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camkii-test.bngl
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begin model
begin parameters
# initial amounts
CaMCa4_init 5
CaMKII_init 1
# Rate constants
kf_N1
kr_N1
kf_N2
kr_N2
kf_C1
kr_C1
kf_C2
kr_C2
kf_CaM4
kr_CaM4
kf_pT286
kr_pT286
kf_ubCaM4
kr_ubCaM4
kf_depho_PP1
kr_depho_PP1
kf_depho_CaN
kr_depho_CaN
end parameters
begin molecule types
Ca
CaMCa4(cmk)
CaMKII(T286~0~p,CaM~0~b,x~1~2~3~4~5~6~7~8~9~10~11~12,L,R)
end molecule types
begin seed species
CaMCa4(cmk) CaMCa4_init
CaMKII(T286~0,CaM~0,x~1,L!1,R!2).CaMKII(T286~0,CaM~0,x~2,L!2,R!3).CaMKII(T286~0,CaM~0,x~3,L!3,R!4).CaMKII(T286~0,CaM~0,x~4,L!4,R!5).CaMKII(T286~0,CaM~0,x~5,L!5,R!6).CaMKII(T286~0,CaM~0,x~6,L!6,R!7).CaMKII(T286~0,CaM~0,x~7,L!7,R!8).CaMKII(T286~0,CaM~0,x~8,L!8,R!9).CaMKII(T286~0,CaM~0,x~9,L!9,R!10).CaMKII(T286~0,CaM~0,x~10,L!10,R!11).CaMKII(T286~0,CaM~0,x~11,L!11,R!12).CaMKII(T286~0,CaM~0,x~12,L!12,R!1) CaMKII_init
end seed species
begin observables
01: Molecules CaMKII_inhibit CaMKII(T286~0,CaM~0,x,L,R)
02: Molecules CaMKII_bound CaMKII(CaM~b)
03: Molecules CaMKII_phosph CaMKII(T286~p)
end observables
begin reaction rules
# CaMCa4 binding
R1: CaMKII(T286~0,CaM~0) + CaMCa4(cmk) -> CaMKII(T286~0,CaM~b) kf1
#autophosphorylation
R2: CaMKII(T286~0,CaM~b,x~1).CaMKII(T286~0,CaM~b,x~2) -> CaMKII(T286~p,CaM~b,x~1).CaMKII(T286~p,CaM~b,x~2) kf2
R2: CaMKII(T286~0,CaM~b,x~2).CaMKII(T286~0,CaM~b,x~3) -> CaMKII(T286~p,CaM~b,x~2).CaMKII(T286~p,CaM~b,x~3) kf2
R2: CaMKII(T286~0,CaM~b,x~3).CaMKII(T286~0,CaM~b,x~4) -> CaMKII(T286~p,CaM~b,x~3).CaMKII(T286~p,CaM~b,x~4) kf2
R2: CaMKII(T286~0,CaM~b,x~4).CaMKII(T286~0,CaM~b,x~5) -> CaMKII(T286~p,CaM~b,x~4).CaMKII(T286~p,CaM~b,x~5) kf2
R2: CaMKII(T286~0,CaM~b,x~5).CaMKII(T286~0,CaM~b,x~6) -> CaMKII(T286~p,CaM~b,x~5).CaMKII(T286~p,CaM~b,x~6) kf2
R2: CaMKII(T286~0,CaM~b,x~6).CaMKII(T286~0,CaM~b,x~7) -> CaMKII(T286~p,CaM~b,x~6).CaMKII(T286~p,CaM~b,x~7) kf2
R2: CaMKII(T286~0,CaM~b,x~7).CaMKII(T286~0,CaM~b,x~8) -> CaMKII(T286~p,CaM~b,x~7).CaMKII(T286~p,CaM~b,x~8) kf2
R2: CaMKII(T286~0,CaM~b,x~8).CaMKII(T286~0,CaM~b,x~9) -> CaMKII(T286~p,CaM~b,x~8).CaMKII(T286~p,CaM~b,x~9) kf2
R2: CaMKII(T286~0,CaM~b,x~9).CaMKII(T286~0,CaM~b,x~10) ->CaMKII(T286~p,CaM~b,x~9).CaMKII(T286~p,CaM~b,x~10) kf2
R2: CaMKII(T286~0,CaM~b,x~10).CaMKII(T286~0,CaM~b,x~11) -> CaMKII(T286~p,CaM~b,x~10).CaMKII(T286~p,CaM~b,x~11) kf2
R2: CaMKII(T286~0,CaM~b,x~11).CaMKII(T286~0,CaM~b,x~12) -> CaMKII(T286~p,CaM~b,x~11).CaMKII(T286~p,CaM~b,x~12) kf2
R2: CaMKII(T286~0,CaM~b,x~12).CaMKII(T286~0,CaM~b,x~1) -> CaMKII(T286~p,CaM~b,x~12).CaMKII(T286~p,CaM~b,x~1) kf2
R3: CaMKII(T286~0,CaM~b,x~1).CaMKII(T286~p,CaM~b,x~2) -> CaMKII(T286~p,CaM~b,x~1).CaMKII(T286~p,CaM~b,x~2) kf3
R3: CaMKII(T286~0,CaM~b,x~2).CaMKII(T286~p,CaM~b,x~3) -> CaMKII(T286~p,CaM~b,x~2).CaMKII(T286~p,CaM~b,x~3) kf3
R3: CaMKII(T286~0,CaM~b,x~3).CaMKII(T286~p,CaM~b,x~4) -> CaMKII(T286~p,CaM~b,x~3).CaMKII(T286~p,CaM~b,x~4) kf3
R3: CaMKII(T286~0,CaM~b,x~4).CaMKII(T286~p,CaM~b,x~5) -> CaMKII(T286~p,CaM~b,x~4).CaMKII(T286~p,CaM~b,x~5) kf3
R3: CaMKII(T286~0,CaM~b,x~5).CaMKII(T286~p,CaM~b,x~6) -> CaMKII(T286~p,CaM~b,x~5).CaMKII(T286~p,CaM~b,x~6) kf3
R3: CaMKII(T286~0,CaM~b,x~6).CaMKII(T286~p,CaM~b,x~7) -> CaMKII(T286~p,CaM~b,x~6).CaMKII(T286~p,CaM~b,x~7) kf3
R3: CaMKII(T286~0,CaM~b,x~7).CaMKII(T286~p,CaM~b,x~8) -> CaMKII(T286~p,CaM~b,x~7).CaMKII(T286~p,CaM~b,x~8) kf3
R3: CaMKII(T286~0,CaM~b,x~8).CaMKII(T286~p,CaM~b,x~9) -> CaMKII(T286~p,CaM~b,x~8).CaMKII(T286~p,CaM~b,x~9) kf3
R3: CaMKII(T286~0,CaM~b,x~9).CaMKII(T286~p,CaM~b,x~10) ->CaMKII(T286~p,CaM~b,x~9).CaMKII(T286~p,CaM~b,x~10) kf3
R3: CaMKII(T286~0,CaM~b,x~10).CaMKII(T286~p,CaM~b,x~11) -> CaMKII(T286~p,CaM~b,x~10).CaMKII(T286~p,CaM~b,x~11) kf3
R3: CaMKII(T286~0,CaM~b,x~11).CaMKII(T286~p,CaM~b,x~12) -> CaMKII(T286~p,CaM~b,x~11).CaMKII(T286~p,CaM~b,x~12) kf3
R3: CaMKII(T286~0,CaM~b,x~12).CaMKII(T286~p,CaM~b,x~1) -> CaMKII(T286~p,CaM~b,x~12).CaMKII(T286~p,CaM~b,x~1) kf3
R3: CaMKII(T286~p,CaM~b,x~1).CaMKII(T286~0,CaM~b,x~2) -> CaMKII(T286~p,CaM~b,x~1).CaMKII(T286~p,CaM~b,x~2) kf3
R3: CaMKII(T286~p,CaM~b,x~2).CaMKII(T286~0,CaM~b,x~3) -> CaMKII(T286~p,CaM~b,x~2).CaMKII(T286~p,CaM~b,x~3) kf3
R3: CaMKII(T286~p,CaM~b,x~3).CaMKII(T286~0,CaM~b,x~4) -> CaMKII(T286~p,CaM~b,x~3).CaMKII(T286~p,CaM~b,x~4) kf3
R3: CaMKII(T286~p,CaM~b,x~4).CaMKII(T286~0,CaM~b,x~5) -> CaMKII(T286~p,CaM~b,x~4).CaMKII(T286~p,CaM~b,x~5) kf3
R3: CaMKII(T286~p,CaM~b,x~5).CaMKII(T286~0,CaM~b,x~6) -> CaMKII(T286~p,CaM~b,x~5).CaMKII(T286~p,CaM~b,x~6) kf3
R3: CaMKII(T286~p,CaM~b,x~6).CaMKII(T286~0,CaM~b,x~7) -> CaMKII(T286~p,CaM~b,x~6).CaMKII(T286~p,CaM~b,x~7) kf3
R3: CaMKII(T286~p,CaM~b,x~7).CaMKII(T286~0,CaM~b,x~8) -> CaMKII(T286~p,CaM~b,x~7).CaMKII(T286~p,CaM~b,x~8) kf3
R3: CaMKII(T286~p,CaM~b,x~8).CaMKII(T286~0,CaM~b,x~9) -> CaMKII(T286~p,CaM~b,x~8).CaMKII(T286~p,CaM~b,x~9) kf3
R3: CaMKII(T286~p,CaM~b,x~9).CaMKII(T286~0,CaM~b,x~10) ->CaMKII(T286~p,CaM~b,x~9).CaMKII(T286~p,CaM~b,x~10) kf3
R3: CaMKII(T286~p,CaM~b,x~10).CaMKII(T286~0,CaM~b,x~11) -> CaMKII(T286~p,CaM~b,x~10).CaMKII(T286~p,CaM~b,x~11) kf3
R3: CaMKII(T286~p,CaM~b,x~11).CaMKII(T286~0,CaM~b,x~12) -> CaMKII(T286~p,CaM~b,x~11).CaMKII(T286~p,CaM~b,x~12) kf3
R3: CaMKII(T286~p,CaM~b,x~12).CaMKII(T286~0,CaM~b,x~1) -> CaMKII(T286~p,CaM~b,x~12).CaMKII(T286~p,CaM~b,x~1) kf3
R4: CaMKII(T286~p)-> CaMKII(T286~0) kf4
R5: CaMKII(CaM~0)-> CaMKII(CaM~0) kf5
end reaction rules
end model
generate_network({overwrite=>1})