From f55ed02efdec00c28959e55f4373e6b1bda939ae Mon Sep 17 00:00:00 2001 From: Sergio Marchetti Date: Sat, 30 May 2026 12:58:39 +0200 Subject: [PATCH] Update elements/neuron/presynapse.md --- elements/neuron/presynapse.md | 210 ++++++++++++++++++---------------- 1 file changed, 112 insertions(+), 98 deletions(-) diff --git a/elements/neuron/presynapse.md b/elements/neuron/presynapse.md index 1c4d528..bc3ad7a 100644 --- a/elements/neuron/presynapse.md +++ b/elements/neuron/presynapse.md @@ -13,7 +13,6 @@ Qui comprendiamo: ```Gen PRESYNAPSE - type: comprehension expansion: @@ -24,21 +23,23 @@ PRESYNAPSE intrication: # Scope - !DAY: INTRICATION [ ref: &ORGANISM.!DAY] - !NIGHT: INTRICATION [ ref: &ORGANISM.!NIGHT] + !DAY: INTRICATION [ ref: &ORGANISM.!DAY ] + !NIGHT: INTRICATION [ ref: &ORGANISM.!NIGHT ] # Context - *AP: INTRICATION [ ref: &SOMA.*AP] - *TunePossible: INTRICATION [ref: &...] # To be defined... + *AP: INTRICATION [ ref: &SOMA.*AP ] + *TunePossible: INTRICATION [ ref: &... ] # To be defined... # Tub - _NT: INTRICATION [ ref: &ASTROSYNAPSE._NT] - _ATP: INTRICATION [ ref: &ASTROCYTE._ATP] - _eCB: INTRICATION [ ref: &POSTSYNAPSE._eCB] + _NT: INTRICATION [ ref: &ASTROSYNAPSE._NT ] + _ATP: INTRICATION [ ref: &ASTROCYTE._ATP ] + _eCB: INTRICATION [ ref: &POSTSYNAPSE._eCB ] instantiation: # Context + *TryTunUpPreVcgg: CONTEXT [] + *TryTunDownPreVcgg: CONTEXT [] # Tub _Ca2: TUB [ full: 60x, active: 30x, empty: 0x ] @@ -68,24 +69,24 @@ MAIN_PRE snippet: # *AP - @: ACCUMULATOR [snippet: NTreleaseLow, RF: active 12x] - @: ACCUMULATOR [snippet: NTreleaseMedium, RF: active 9x] - @: ACCUMULATOR [snippet: NTreleaseHigh, RF: active 6x] + @: ACCUMULATOR [ snippet: NTreleaseLow, rf: active 12x ] + @: ACCUMULATOR [ snippet: NTreleaseMedium, rf: active 9x ] + @: ACCUMULATOR [ snippet: NTreleaseHigh, rf: active 6x ] - @: ACCUMULATOR [snippet: TracesAccLow, RF: active 3x] - @: ACCUMULATOR [snippet: TracesAccMedium, RF: active 6x] - @: ACCUMULATOR [snippet: TracesAccHigh, RF: active 10x] + @: ACCUMULATOR [ snippet: TracesAccLow, rf: active 3x ] + @: ACCUMULATOR [ snippet: TracesAccMedium, rf: active 6x ] + @: ACCUMULATOR [ snippet: TracesAccHigh, rf: active 10x ] # NOT *AP - @: ACCUMULATOR [snippet: eCBClearenceMedium, RF: active 24x] - @: ACCUMULATOR [snippet: eCBClearenceLow, RF: active 48x] + @: ACCUMULATOR [ snippet: eCBClearenceMedium, rf: active 24x ] + @: ACCUMULATOR [ snippet: eCBClearenceLow, rf: active 48x ] - @: ACCUMULATOR [snippet: RPShuttleLow, RF: active 24x] - @: ACCUMULATOR [snippet: RPShuttleMedium, RF: active 48x] + @: ACCUMULATOR [ snippet: RPShuttleLow, rf: active 24x ] + @: ACCUMULATOR [ snippet: RPShuttleMedium, rf: active 48x ] - @: ACCUMULATOR [snippet: RefillGlutamine, RF: active 24x] + @: ACCUMULATOR [ snippet: RefillGlutamine, rf: active 24x ] - @: ACCUMULATOR [snippet: TracesClearance, RF: active 30x] + @: ACCUMULATOR [ snippet: TracesClearance, rf: active 30x ] ``` **Tubs:** @@ -119,11 +120,12 @@ In tutti i casi di NT ```Gen NTreleaseLow + type: accumulator - in_context: *AP + in_context: *AP - hypothesis: _Ca2 mediumness AND _Rrp mediumness AND NOT _ATP empty - action: [_Rrp decrease, _NT increase, _ATP decrease] + hypothesis: _Ca2 mediumness AND _Rrp mediumness AND NOT _ATP empty + action: [ _Rrp decrease, _NT increase, _ATP decrease ] trace: None ``` @@ -131,13 +133,14 @@ NTreleaseLow ```Gen NTreleaseMedium + type: accumulator - in_context: *AP + in_context: *AP hypothesis: ( _Ca2 fullness AND _Rrp mediumness ) OR ( _Ca2 mediumness AND _Rrp fullness ) AND NOT _ATP empty - action: [_Rrp decrease, _NT increase, _ATP decrease] + action: [ _Rrp decrease, _NT increase, _ATP decrease ] trace: None ``` @@ -145,12 +148,13 @@ NTreleaseMedium ```Gen NTreleaseHigh + type: accumulator - in_context: *AP + in_context: *AP - hypothesis: ( _Ca2 fullness AND _Rrp fullness ) AND - NOT _ATP empty - action: [_Rrp decrease, NT increase, _ATP decrease] + hypothesis: _Ca2 fullness AND _Rrp fullness AND + NOT _ATP empty + action: [ _Rrp decrease, NT increase, _ATP decrease ] trace: None ``` @@ -168,8 +172,9 @@ Serve a: ```Gen Ca2TracesAccuLow + type: accumulator - in_context: *AP + in_context: *AP hypothesis: _Ca2 emptiness action: [ _CaTraceLow increase ] @@ -180,8 +185,9 @@ Ca2TracesAccuLow ```Gen Ca2TracesAccMedium + type: accumulator - in_context: *AP + in_context: *AP hypothesis: _Ca2 mediumness action: [ _CaTraceMed increase ] @@ -192,8 +198,9 @@ Ca2TracesAccMedium ```Gen Ca2TracesAccumulationHigh + type: accumulator - in_context: *AP + in_context: *AP hypothesis: _Ca2 fullness action: [ _CaTraceHigh increase ] @@ -210,8 +217,9 @@ Qui non facciamo un flush di eCB, riduciamo ogni mezzo secondo (context) di un R ```Gen eCBClearance: ( active: 24x ) # Slow + type: accumulator - in_context: NOT *AP + in_context: NOT *AP hypothesis: NOT _eCB empty action: [ _eCB decrease ] @@ -228,13 +236,14 @@ Rate: 0.00 – 0.25 ```Gen RPShuttleLow + type: accumulator - in_context: NOT *AP + in_context: NOT *AP hypothesis: _CaTraceLow fullness OR _RP emptiness OR _Rrp fullness - action: [RP decrease, _Rrp increase] + action: [ _RP decrease, _Rrp increase ] trace: None ``` @@ -246,14 +255,15 @@ Rate: 0.50 – 0.97 ```Gen RPShuttleMedium + type: accumulator - in_context: *AP + in_context: *AP hypothesis: ( _CaTraceMedium fullness AND _RP mediumness AND _Rrp mediumness ) OR ( _CaTraceHigh fullness AND _RP mediumness AND _Rrp mediumness ) OR # signal boost ( _CaTraceMedium fullness AND _RP fullness AND _Rrp mediumness ) OR # supply boost ( _CaTraceMedium fullness AND _RP mediumness AND _Rrp emptiness ) # vacancy boost - action: [RP decrease, _Rrp increase] + action: [ _RP decrease, _Rrp increase ] trace: None ``` @@ -265,13 +275,14 @@ Rate: 1.25 – 1.94 ```Gen RPShuttleHigh + type: accumulator - in_context: *AP + in_context: *AP hypothesis: ( _CaTraceHigh fullness AND _RP fullness AND _Rrp mediumness ) OR # signal + supply ( _CaTraceHigh fullness AND _RP mediumness AND _Rrp emptiness ) OR # signal + vacancy ( _CaTraceMedium fullness AND _RP fullness AND _Rrp emptiness ) # supply + vacancy - action: [ _RP decrease, _Rrp increase] + action: [ _RP decrease, _Rrp increase ] trace: None ``` @@ -311,8 +322,9 @@ Qui facciamo un flush di CaTraceX. Deve essere fatto a valle del tuning. ```Gen Ca2TracesClearance + type: accumulator - in_context: NOT *TunePossible + in_context: NOT *TunePossible hypothesis: NOT _CaTraceHigh empty action: [ _CaTRaceHigh decrease ] @@ -333,32 +345,21 @@ Ca2TracesClearance TUNE_VGCC_PRE type: behaviour - # qui stiamo aggiungendo o eliminando VGCC_PRE. Fra un massimo full e minimo empty (empty puo' non essere 0) # contained_by: PRESYNAPSE non e' contenuto, si attacca. activity_scope: !DAY - context_intricated: - - *TunePossible ( contained_by: DAY-N ) - - tub_passed: - _VgccPre: TUB [pass.@VGCC_PRE] - - tub_local: - - tub_intricated: - snippet: # *TunePossible - CheckVgccPreTun: CONTEXTOR [RF: active 60x] + @: CONTEXTOR [ snippet: CheckVgccPreTun, rf: active 60x ] - *TryTunUpPreVcgg - PossibleUpPreVgccTun: ACCUMULATOR [RF:active 10x] + # *TryTunUpPreVcgg + @: ACCUMULATOR [ snippet: PossibleUpPreVgccTun, rf:active 10x ] - *TryTunDownPreVcgg - PossibleDownPreVgccTun: ACCUMULATOR [RF:active 10x] + # *TryTunDownPreVcgg + @: ACCUMULATOR [ snippet: PossibleDownPreVgccTun, rf:active 10x ] ``` #### *TunePossible @@ -369,13 +370,14 @@ Qui controlliamo che ci siano le condizioni per aumentare o diminuire la quantit ```Gen CheckVgccPreTun + type contextor + + in_context: *TunePossible - in_context: *TunePossible - - condition: ( CaTraceHigh fullness ) + condition: _CaTraceHigh fullness out_context: *TryTunUpPreVcgg - condition: ( CaTraceLow fullness ) + condition: _CaTraceLow fullness out_context: *TryTunDownPreVcgg ``` @@ -383,8 +385,9 @@ CheckVgccPreTun ```Gen PossibleUpPreVgccTun + type: accumulator - in_context: TryTunUpPreVcgg_ctx + in_context: *TryTunUpPreVcgg hypothesis: action: @@ -395,8 +398,9 @@ PossibleUpPreVgccTun ```Gen PossibleDownPreVgccTun + type: accumulator - in_context: TryTunDownPreVcgg_ctx + in_context: *TryTunDownPreVcgg hypothesis: action: @@ -409,10 +413,21 @@ Voltage-Controlled Gated Channels: Qui per ora non gestiamo l'evoluzione della d ```Gen VGCC-PRE - type: comprehension + type: comprehension -instantiate_behaviour: - BEHAVIOR_VGCC_PRE: behaviour [] + # Scope + !DAY: INTRICATION [ ref: &ORGANISM.!DAY ] + !NIGHT: INTRICATION [ ref: &ORGANISM.!NIGHT ] + + # Context + *AP: INTRICATION [ ref: &SOMA.*AP ] + + # Tub + _NT: INTRICATION [ ref: &ASTROSYNAPSE._NT ] + _Ca2: INTRICATION [ ref: &PRESYNAPSE._Ca2 ] + + # Behaviour + @: BEHAVIOUR [ behaviour: VGCC_PRE_BEH ] ``` ### BEHAVIOR_VGCC_PRE @@ -420,26 +435,20 @@ instantiate_behaviour: Voltage-Controlled Gated Channels: Qui per ora non gestiamo l'evoluzione della depolarizzazione. Alla scomparsa dell'AP, i VGCC smettono di funzionare. ```Gen -BEHAVIOR_VGCC_PRE - - activity_scope: !DAY +VGCC_PRE_BEH type: behaviour - tub_intricated: - - _Ca2 ( contained_by: PRESYNAPSE-BHE ) - - NT ( contained_by: SYN ) - - context_intricated: - - AP ( contained_by: SOMA ) - + within_scope: !DAY + snippets: + # *AP + @: ACCUMULATOR [ snippet: Ca2enterLow, rf: active 12x ] + @: ACCUMULATOR [ snippet: Ca2enterMedium, rf: active 6x ] + @: ACCUMULATOR [ snippet: Ca2enterHigh, rf: active 3x ] - Ca2enterLow: ACCUMULATOR [RF: active 12x] - Ca2enterMedium: ACCUMULATOR [RF: active 6x] - Ca2enterHigh: ACCUMULATOR [RF: active 3x] - - Ca2ClearanceLow: ACCUMULATOR [RF: active 24x] - Ca2ClearanceHigh: ACCUMULATOR [RF: active 4x] + # NOT *AP + @: ACCUMULATOR [ snippet: Ca2ClearanceLow, rf: active 24x ] + @: ACCUMULATOR [ snippet: Ca2ClearanceHigh, rf: active 4x ] ``` @@ -469,11 +478,12 @@ Devo controllare che le condizioni sotto siano esaustive. Qui ho confuso high co ```Gen Ca2enterLow + type: accumulator - in_context: *AP + in_context: *AP - hypothesis: (_Ca2 empty) AND (eCB empty) - action: [_Ca2 increase, _ATP decrease] + hypothesis: _Ca2 empty AND _eCB empty + action: [ _Ca2 increase, _ATP decrease ] trace: None ``` @@ -481,13 +491,14 @@ Ca2enterLow ```Gen Ca2enterMedium + type: accumulator - in_context: *AP + in_context: *AP - hypothesis: (_Ca2 mediumness) OR - ((eCB mediumness) AND (_Ca2 empty)) OR - ((eCB full) AND (_Ca2 empty) AND (NT empty)) - action: [_Ca2 increase, _ATP decrease] + hypothesis: _Ca2 mediumness OR + ( _eCB mediumness AND _Ca2 empty ) OR + ( _eCB full AND _Ca2 empty AND _NT empty ) + action: [ _Ca2 increase, _ATP decrease ] trace: None ``` @@ -495,12 +506,13 @@ Ca2enterMedium ```Gen Ca2enterHigh + type: accumulator - in_context: *AP + in_context: *AP - hypothesis: (_Ca2 mediumness) AND (eCB full) OR - (eCB mediumness) - action: [_Ca2 increase, _ATP decrease] + hypothesis: ( _Ca2 mediumness AND _eCB full ) OR + _eCB mediumness + action: [ _Ca2 increase, _ATP decrease ] trace: None ``` @@ -524,11 +536,12 @@ Qui disinguiamo: ```Gen Ca2ClearanceLow + type: accumulator - in_context: NOT *AP + in_context: NOT *AP - hypothesis: (NOT _Ca2 fullness) AND (NOT _Ca2 empty) - action: [_Ca2 decrease] + hypothesis: NOT _Ca2 fullness AND NOT _Ca2 empty + action: [ _Ca2 decrease ] trace: None ``` @@ -536,10 +549,11 @@ Ca2ClearanceLow ```Gen Ca2ClearanceHigh + type: accumulator - in_context: NOT *AP + in_context: NOT *AP - hypothesis: NOT (Ca2 empty) + hypothesis: NOT _Ca2 empty action: [Ca2 decrease] trace: None ```