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camkii-test2_v2.bngl
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camkii-test2_v2.bngl
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begin model
begin parameters
# initial amounts
CaMCa4_init 13
CaMKII_init 5
# Rate constants
kf1 1/10000
kr1 1
kf2 1
kf3 1
kf4 1
kr4 1
kf5 1
end parameters
begin molecule types
CaMCa4(cmk)
bCaMKII(T1~0~p,C1~0~b,T2~0~p,C2~0~b,T3~0~p,C3~0~b,T4~0~p,C4~0~b,T5~0~p,C5~0~b,T6~0~p,C6~0~b)
gCaMKII(T~0~p,C~0~b,S~0~p,T~0~p,C~0~b,S~0~p,T~0~p,C~0~b,S~0~p,T~0~p,C~0~b,S~0~p,T~0~p,C~0~b,S~0~p,T~0~p,C~0~b,S~0~p)
end molecule types
begin seed species
CaMCa4(cmk) CaMCa4_init
bCaMKII(T1~0,C1~0,T2~0,C2~0,T3~0,C3~0,T4~0,C4~0,T5~0,C5~0,T6~0,C6~0) CaMKII_init
gCaMKII(T~0,C~0,S~p,T~0,C~0,S~p,T~0,C~0,S~p,T~0,C~0,S~p,T~0,C~0,S~p,T~0,C~0,S~p) CaMKII_init
end seed species
begin reaction rules
# CaMCa4 binding
# R1 works good; seems BioNetGen knows which graph patterns are isomorphic; can test it by set max_iter=1, 2
R1_1: bCaMKII(T1~0,C1~0) + CaMCa4(cmk) -> bCaMKII(T1~0,C1~b) kf1
R1_2: bCaMKII(T2~0,C2~0) + CaMCa4(cmk) -> bCaMKII(T2~0,C2~b) kf1
R1_3: bCaMKII(T3~0,C3~0) + CaMCa4(cmk) -> bCaMKII(T3~0,C3~b) kf1
R1_4: bCaMKII(T4~0,C4~0) + CaMCa4(cmk) -> bCaMKII(T4~0,C4~b) kf1
R1_5: bCaMKII(T5~0,C5~0) + CaMCa4(cmk) -> bCaMKII(T5~0,C5~b) kf1
R1_6: bCaMKII(T6~0,C6~0) + CaMCa4(cmk) -> bCaMKII(T6~0,C6~b) kf1
# autophosphorylation
R2_1: bCaMKII(T1~0,C1~b,T2~0,C2~b)-> bCaMKII(T1~p,C1~b,T2~p,C2~b) kf2
R2_2: bCaMKII(T2~0,C2~b,T3~0,C3~b)-> bCaMKII(T2~p,C2~b,T3~p,C3~b) kf2
R2_3: bCaMKII(T3~0,C3~b,T4~0,C4~b)-> bCaMKII(T3~p,C3~b,T4~p,C4~b) kf2
R2_4: bCaMKII(T4~0,C4~b,T5~0,C5~b)-> bCaMKII(T4~p,C4~b,T5~p,C5~b) kf2
R2_5: bCaMKII(T5~0,C5~b,T6~0,C6~b)-> bCaMKII(T5~p,C5~b,T6~p,C6~b) kf2
R2_6: bCaMKII(T6~0,C6~b,T1~0,C1~b)-> bCaMKII(T6~p,C6~b,T1~p,C1~b) kf2
R4_1: bCaMKII(T1~p) -> bCaMKII(T1~0) kf4
R4_2: bCaMKII(T2~p) -> bCaMKII(T2~0) kf4
R4_3: bCaMKII(T3~p) -> bCaMKII(T3~0) kf4
R4_4: bCaMKII(T4~p) -> bCaMKII(T4~0) kf4
R4_5: bCaMKII(T5~p) -> bCaMKII(T5~0) kf4
R4_6: bCaMKII(T6~p) -> bCaMKII(T6~0) kf4
R5_1: bCaMKII(C1~b) -> bCaMKII(C1~0) kf5
R5_2: bCaMKII(C2~b) -> bCaMKII(C2~0) kf5
R5_3: bCaMKII(C3~b) -> bCaMKII(C3~0) kf5
R5_4: bCaMKII(C4~b) -> bCaMKII(C4~0) kf5
R5_5: bCaMKII(C5~b) -> bCaMKII(C5~0) kf5
R5_6: bCaMKII(C6~b) -> bCaMKII(C6~0) kf5
#========================================================================
R6: gCaMKII(T~0,C~0) + CaMCa4(cmk) -> gCaMKII(T~0,C~b) kf1
R7: gCaMKII(T~p) -> gCaMKII(T~0) kf4
R8: gCaMKII(C~b) -> gCaMKII(C~0) kf5
R9: gCaMKII(S~p) -> gCaMKII(S~0) kf2
#==========================================================================
R27: bCaMKII(T1~p)+gCaMKII(T~0,C~b)-> bCaMKII(T1~p)+gCaMKII(T~p,C~b) kf2
R27: bCaMKII(T2~p)+gCaMKII(T~0,C~b)-> bCaMKII(T2~p)+gCaMKII(T~p,C~b) kf2
R27: bCaMKII(T3~p)+gCaMKII(T~0,C~b)-> bCaMKII(T3~p)+gCaMKII(T~p,C~b) kf2
R27: bCaMKII(T4~p)+gCaMKII(T~0,C~b)-> bCaMKII(T4~p)+gCaMKII(T~p,C~b) kf2
R27: bCaMKII(T5~p)+gCaMKII(T~0,C~b)-> bCaMKII(T5~p)+gCaMKII(T~p,C~b) kf2
R27: bCaMKII(T6~p)+gCaMKII(T~0,C~b)-> bCaMKII(T6~p)+gCaMKII(T~p,C~b) kf2
end reaction rules
end model
generate_network({overwrite=>1})