant
 
 src_IOF
Compartment: default
Initial amount: 0.0
Constant
 
 src_CL
Compartment: default
Initial amount: 0.0
Constant
 
 snk_Inh
Compartment: default
Initial amount: 0.0
Constant
 
 snk_P4
Compartment: default
Initial amount: 0.0
Constant
 
 snk_E2
Compartment: default
Initial amount: 0.0
Constant
 
 snk_GnRH_Pit
Compartment: default
Initial amount: 0.0
Constant
 
 snk_LH
Compartment: default
Initial amount: 0.0
Constant
 
 snk_FSH
Compartment: default
Initial amount: 0.0
Constant
 
 snk_IOF
Compartment: default
Initial amount: 0.0
Constant
 
 snk_CL
Compartment: default
Initial amount: 0.0
Constant
 
 snk_Enz
Compartment: default
Initial amount: 0.0
Constant
 
 snk_OT
Compartment: default
Initial amount: 0.0
Constant
 
 snk_PGF
Compartment: default
Initial amount: 0.0
Constant
 
 snk_Foll
Compartment: default
Initial amount: 0.0
Constant
 
 PGF_syn
Compartment: default
Initial concentration: 0.0
 
Global Parameters (69)
 
   k_G
Value: 2.75
Constant
 
   GnRH_max
Value: 16.0
Constant
 
   h_P4&E2_G
Value: 2.05
Constant
 
   T_E2_G1
Value: 0.0972
Constant
 
   T_p4_G1
Value: 0.35
Constant
 
   h_p4_G2
Value: 1.91
Constant
 
   T_p4_G2
Value: 0.252
Constant
 
   h_e2_g2
Value: 0.99
Constant
 
   T_e2_g2
Value: 0.648
Constant
 
   cl_G
Value: 1.63
Constant
 
   h_inh_fsh
Value: 4.21
Constant
 
   T_inh_fsh
Value: 0.118
Constant
 
   h_p4_fsh
Value: 0.293
Constant
 
   T_p4_fsh
Value: 0.152
Constant
 
   h_e2_fsh
Value: 0.396
Constant
 
   T_e2_fsh
Value: 0.312
Constant
 
   h_gnrh_fsh
Value: 1.23
Constant
 
   T_gnrh_fsh
Value: 0.0708
Constant
 
   cl_fsh
Value: 2.73
Constant
 
   b_fsh
Value: 0.948
Constant
 
   h_e2_lh
Value: 0.376
Constant
 
   T_e2_lh
Value: 0.243
Constant
 
   h_p4_lh
Value: 2.71
Constant
 
   T_p4_lh
Value: 0.0269
Constant
 
   h_gnrh_lh
Value: 2.22
Constant
 
   T_gnrh_lh
Value: 0.69
Constant
 
   b_lh
Value: 0.0141
Constant
 
   cl_lh
Value: 12.0
Constant
 
   h_fsh_foll
Value: 0.562
Constant
 
   T_fsh_foll
Value: 0.57
Constant
 
   T_foll_fsh
Value: 0.22
Constant
 
   h_p4_fsh_2
Value: 1.1
Constant
 
   T_p4_foll
Value: 0.126
Constant
 
   h_lh_foll
Value: 3.49
Constant
 
   T_lh_Foll
Value: 0.171
Constant
 
   h_enz_pgf
Value: 53.91
Constant
 
   T_enz_pgf
Value: 1.43
Constant
 
   T_ot_pgf
Value: 1.087
Constant
 
   cl_pgf
Value: 1.23
Constant
 
   SF_CL
Value: 0.2
Constant
 
   h_cl_cl
Value: 0.0353
Constant
 
   T_cl_cl
Value: 0.1
Constant
 
   h_iof_cl
Value: 41.39
Constant
 
   T_iof_cl
Value: 1.32
Constant
 
   k_cl_p4
Value: 2.25
Constant
 
   cl_p4
Value: 1.41
Constant
 
   k_foll_e2
Value: 2.19
Constant
 
   cl_e2
Value: 1.23
Constant
 
   k_foll_inh
Value: 1.41
Constant
 
   cl_inh
Value: 0.475
Constant
 
   h_p4_enz
Value: 3.58
Constant
 
   T_p4_enz
Value: 0.77
Constant
 
   cl_enz
Value: 2.98
Constant
 
   h_e2cl_ot
Value: 1.59
Constant
 
   T_e2_ot
Value: 0.143
Constant
 
   cl_ot
Value: 0.644
Constant
 
   h_pg_iof
Value: 39.68
Constant
 
   T_pg_ot
Value: 1.22
Constant
 
   T_cl_iof
Value: 0.6
Constant
 
   cl_iof
Value: 0.298
Constant
 
 D
Value: 3.7
Constant
 
 beta
Value: 100.0
Constant
 
 c_PGF_syn
Value: 5.5
Constant
 
  t_mod
Value: 150.0
 
 t_D
Constant
 
  Total_PGF_2alpha
Value: 3.62064120302475E-4
 
 quantity_1
Constant
 
 Initial for D
Value: 3.7
Constant
 
 Initial for beta
Value: 100.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000481

Curator's comment: (updated: 23 Sep 2013 11:43:09 BST)

Figure 5B of the reference publication has been reproduced here. The plot varies slightly in terms of the period. This is because in the the paper, the simulation is done for the negative time period, i.e. before the administration of PGF_syn at time=0.
The simulation was done using Copasi v4.8 (Build 55) and the plot was generated using gnuplot.

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