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started writing a script for benchmarks of the incremental KaSa implementation
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‎examples/benchmarks/incremental-KaSa/models/Repressilator.ka‎

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%var: 'Na' 6.022e23 // Avogadro's [mol^-1]
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%var: 'V' 1.4e-15 // Cell volume [L]
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//
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%var: 'c0' 1e9 // M^-1 s^-1
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%var: 'c1' 224 // s^-1
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%var: 'c2' 9 // s^-1
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%var: 'c3' 0.5 // s^-1
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%var: 'c4' 5e-4 // s^-1
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%var: 'c5' 0.167 // s^-1
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%var: 'c6' 0.0057762265 // s^-1
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%var: 'c7' 0.0011552453 // s^-1
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//
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%var: 'tF' 1e-4 // telegraph factor
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%var: 'rF' 1000 // rna factor
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%var: 'pF' 1000 // protein factor
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%var: 'l0' 'c0'/'Na'/'V'*'tF'/'pF'
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%var: 'l1' 'c1'*'tF'
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%var: 'l2' 'c2'*'tF'
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%var: 'l3' 'c3'*'rF'
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%var: 'l4' 'c4'*'rF'
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%var: 'm0' 'c0'/'Na'/'V'*'tF'/'pF'
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%var: 'm1' 'c1'*'tF'
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%var: 'm2' 'c2'*'tF'
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%var: 'm3' 'c3'*'rF'
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%var: 'm4' 'c4'*'rF'
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%agent: Null()
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%agent: gTetR(lac1,lac2)
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%agent: pLacI(tet)
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%agent: pTetR(cI)
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%agent: gCI(tet1,tet2)
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%agent: gLacI(cI1,cI2)
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%agent: mTetR()
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%agent: mCI()
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%agent: mLacI()
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%agent: pCI(lac)
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%init: 1 Null()
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%init: 1 gTetR(lac1[1],lac2[2]),pLacI(tet[1]),pLacI(tet[2])
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%init: 1 gCI(tet1[1],tet2[2]),pTetR(cI[1]),pTetR(cI[2])
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%init: 1 gLacI(cI1[1],cI2[2]),pCI(lac[1]),pCI(lac[2])
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%init: 3163 mTetR()
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%init: 6819 mCI()
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%init: 129 mLacI()
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%init: 183453 pTetR(cI)
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%init: 2006198 pCI(lac)
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%init: 165670 pLacI(tet)
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%var: 'k0' 'c0'/'Na'/'V'*'tF'/'pF'
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%var: 'k1' 'c1'*'tF'
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%var: 'k2' 'c2'*'tF'
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%var: 'k3' 'c3'*'rF'
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%var: 'k4' 'c4'*'rF'
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// working_set
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//00//
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gTetR(lac1[.],lac2[.]) , pLacI(tet[.]) <-> gTetR(lac1[1],lac2[.]),pLacI(tet[1]) @'k0', 'k1'
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gTetR(lac2[.],lac1[.]) , pLacI(tet[.]) <-> gTetR(lac2[1],lac1[.]),pLacI(tet[1]) @'k0', 'k1'
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gTetR(lac1[_],lac2[.]) , pLacI(tet[.]) <-> gTetR(lac1[_],lac2[1]),pLacI(tet[1]) @'k0', 'k2'
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gTetR(lac2[_],lac1[.]) , pLacI(tet[.]) <-> gTetR(lac2[_],lac1[1]),pLacI(tet[1]) @'k0', 'k2'
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gTetR(lac1[.],lac2[.]),. -> gTetR(lac1[.],lac2[.]) , mTetR() @'k3'
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//05//
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gTetR(lac1[_]),. -> gTetR(lac1[_]) , mTetR() @'k4'
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gTetR(lac2[_]),. -> gTetR(lac2[_]) , mTetR() @'k4'
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mTetR(),. -> mTetR() , pTetR(cI[.]) @'c5'/'rF'*'pF'
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mTetR() , Null() -> .,Null() @'c6'{0}
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pTetR(cI[.]) , Null() -> .,Null() @'c7'{0}
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//10//
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gCI(tet1[.],tet2[.]) , pTetR(cI[.]) <-> gCI(tet1[1],tet2[.]),pTetR(cI[1]) @'l0', 'l1'
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gCI(tet2[.],tet1[.]) , pTetR(cI[.]) <-> gCI(tet2[1],tet1[.]),pTetR(cI[1]) @'l0', 'l1'
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gCI(tet1[_],tet2[.]) , pTetR(cI[.]) <-> gCI(tet1[_],tet2[1]),pTetR(cI[1]) @'l0', 'l2'
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gCI(tet2[_],tet1[.]) , pTetR(cI[.]) <-> gCI(tet2[_],tet1[1]),pTetR(cI[1]) @'l0', 'l2'
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gCI(tet1[.],tet2[.]),. -> gCI(tet1[.],tet2[.]) ,mCI() @'l3'
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//15//
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gCI(tet1[_]),. -> gCI(tet1[_]) , mCI() @'l4'
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gCI(tet2[_]),. -> gCI(tet2[_]) , mCI() @'l4'
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mCI(),. -> mCI() , pCI(lac[.]) @'c5'/'rF'*'pF'
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mCI() , Null() -> .,Null() @'c6'{0}
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pCI(lac[.]) , Null() -> .,Null() @'c7'{0}
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//20//
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gLacI(cI1[.],cI2[.]) , pCI(lac[.]) <-> gLacI(cI1[1],cI2[.]),pCI(lac[1]) @'m0','m1'
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gLacI(cI2[.],cI1[.]) , pCI(lac[.]) <-> gLacI(cI2[1],cI1[.]),pCI(lac[1]) @'m0','m1'
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gLacI(cI1[_],cI2[.]) , pCI(lac[.]) <-> gLacI(cI1[_],cI2[1]),pCI(lac[1]) @'m0','m2'
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gLacI(cI2[_],cI1[.]) , pCI(lac[.]) <-> gLacI(cI2[_],cI1[1]),pCI(lac[1]) @'m0','m2'
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gLacI(cI1[.],cI2[.]),. -> gLacI(cI1[.],cI2[.]) , mLacI() @ 'm3'
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//25//
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gLacI(cI1[_]),. -> gLacI(cI1[_]), mLacI() @'m4'
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gLacI(cI2[_]),. -> gLacI(cI2[_]) , mLacI() @'m4'
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mLacI(),. -> mLacI() , pLacI(tet[.]) @'c5'/'rF'*'pF'
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mLacI() , Null() -> .,Null() @'c6'{0}
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pLacI(tet[.]) , Null() -> .,Null() @'c7'{0}
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//30//

‎examples/benchmarks/incremental-KaSa/models/causality_05_sos.ka‎

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/////////////////////
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// stories
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%var: 'cflow' 0
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%mod: [true] do $TRACK 'sos recruited' [true];
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%mod: ('sos recruited' - 'cflow' = 10 ) do ($TRACK 'sos recruited' [false];$STOP;)
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//////////////////////////////////////////////////////////////////////////////
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// agent interfaces
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%agent: EGF(r)
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%agent: EGFR(CR,C,N,L,Y1016{u p},Y1092{u p},Y1172{u p})
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%agent: SoS(PR,S{u p})
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%agent: Shc(Y{u p},PTB{u p})
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%agent: Grb2(SH3c,SH3n,SH2{u p})
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//------------------------------------------------------------------------------
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// "mad computer scientist" rate constants
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%var: 'k_on' 1
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%var: 'k_cat' 1
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%var: 'k_off' 1
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//------------------------------------------------------------------------------
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// more reasonable rate constants
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// %var: 'k_on K' 0.01 # molecule^-1 s^-1
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// %var: 'k_off K' 2.5 # s^-1
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// %var: 'k_cat K' 1 # s^-1
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//////////////////////////////////////////////////////////////////////////////
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// initial mixture
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%init: 10 EGF(r)
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%init: 10 EGFR(CR,C,N,L,Y1016{u},Y1092{u},Y1172{u})
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%init: 20 SoS(PR,S{u})
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%init: 16 Shc(Y{u},PTB{u})
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%init: 10 Grb2(SH3c,SH3n,SH2{u})
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//////////////////////////////////////////////////////////////////////////////
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// observables
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%obs: 'long' |Shc(PTB[_],Y[1]),Grb2(SH2[1],SH3n[2]),SoS(PR[2])|
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%obs: 'short' |EGFR(Y1092{p}[2]),Grb2(SH2[2],SH3n[1]),SoS(PR[1])|
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%var: 'sos recruited' |Grb2(SH2[_],SH3n[2]),SoS(PR[2])|
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//////////////////////////////////////////////////////////////////////////////
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// rules for "Sos recruitment"
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// working_set
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//00//
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'EGFR.EGFR'//rule1//
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EGF(r[2]), EGFR(L[2],CR[.],N[.],C[.]), EGF(r[3]), EGFR(L[3],CR[.],N[.],C[.]) ->//rule1//
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EGF(r[2]), EGFR(L[2],CR[1],N[.],C[.]), EGF(r[3]), EGFR(L[3],CR[1],N[.],C[.]) @ 'k_on'/2//rule1//
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'EGFR/EGFR'//rule2//
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EGF(r[2]), EGFR(L[2],CR[1],N[.],C[.]), EGF(r[3]), EGFR(L[3],CR[1],N[.],C[.]) ->//rule2//
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EGF(r[2]), EGFR(L[2],CR[.],N[.],C[.]), EGF(r[3]), EGFR(L[3],CR[.],N[.],C[.]) @ 'k_off'/2//rule2//
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'EGF.EGFR' EGF(r[.]), EGFR(L[.],CR[.]) -> EGF(r[1]), EGFR(L[1],CR[.]) @ 'k_on'
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'EGF/EGFR' EGF(r[1]), EGFR(L[1],CR[.]) -> EGF(r[.]), EGFR(L[.],CR[.]) @ 'k_off'
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'Shc.Grb2' Shc(Y[.]{p}), Grb2(SH2[.]) -> Shc(Y[1]{p}), Grb2(SH2[1]) @ 5*'k_on'
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//05//
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'Shc/Grb2' Shc(Y{p}[1]), Grb2(SH2[1]) -> Shc(Y{p}[.]), Grb2(SH2[.]) @ 'k_off'
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'EGFR.Grb2' EGFR(Y1092{p}[.]), Grb2(SH2[.]) -> EGFR(Y1092{p}[1]), Grb2(SH2[1]) @ 'k_on'
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'EGFR/Grb2' EGFR(Y1092{p}[1]), Grb2(SH2[1]) -> EGFR(Y1092{p}[.]), Grb2(SH2[.]) @ 'k_off'
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'EGFR.Shc' EGFR(Y1172{p}[.]), Shc(PTB[.]) -> EGFR(Y1172{p}[1]), Shc(PTB[1]) @ 'k_on'
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'EGFR/Shc' EGFR(Y1172{p}[1]), Shc(PTB[1]) -> EGFR(Y1172{p}[.]), Shc(PTB[.]) @ 'k_off'
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//10//
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'Grb2.SoS' Grb2(SH3n[.]), SoS(PR[.],S[.]{u}) -> Grb2(SH3n[1]), SoS(PR[1],S[.]{u}) @ 'k_on'
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'Grb2/SoS' Grb2(SH3n[1]), SoS(PR[1]) -> Grb2(SH3n[.]), SoS(PR[.]) @ 'k_off'
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'EGFR.int' EGFR(CR[1],N[.],C[.]), EGFR(CR[1],N[.],C[.]) -> EGFR(CR[1],N[2],C[.]), EGFR(CR[1],N[.],C[2]) @ 'k_on'
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'EGFR/int' EGFR(CR[1],N[2],C[.]), EGFR(CR[1],N[.],C[2]) -> EGFR(CR[1],N[.],C[.]), EGFR(CR[1],N[.],C[.]) @ 'k_off'
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'pY1092@EGFR' EGFR(N[1]), EGFR(C[1],Y1092{u}[.]) -> EGFR(N[1]), EGFR(C[1],Y1092{p}[.]) @ 'k_cat'
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//15//
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'pY1172@EGFR' EGFR(N[1]), EGFR(C[1],Y1172[.]{u}) -> EGFR(N[1]), EGFR(C[1],Y1172[.]{p}) @ 'k_cat'
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'uY1092@EGFR' EGFR(Y1092[.]{p}) -> EGFR(Y1092[.]{u}) @ 'k_cat'
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'uY1172@EGFR' EGFR(Y1172{p}[.]) -> EGFR(Y1172{u}[.]) @ 'k_cat'
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'pY@Shc' EGFR(Y1172{p}[1]), Shc(PTB[1],Y{u}[.]) -> EGFR(Y1172{p}[1]), Shc(PTB[1],Y{p}[.]) @ 'k_cat'
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'uY@Shc' Shc(Y{p}[.]) -> Shc(Y{u}[.]) @ 'k_cat'
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//20//

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