Apply a slightly nicer .aeon printer from the new version.

sybila · Sep 24, 2024 · ee1b2ac · ee1b2ac
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diff --git a/models/[id-001]__[var-302]__[in-19]__[SIGNALING-IN-MACROPHAGE-ACTIVATION]/model.aeon b/models/[id-001]__[var-302]__[in-19]__[SIGNALING-IN-MACROPHAGE-ACTIVATION]/model.aeon
diff --git a/models/[id-002]__[var-130]__[in-9]__[SIGNAL-TRANSDUCTION-IN-FIBROBLASTS]/model.aeon b/models/[id-002]__[var-130]__[in-9]__[SIGNAL-TRANSDUCTION-IN-FIBROBLASTS]/model.aeon
diff --git a/models/[id-003]__[var-19]__[in-1]__[MAMMALIAN-CELL-CYCLE]/model.aeon b/models/[id-003]__[var-19]__[in-1]__[MAMMALIAN-CELL-CYCLE]/model.aeon
@@ -49,22 +49,22 @@ v_cMYC -| v_p21
 v_Akt1 -| v_p21
 v_CDK4 -| v_p21
 v_ERa -> v_p21
-$v_Akt1: ((((v_ErbB2_3 | v_IGF1R) | v_ErbB1_2) | v_ErbB1_3) | v_ErbB1)
-$v_CDK2: (v_CycE1 & !(v_p21 | v_p27))
-$v_CDK4: (v_CycD1 & !(v_p21 | v_p27))
+$v_Akt1: v_ErbB2_3 | v_IGF1R | v_ErbB1_2 | v_ErbB1_3 | v_ErbB1
+$v_CDK2: v_CycE1 & !(v_p21 | v_p27)
+$v_CDK4: v_CycD1 & !(v_p21 | v_p27)
 $v_CDK6: v_CycD1
-$v_CycD1: ((v_Akt1 & (v_cMYC & v_ERa)) | (v_MEK1 & (v_ERa & v_cMYC)))
+$v_CycD1: (v_Akt1 & v_cMYC & v_ERa) | (v_MEK1 & v_ERa & v_cMYC)
 $v_CycE1: v_cMYC
-$v_ERa: (v_Akt1 | v_MEK1)
+$v_ERa: v_Akt1 | v_MEK1
 $v_ErbB1: v_EGF
-$v_ErbB1_2: (v_ErbB1 & v_ErbB2)
-$v_ErbB1_3: (v_ErbB1 & v_ErbB3)
+$v_ErbB1_2: v_ErbB1 & v_ErbB2
+$v_ErbB1_3: v_ErbB1 & v_ErbB3
 $v_ErbB2: v_EGF
-$v_ErbB2_3: (v_ErbB2 & v_ErbB3)
+$v_ErbB2_3: v_ErbB2 & v_ErbB3
 $v_ErbB3: v_EGF
-$v_IGF1R: ((v_ERa & !v_ErbB2_3) | (v_Akt1 & !v_ErbB2_3))
-$v_MEK1: ((((v_ErbB2_3 | v_ErbB1_2) | v_IGF1R) | v_ErbB1_3) | v_ErbB1)
-$v_cMYC: ((v_MEK1 | v_Akt1) | v_ERa)
-$v_p21: (v_ERa & !((v_CDK4 | v_Akt1) | v_cMYC))
-$v_p27: (v_ERa & !(((v_cMYC | v_CDK4) | v_Akt1) | v_CDK2))
-$v_pRB: ((v_CDK4 & v_CDK6) | (v_CDK2 & (v_CDK6 & v_CDK4)))
+$v_IGF1R: (v_ERa & !v_ErbB2_3) | (v_Akt1 & !v_ErbB2_3)
+$v_MEK1: v_ErbB2_3 | v_ErbB1_2 | v_IGF1R | v_ErbB1_3 | v_ErbB1
+$v_cMYC: v_MEK1 | v_Akt1 | v_ERa
+$v_p21: v_ERa & !(v_CDK4 | v_Akt1 | v_cMYC)
+$v_p27: v_ERa & !(v_cMYC | v_CDK4 | v_Akt1 | v_CDK2)
+$v_pRB: (v_CDK4 & v_CDK6) | (v_CDK2 & v_CDK6 & v_CDK4)
diff --git a/models/[id-004]__[var-225]__[in-22]__[ERBB-RECEPTOR-SIGNALING]/model.aeon b/models/[id-004]__[var-225]__[in-22]__[ERBB-RECEPTOR-SIGNALING]/model.aeon
diff --git a/models/[id-005]__[var-28]__[in-0]__[FA-BRCA-PATHWAY]/model.aeon b/models/[id-005]__[var-28]__[in-0]__[FA-BRCA-PATHWAY]/model.aeon
@@ -121,31 +121,31 @@ v_CHKREC -| v_ATR
 v_ssDNARPA -> v_ATR
 v_MUS81 -> v_FAN1
 v_FANCD2I -> v_FAN1
-$v_ADD: ((v_ADD & !v_PCNATLS) | ((v_MUS81 & (v_FAN1 | v_XPF)) & !v_PCNATLS))
-$v_ATM: ((v_DSB & !v_CHKREC) | (v_ATR & !v_CHKREC))
-$v_ATR: (((v_FANCM & !v_CHKREC) | (v_ATM & !v_CHKREC)) | (v_ssDNARPA & !v_CHKREC))
-$v_BRCA1: ((v_DSB & ((v_ATM | v_CHK2) | v_ATR)) & !v_CHKREC)
-$v_CHK1: (((v_ATM & !v_CHKREC) | (v_DNAPK & !v_CHKREC)) | (v_ATR & !v_CHKREC))
-$v_CHK2: (((v_ATM & !v_CHKREC) | (v_DNAPK & !v_CHKREC)) | (v_ATR & !v_CHKREC))
-$v_CHKREC: ((((v_PCNATLS & !v_DSB) | (v_NHEJ & !v_DSB)) | (v_HRR & !v_DSB)) | !((((((v_NHEJ | v_ICL) | v_PCNATLS) | v_HRR) | v_DSB) | v_CHKREC) | v_ADD))
-$v_DNAPK: ((v_DSB & v_KU) & !v_CHKREC)
-$v_DSB: (((v_XPF & !(v_HRR | v_NHEJ)) | (v_DSB & !(v_HRR | v_NHEJ))) | (v_FAN1 & !(v_HRR | v_NHEJ)))
-$v_FAN1: (v_MUS81 & v_FANCD2I)
-$v_FANCD1N: ((v_ssDNARPA & v_BRCA1) | ((v_FANCD2I & v_ssDNARPA) & !v_CHKREC))
-$v_FANCD2I: ((v_FAcore & ((v_ATM | v_ATR) | (v_DSB & v_H2AX))) & !v_USP1)
-$v_FANCJBRCA1: ((v_ssDNARPA & (v_ATM | v_ATR)) | (v_ICL & (v_ATM | v_ATR)))
-$v_FANCM: (v_ICL & !v_CHKREC)
-$v_FAcore: ((v_FANCM & (v_ATM | v_ATR)) & !v_CHKREC)
-$v_H2AX: ((v_DSB & ((v_ATM | v_DNAPK) | v_ATR)) & !v_CHKREC)
-$v_HRR: ((v_DSB & ((v_BRCA1 & v_FANCD1N) & v_RAD51)) & !v_CHKREC)
-$v_ICL: (v_ICL & !v_DSB)
-$v_KU: (v_DSB & !((v_CHKREC | v_MRN) | v_FANCD2I))
-$v_MRN: ((v_DSB & v_ATM) & !((v_RAD51 | (v_KU & v_FANCD2I)) | v_CHKREC))
+$v_ADD: (v_ADD & !v_PCNATLS) | (v_MUS81 & (v_FAN1 | v_XPF) & !v_PCNATLS)
+$v_ATM: (v_DSB & !v_CHKREC) | (v_ATR & !v_CHKREC)
+$v_ATR: (v_FANCM & !v_CHKREC) | (v_ATM & !v_CHKREC) | (v_ssDNARPA & !v_CHKREC)
+$v_BRCA1: v_DSB & (v_ATM | v_CHK2 | v_ATR) & !v_CHKREC
+$v_CHK1: (v_ATM & !v_CHKREC) | (v_DNAPK & !v_CHKREC) | (v_ATR & !v_CHKREC)
+$v_CHK2: (v_ATM & !v_CHKREC) | (v_DNAPK & !v_CHKREC) | (v_ATR & !v_CHKREC)
+$v_CHKREC: (v_PCNATLS & !v_DSB) | (v_NHEJ & !v_DSB) | (v_HRR & !v_DSB) | !(v_NHEJ | v_ICL | v_PCNATLS | v_HRR | v_DSB | v_CHKREC | v_ADD)
+$v_DNAPK: v_DSB & v_KU & !v_CHKREC
+$v_DSB: (v_XPF & !(v_HRR | v_NHEJ)) | (v_DSB & !(v_HRR | v_NHEJ)) | (v_FAN1 & !(v_HRR | v_NHEJ))
+$v_FAN1: v_MUS81 & v_FANCD2I
+$v_FANCD1N: (v_ssDNARPA & v_BRCA1) | (v_FANCD2I & v_ssDNARPA & !v_CHKREC)
+$v_FANCD2I: v_FAcore & (v_ATM | v_ATR | (v_DSB & v_H2AX)) & !v_USP1
+$v_FANCJBRCA1: (v_ssDNARPA & (v_ATM | v_ATR)) | (v_ICL & (v_ATM | v_ATR))
+$v_FANCM: v_ICL & !v_CHKREC
+$v_FAcore: v_FANCM & (v_ATM | v_ATR) & !v_CHKREC
+$v_H2AX: v_DSB & (v_ATM | v_DNAPK | v_ATR) & !v_CHKREC
+$v_HRR: v_DSB & v_BRCA1 & v_FANCD1N & v_RAD51 & !v_CHKREC
+$v_ICL: v_ICL & !v_DSB
+$v_KU: v_DSB & !(v_CHKREC | v_MRN | v_FANCD2I)
+$v_MRN: v_DSB & v_ATM & !(v_RAD51 | (v_KU & v_FANCD2I) | v_CHKREC)
 $v_MUS81: v_ICL
-$v_NHEJ: (((v_KU & (v_DNAPK & v_DSB)) & !(v_ATM & v_ATR)) | ((v_XPF & (v_DNAPK & v_DSB)) & !((v_FANCJBRCA1 & v_ssDNARPA) | v_CHKREC)))
-$v_PCNATLS: (((v_FAcore & v_ADD) & !(v_FAN1 | v_USP1)) | (v_ADD & !(v_FAN1 | v_USP1)))
-$v_RAD51: ((v_ssDNARPA & v_FANCD1N) & !v_CHKREC)
-$v_USP1: (((v_FANCD1N & v_FANCD2I) & !v_FANCM) | (v_PCNATLS & !v_FANCM))
-$v_XPF: (((v_p53 & v_MUS81) & !(v_FAcore & (v_FAN1 & v_FANCD2I))) | (v_MUS81 & !v_FANCM))
-$v_p53: ((((v_ATM & v_CHK2) & !v_CHKREC) | ((v_ATR & v_CHK1) & !v_CHKREC)) | (v_DNAPK & !v_CHKREC))
-$v_ssDNARPA: ((v_DSB & ((v_FANCJBRCA1 & v_FANCD2I) | v_MRN)) & !(v_KU | v_RAD51))
+$v_NHEJ: (v_KU & v_DNAPK & v_DSB & !(v_ATM & v_ATR)) | (v_XPF & v_DNAPK & v_DSB & !((v_FANCJBRCA1 & v_ssDNARPA) | v_CHKREC))
+$v_PCNATLS: (v_FAcore & v_ADD & !(v_FAN1 | v_USP1)) | (v_ADD & !(v_FAN1 | v_USP1))
+$v_RAD51: v_ssDNARPA & v_FANCD1N & !v_CHKREC
+$v_USP1: (v_FANCD1N & v_FANCD2I & !v_FANCM) | (v_PCNATLS & !v_FANCM)
+$v_XPF: (v_p53 & v_MUS81 & !(v_FAcore & v_FAN1 & v_FANCD2I)) | (v_MUS81 & !v_FANCM)
+$v_p53: (v_ATM & v_CHK2 & !v_CHKREC) | (v_ATR & v_CHK1 & !v_CHKREC) | (v_DNAPK & !v_CHKREC)
+$v_ssDNARPA: v_DSB & ((v_FANCJBRCA1 & v_FANCD2I) | v_MRN) & !(v_KU | v_RAD51)
diff --git a/models/[id-006]__[var-62]__[in-6]__[HGF-SIGNALING-IN-KERATINOCYTES]/model.aeon b/models/[id-006]__[var-62]__[in-6]__[HGF-SIGNALING-IN-KERATINOCYTES]/model.aeon
@@ -101,65 +101,65 @@ v_HGF -> v_MET
 v_C3G -> v_Rap1
 v_MET -> v_PLC_g
 v_EGFR -> v_PLC_g
-$v_AP1: (v_cFOS & v_cJUN)
-$v_ATF2: (v_JNK & v_p38)
-$v_Akt: (v_PI3K & !v_PTEN)
+$v_AP1: v_cFOS & v_cJUN
+$v_ATF2: v_JNK & v_p38
+$v_Akt: v_PI3K & !v_PTEN
 $v_C3G: v_CRKL
 $v_CCL20: v_Erk
-$v_CDK2: (v_CyclinD & (!v_CDKN1A | !v_CDKN2A))
+$v_CDK2: v_CyclinD & (!v_CDKN1A | !v_CDKN2A)
 $v_CDKN1A: v_STAT3
-$v_CDKN2A: (v_Elk1 | v_ETS)
+$v_CDKN2A: v_Elk1 | v_ETS
 $v_CREB: v_RSK
 $v_CRKL: v_Grb2
-$v_CTGF: (v_Erk | v_p38)
+$v_CTGF: v_Erk | v_p38
 $v_Ca: v_IP3
-$v_Cdc42_Rac1: (v_Akt & (v_Ras & v_DOCK180))
-$v_CellMigration: (v_IL8 & ((v_CTGF & v_CCL20) & v_PTGS2))
-$v_CyclinD: (v_Elk1 | v_ATF2)
+$v_Cdc42_Rac1: v_Akt & v_Ras & v_DOCK180
+$v_CellMigration: v_IL8 & v_CTGF & v_CCL20 & v_PTGS2
+$v_CyclinD: v_Elk1 | v_ATF2
 $v_DAG: v_PLC_g
 $v_DOCK180: v_CRKL
 $v_ECM: v_MMP1_10
-$v_EGFR: (v_HBEGF | v_EGF)
+$v_EGFR: v_HBEGF | v_EGF
 $v_EGR1: v_Erk
 $v_ETS: v_Erk
-$v_Elk1: (v_JNK | v_Erk)
+$v_Elk1: v_JNK | v_Erk
 $v_Erk: v_Mek
-$v_Fak: ((v_Integrins & v_Rap1) & !v_PTEN)
+$v_Fak: v_Integrins & v_Rap1 & !v_PTEN
 $v_Grb2: v_Shc
-$v_HBEGF: (v_p38 | v_Erk)
-$v_IL8: (v_Erk | v_p38)
+$v_HBEGF: v_p38 | v_Erk
+$v_IL8: v_Erk | v_p38
 $v_IP3: v_PLC_g
 $v_Integrins: v_ECM
-$v_JNK: (v_PAK2 | (v_Mekk7 & v_Mkk4))
+$v_JNK: v_PAK2 | (v_Mekk7 & v_Mkk4)
 $v_MET: v_HGF
 $v_MLK3: v_Cdc42_Rac1
 $v_MMP1_10: v_Plasmin
-$v_Mek: (v_Mekk1 | v_Raf)
+$v_Mek: v_Mekk1 | v_Raf
 $v_Mekk1: v_Cdc42_Rac1
 $v_Mekk4: v_Cdc42_Rac1
 $v_Mekk7: v_Mekk1
 $v_Mkk3: v_MLK3
-$v_Mkk4: ((v_MLK3 | v_Mekk1) | v_Mekk4)
+$v_Mkk4: v_MLK3 | v_Mekk1 | v_Mekk4
 $v_Mkk6: v_MLK3
 $v_PAK1: v_Cdc42_Rac1
 $v_PAK2: v_Cdc42_Rac1
 $v_PAK3: v_Cdc42_Rac1
-$v_PI3K: (v_MET | (v_EGFR & v_Fak))
-$v_PKC: ((v_DAG & v_Ca) & !v_AKAP12)
-$v_PLC_g: (v_MET | v_EGFR)
-$v_PTGS2: (v_ATF2 | (v_cFOS & v_cJUN))
-$v_Plasmin: (v_uPA & v_PAI_1)
-$v_Proliferation: (v_CDK2 & v_CyclinD)
+$v_PI3K: v_MET | (v_EGFR & v_Fak)
+$v_PKC: v_DAG & v_Ca & !v_AKAP12
+$v_PLC_g: v_MET | v_EGFR
+$v_PTGS2: v_ATF2 | (v_cFOS & v_cJUN)
+$v_Plasmin: v_uPA & v_PAI_1
+$v_Proliferation: v_CDK2 & v_CyclinD
 $v_RSK: v_Erk
-$v_Raf: (v_Ras & (v_PAK3 & v_PKC))
+$v_Raf: v_Ras & v_PAK3 & v_PKC
 $v_Rap1: v_C3G
 $v_Ras: v_SOS
 $v_SOS: v_Grb2
 $v_STAT3: v_Erk
-$v_Shc: ((v_MET | v_Fak) | v_EGFR)
+$v_Shc: v_MET | v_Fak | v_EGFR
 $v_cFOS: v_Erk
-$v_cJUN: (v_JNK & v_p38)
+$v_cJUN: v_JNK & v_p38
 $v_cMYC: v_Erk
-$v_p38: (((v_Mkk3 & v_Mkk6) & !v_DUSP1) | v_PAK1)
+$v_p38: (v_Mkk3 & v_Mkk6 & !v_DUSP1) | v_PAK1
 $v_uPA: v_uPAR
 $v_uPAR: v_AP1
diff --git a/models/[id-007]__[var-5]__[in-0]__[CORTICAL-AREA-DEVELOPMENT]/model.aeon b/models/[id-007]__[var-5]__[in-0]__[CORTICAL-AREA-DEVELOPMENT]/model.aeon
@@ -12,8 +12,8 @@ v_Emx2 -| v_Pax6
 v_Sp8 -> v_Fgf8
 v_Emx2 -| v_Fgf8
 v_Fgf8 -> v_Fgf8
-$v_Coup_fti: (!(v_Fgf8 | v_Sp8) | !(v_Sp8 | v_Fgf8))
-$v_Emx2: (v_Coup_fti & !((v_Fgf8 | v_Sp8) | v_Pax6))
-$v_Fgf8: ((v_Fgf8 & v_Sp8) & !v_Emx2)
-$v_Pax6: (v_Sp8 & !(v_Emx2 | v_Coup_fti))
-$v_Sp8: (v_Fgf8 & !v_Emx2)
+$v_Coup_fti: !(v_Fgf8 | v_Sp8) | !(v_Sp8 | v_Fgf8)
+$v_Emx2: v_Coup_fti & !(v_Fgf8 | v_Sp8 | v_Pax6)
+$v_Fgf8: v_Fgf8 & v_Sp8 & !v_Emx2
+$v_Pax6: v_Sp8 & !(v_Emx2 | v_Coup_fti)
+$v_Sp8: v_Fgf8 & !v_Emx2
diff --git a/models/[id-008]__[var-25]__[in-3]__[DEATH-RECEPTOR-SIGNALING]/model.aeon b/models/[id-008]__[var-25]__[in-3]__[DEATH-RECEPTOR-SIGNALING]/model.aeon
@@ -44,27 +44,27 @@ v_MOMP -> v_Cyt_c
 v_FASL -> v_DISC_FAS
 v_FADD -> v_DISC_FAS
 $v_ATP: !v_MPT
-$v_BAX: (v_CASP8 & !v_BCL2)
+$v_BAX: v_CASP8 & !v_BCL2
 $v_BCL2: v_NFkB
-$v_CASP3: (v_apoptosome & !v_XIAP)
-$v_CASP8: (((v_CASP3 & !v_cFLIP) | (v_DISC_FAS & !v_cFLIP)) | (v_DISC_TNF & !v_cFLIP))
+$v_CASP3: v_apoptosome & !v_XIAP
+$v_CASP8: (v_CASP3 & !v_cFLIP) | (v_DISC_FAS & !v_cFLIP) | (v_DISC_TNF & !v_cFLIP)
 $v_Cyt_c: v_MOMP
-$v_DISC_FAS: (v_FASL & v_FADD)
-$v_DISC_TNF: (v_TNFR & v_FADD)
+$v_DISC_FAS: v_FASL & v_FADD
+$v_DISC_TNF: v_TNFR & v_FADD
 $v_IKK: v_RIP1ub
-$v_MOMP: (v_BAX | v_MPT)
-$v_MPT: (v_ROS & !v_BCL2)
-$v_NFkB: (v_IKK & !v_CASP3)
-$v_NonACD: (!v_ATP | !v_ATP)
-$v_RIP1: ((v_TNFR & !v_CASP8) | (v_DISC_FAS & !v_CASP8))
+$v_MOMP: v_BAX | v_MPT
+$v_MPT: v_ROS & !v_BCL2
+$v_NFkB: v_IKK & !v_CASP3
+$v_NonACD: !v_ATP | !v_ATP
+$v_RIP1: (v_TNFR & !v_CASP8) | (v_DISC_FAS & !v_CASP8)
 $v_RIP1k: v_RIP1
-$v_RIP1ub: (v_cIAP & v_RIP1)
-$v_ROS: ((v_RIP1k & !v_NFkB) | (v_MPT & !v_NFkB))
+$v_RIP1ub: v_cIAP & v_RIP1
+$v_ROS: (v_RIP1k & !v_NFkB) | (v_MPT & !v_NFkB)
 $v_SMAC: v_MOMP
 $v_TNFR: v_TNF
-$v_XIAP: (v_NFkB & !v_SMAC)
+$v_XIAP: v_NFkB & !v_SMAC
 $v_apoptosis: v_CASP3
-$v_apoptosome: ((v_Cyt_c & v_ATP) & !v_XIAP)
+$v_apoptosome: v_Cyt_c & v_ATP & !v_XIAP
 $v_cFLIP: v_NFkB
-$v_cIAP: ((v_NFkB & !v_SMAC) | (v_cIAP & !v_SMAC))
+$v_cIAP: (v_NFkB & !v_SMAC) | (v_cIAP & !v_SMAC)
 $v_survival: v_NFkB
diff --git a/models/[id-009]__[var-60]__[in-13]__[YEAST-APOPTOSIS]/model.aeon b/models/[id-009]__[var-60]__[in-13]__[YEAST-APOPTOSIS]/model.aeon
@@ -114,23 +114,23 @@ v_AdenylateCyclase -> v_CAMP
 v_H2O2 -> v_HOS3
 $v_AIF1_MT: v_HK
 $v_AIF1_NUC: v_AIF1_MT
-$v_AdenylateCyclase: (v_RAS2 | v_Stress)
-$v_Apoptosis: (((((((((((((v_YCA1 & (((((!v_POR1_2 | !v_H2O2) | !v_BIR1) | !v_SNO1) | !v_AceticAcid) | !v_FVY10)) & !(v_BIR1 & (v_SNO1 & v_FVY10))) | ((v_CPR3 & ((((!v_POR1_2 | !v_H2O2) | !v_BIR1) | !v_AceticAcid) | !v_FVY10)) & !v_SNO1)) | (v_BIR1 & ((((!v_POR1_2 & !v_H2O2) & !v_SNO1) & !v_AceticAcid) & !v_FVY10))) | (v_DNA_Frag & ((((((!v_POR1_2 | !v_H2O2) | !v_BIR1) | !v_SNO1) | !v_AceticAcid) | !v_FVY10) | ((((v_POR1_2 & v_H2O2) & v_BIR1) & v_AceticAcid) & v_FVY10)))) | (v_ROS_CYT & ((((((!v_POR1_2 | !v_H2O2) | !v_BIR1) | !v_SNO1) | !v_AceticAcid) | !v_FVY10) | (((v_POR1_2 & v_H2O2) & v_BIR1) & v_AceticAcid)))) | (v_SNO1 & (((((!v_POR1_2 | !v_H2O2) | !v_BIR1) | !v_AceticAcid) & !v_FVY10) | ((v_H2O2 & v_FVY10) & ((!v_POR1_2 & !v_ROS_CYT) & !v_DNA_Frag))))) | ((v_POR1_2 & (((!v_H2O2 | !v_BIR1) | !v_AceticAcid) | !v_FVY10)) & !v_SNO1)) | ((v_H2O2 & (((!v_POR1_2 | !v_BIR1) | !v_AceticAcid) | !v_FVY10)) & !v_SNO1)) | ((v_FVY10 & (((!v_POR1_2 | !v_H2O2) | !v_BIR1) | !v_AceticAcid)) & !v_SNO1)) | (v_CU2 & (v_CPR3 | ((((!v_POR1_2 | !v_H2O2) | !v_BIR1) | !v_AceticAcid) & (!v_SNO1 & !v_FVY10))))) | (v_AceticAcid & ((((((v_POR1_2 & v_H2O2) & v_BIR1) & (!v_SNO1 | !v_FVY10)) | ((((!v_POR1_2 | !v_H2O2) | !v_BIR1) | !v_FVY10) & !v_SNO1)) | (((v_BIR1 & v_SNO1) & v_FVY10) & (!v_POR1_2 & !v_H2O2))) | ((v_SNO1 & v_FVY10) & (((((!v_POR1_2 & !v_H2O2) & !v_BIR1) & !v_YCA1) & !v_ROS_CYT) & !v_DNA_Frag))))) | !((((((((((v_POR1_2 | v_H2O2) | v_BIR1) | v_CPR3) | v_SNO1) | v_AceticAcid) | v_FVY10) | v_CU2) | v_YCA1) | v_ROS_CYT) | v_DNA_Frag))
+$v_AdenylateCyclase: v_RAS2 | v_Stress
+$v_Apoptosis: (v_YCA1 & (!v_POR1_2 | !v_H2O2 | !v_BIR1 | !v_SNO1 | !v_AceticAcid | !v_FVY10) & !(v_BIR1 & v_SNO1 & v_FVY10)) | (v_CPR3 & (!v_POR1_2 | !v_H2O2 | !v_BIR1 | !v_AceticAcid | !v_FVY10) & !v_SNO1) | (v_BIR1 & !v_POR1_2 & !v_H2O2 & !v_SNO1 & !v_AceticAcid & !v_FVY10) | (v_DNA_Frag & (!v_POR1_2 | !v_H2O2 | !v_BIR1 | !v_SNO1 | !v_AceticAcid | !v_FVY10 | (v_POR1_2 & v_H2O2 & v_BIR1 & v_AceticAcid & v_FVY10))) | (v_ROS_CYT & (!v_POR1_2 | !v_H2O2 | !v_BIR1 | !v_SNO1 | !v_AceticAcid | !v_FVY10 | (v_POR1_2 & v_H2O2 & v_BIR1 & v_AceticAcid))) | (v_SNO1 & (((!v_POR1_2 | !v_H2O2 | !v_BIR1 | !v_AceticAcid) & !v_FVY10) | (v_H2O2 & v_FVY10 & !v_POR1_2 & !v_ROS_CYT & !v_DNA_Frag))) | (v_POR1_2 & (!v_H2O2 | !v_BIR1 | !v_AceticAcid | !v_FVY10) & !v_SNO1) | (v_H2O2 & (!v_POR1_2 | !v_BIR1 | !v_AceticAcid | !v_FVY10) & !v_SNO1) | (v_FVY10 & (!v_POR1_2 | !v_H2O2 | !v_BIR1 | !v_AceticAcid) & !v_SNO1) | (v_CU2 & (v_CPR3 | ((!v_POR1_2 | !v_H2O2 | !v_BIR1 | !v_AceticAcid) & !v_SNO1 & !v_FVY10))) | (v_AceticAcid & ((v_POR1_2 & v_H2O2 & v_BIR1 & (!v_SNO1 | !v_FVY10)) | ((!v_POR1_2 | !v_H2O2 | !v_BIR1 | !v_FVY10) & !v_SNO1) | (v_BIR1 & v_SNO1 & v_FVY10 & !v_POR1_2 & !v_H2O2) | (v_SNO1 & v_FVY10 & !v_POR1_2 & !v_H2O2 & !v_BIR1 & !v_YCA1 & !v_ROS_CYT & !v_DNA_Frag))) | !(v_POR1_2 | v_H2O2 | v_BIR1 | v_CPR3 | v_SNO1 | v_AceticAcid | v_FVY10 | v_CU2 | v_YCA1 | v_ROS_CYT | v_DNA_Frag)
 $v_BIR1: !v_NMA111_NUC
-$v_CAMP: (v_AdenylateCyclase | v_TOR1)
+$v_CAMP: v_AdenylateCyclase | v_TOR1
 $v_CDC48: v_HK
 $v_CDC6: v_Adozelesin
-$v_CytC_CYT: (v_CDC48 | v_CytC_MT)
-$v_CytC_MT: (v_MCD1_MT | v_AceticAcid)
-$v_DNA_Frag: (v_Tat_D | !(v_STM1_NUC | v_Tat_D))
+$v_CytC_CYT: v_CDC48 | v_CytC_MT
+$v_CytC_MT: v_MCD1_MT | v_AceticAcid
+$v_DNA_Frag: v_Tat_D | !(v_STM1_NUC | v_Tat_D)
 $v_DRE2_TAH18: v_HK
 $v_DesCyclinCCDK8: !v_SLT2
 $v_EMC4: v_HK
 $v_ESP1: v_H2O2
 $v_FIS1: v_HK
 $v_FVY10: v_HK
-$v_H2B: ((((v_STE20_NUC | v_NUC1_NUC) | v_RPD3) | v_HOS3) | v_AIF1_NUC)
-$v_HOG1: ((((v_PTP3 & !v_PTP2) | v_Stress) | (v_PTP2 & !v_PTP3)) | !((v_PTP2 | v_Stress) | v_PTP3))
+$v_H2B: v_STE20_NUC | v_NUC1_NUC | v_RPD3 | v_HOS3 | v_AIF1_NUC
+$v_HOG1: (v_PTP3 & !v_PTP2) | v_Stress | (v_PTP2 & !v_PTP3) | !(v_PTP2 | v_Stress | v_PTP3)
 $v_HOG1_Dep: v_HOG1
 $v_HOS3: v_H2O2
 $v_KAP123: v_NUC1_MT
@@ -141,34 +141,34 @@ $v_MDV1: v_HK
 $v_MEC1: v_AbnormalTelomer
 $v_MMI1: v_HK
 $v_MSN2_4: v_PKA
-$v_MT_ALT: (((v_PKA | v_RAS2) | v_MT_Frag) | v_MMI1)
-$v_MT_Frag: (((v_H2O2 & !v_DRE2_TAH18) | (v_MDV1 & !v_FIS1)) | v_MT_ALT)
+$v_MT_ALT: v_PKA | v_RAS2 | v_MT_Frag | v_MMI1
+$v_MT_Frag: (v_H2O2 & !v_DRE2_TAH18) | (v_MDV1 & !v_FIS1) | v_MT_ALT
 $v_NDI1: v_HK
 $v_NMA111_CYT: v_Heat
 $v_NMA111_NUC: v_NMA111_CYT
 $v_NUC1_MT: v_H2O2
 $v_NUC1_NUC: v_KAP123
-$v_PKA: (v_Heat | v_RAS2)
+$v_PKA: v_Heat | v_RAS2
 $v_POR1_2: v_HK
 $v_PTP2: v_RLM1
 $v_PTP3: v_HOG1_Dep
 $v_Protosom: v_CDC6
-$v_RAS2: (v_RedActinDyn | v_TOR1)
-$v_RLM1: (v_SLT2 | v_HOG1)
-$v_ROS_CYT: ((((((((((v_DesCyclinCCDK8 | (v_AceticAcid & !v_SVF1)) | (v_H2O2 & !v_SVF1)) | (v_H2O2 & !v_EMC4)) | v_CDC48) | v_ESP1) | v_RedActinDyn) | v_SOD1) | v_Salt) | v_RAS2) | v_NDI1)
-$v_ROS_MT: (v_NDI1 & !v_SOD2)
+$v_RAS2: v_RedActinDyn | v_TOR1
+$v_RLM1: v_SLT2 | v_HOG1
+$v_ROS_CYT: v_DesCyclinCCDK8 | (v_AceticAcid & !v_SVF1) | (v_H2O2 & !v_SVF1) | (v_H2O2 & !v_EMC4) | v_CDC48 | v_ESP1 | v_RedActinDyn | v_SOD1 | v_Salt | v_RAS2 | v_NDI1
+$v_ROS_MT: v_NDI1 & !v_SOD2
 $v_RPD3: v_Stress
 $v_SDP1: v_MSN2_4
-$v_SLT2: ((((((v_Stress & (!v_SDP1 | !v_PTP2)) | (v_PTP2 & (!v_SDP1 | !v_Stress))) | v_RLM1) | (v_SDP1 & (!v_PTP2 | !v_Stress))) | v_Heat) | !((((v_SDP1 | v_PTP2) | v_RLM1) | v_Stress) | v_Heat))
+$v_SLT2: (v_Stress & (!v_SDP1 | !v_PTP2)) | (v_PTP2 & (!v_SDP1 | !v_Stress)) | v_RLM1 | (v_SDP1 & (!v_PTP2 | !v_Stress)) | v_Heat | !(v_SDP1 | v_PTP2 | v_RLM1 | v_Stress | v_Heat)
 $v_SNO1: v_HK
 $v_SOD1: v_Heat
 $v_SOD2: v_HK
 $v_SRO7: v_HK
 $v_STE20_CYT: v_MAPK
 $v_STE20_NUC: v_STE20_CYT
 $v_STM1_CYT: v_HK
-$v_STM1_NUC: (v_STM1_CYT & !v_Protosom)
+$v_STM1_NUC: v_STM1_CYT & !v_Protosom
 $v_SVF1: v_HK
 $v_TOR1: v_Stress
 $v_Tat_D: v_MG2
-$v_YCA1: (((((v_ROS_CYT | v_MT_Frag) | v_RedActinDyn) | (v_Salt & !v_SRO7)) | v_CytC_CYT) | v_MEC1)
+$v_YCA1: v_ROS_CYT | v_MT_Frag | v_RedActinDyn | (v_Salt & !v_SRO7) | v_CytC_CYT | v_MEC1
diff --git a/models/[id-010]__[var-13]__[in-2]__[CARDIAC-DEVELOPMENT]/model.aeon b/models/[id-010]__[var-13]__[in-2]__[CARDIAC-DEVELOPMENT]/model.aeon
@@ -35,16 +35,16 @@ v_Nkx2_5 -> v_GATAs
 v_Tbx5 -> v_GATAs
 v_Mesp1 -> v_GATAs
 v_Foxc1_2 -> v_Tbx1
-$v_Bmp2: (v_exogen_BMP2_II & !v_canWnt)
-$v_Dkk1: (v_Mesp1 | (v_canWnt & !v_exogen_BMP2_II))
-$v_Fgf8: ((v_Tbx1 & !v_Mesp1) | (v_Foxc1_2 & !v_Mesp1))
-$v_Foxc1_2: (v_canWnt & v_exogen_canWnt_II)
-$v_GATAs: ((v_Nkx2_5 | v_Tbx5) | v_Mesp1)
-$v_Isl1: (((v_Mesp1 | v_Tbx1) | v_Fgf8) | (v_canWnt & v_exogen_canWnt_II))
-$v_Mesp1: (v_canWnt & !v_exogen_BMP2_II)
-$v_Nkx2_5: ((((v_Tbx5 | v_Tbx1) | (v_Mesp1 & v_Dkk1)) | (v_Bmp2 & v_GATAs)) | (v_Isl1 & v_GATAs))
+$v_Bmp2: v_exogen_BMP2_II & !v_canWnt
+$v_Dkk1: v_Mesp1 | (v_canWnt & !v_exogen_BMP2_II)
+$v_Fgf8: (v_Tbx1 & !v_Mesp1) | (v_Foxc1_2 & !v_Mesp1)
+$v_Foxc1_2: v_canWnt & v_exogen_canWnt_II
+$v_GATAs: v_Nkx2_5 | v_Tbx5 | v_Mesp1
+$v_Isl1: v_Mesp1 | v_Tbx1 | v_Fgf8 | (v_canWnt & v_exogen_canWnt_II)
+$v_Mesp1: v_canWnt & !v_exogen_BMP2_II
+$v_Nkx2_5: v_Tbx5 | v_Tbx1 | (v_Mesp1 & v_Dkk1) | (v_Bmp2 & v_GATAs) | (v_Isl1 & v_GATAs)
 $v_Tbx1: v_Foxc1_2
-$v_Tbx5: (((v_Tbx5 & !((v_canWnt | (v_Dkk1 & (!v_Tbx5 & !v_Mesp1))) | v_Tbx1)) | (v_Nkx2_5 & !((v_canWnt | (v_Dkk1 & (!v_Tbx5 & !v_Mesp1))) | v_Tbx1))) | (v_Mesp1 & !((v_canWnt | (v_Dkk1 & (!v_Tbx5 & !v_Mesp1))) | v_Tbx1)))
+$v_Tbx5: (v_Tbx5 & !(v_canWnt | (v_Dkk1 & !v_Tbx5 & !v_Mesp1) | v_Tbx1)) | (v_Nkx2_5 & !(v_canWnt | (v_Dkk1 & !v_Tbx5 & !v_Mesp1) | v_Tbx1)) | (v_Mesp1 & !(v_canWnt | (v_Dkk1 & !v_Tbx5 & !v_Mesp1) | v_Tbx1))
 $v_canWnt: v_exogen_canWnt_II
 $v_exogen_BMP2_II: v_exogen_BMP2_I
 $v_exogen_canWnt_II: v_exogen_CanWnt_I