messo a posto i titoli e iniziato il tun vgcc

neuron/presynapse.md

@@ -133,10 +133,7 @@ container: PRESYNAPSE
 
 ### AP_ctx: PRESYNAPSE
 
-#### ms: AP_ctx: PRESYNAPSE
+#### NTreleaseLow: int: ms
-
-
-##### NTreleaseLow: interacting
 
 Il rilascio di NT lo facciamo nel contesto di AP. Biologicamente dovrebbe avvenire solo in base alle concentrazioni, quindi anche al difuori degli AP.
 
@@ -168,7 +165,7 @@ interacting: NTreleaseLow
     trace: None
 ```
 
-##### NTreleaseMedium: interacting
+#### NTreleaseMedium: int: ms
 
 In tutti i casi di NT
 
@@ -186,7 +183,7 @@ interacting: NTreleaseMedium
     trace: None
 ```
 
-##### NTreleaseHigh: interacting
+#### NTreleaseHigh: int: ms
 
 ```Gen
 interacting: NTreleaseHigh
@@ -201,14 +198,17 @@ interacting: NTreleaseHigh
     trace: None
 ```
 
-##### Ca2+TracesAccumulationLow: interacting
+#### Ca2+TracesAccumulationLow: int: ms
 
-Serve a dare la velocita' al trasporto di vesicles da RP a RRP.
+Serve a: 
- - The biological meaning is that a synapse that has just been through a burst is primed for fast recovery — the molecular machinery for vesicle docking is already engaged, calcium-dependent priming factors are still elevated, and the system is in a ready state. A synapse that has been silent for several seconds has cooled down and replenishes slowly.
+- fare il tuning dei VGCC
-
+- dare la velocita' al trasporto di vesicles da RP a RRP, anche se non avendo ancora compreso ATP, la velocita' non cambia molto la sostanza. 
- - So after one second of silence CaTrace has fallen to ~37% of its peak value, after two seconds to ~14%, after three seconds to ~5%. It asymptotes toward zero but never exactly reaches it. Between spikes, Ca2+ falls toward zero as the pumps clear it. The result is that CaTrace encodes not the instantaneous calcium level but the recent history of calcium activity — a smoothed, time-averaged measure of how active the synapse has been over the past one to two seconds.
+- le tracce vengono eliminate quando il neurone e' in pausa, lontano da uno spike train, TunPossible_ctx
- - Abbiamo 3 tracce, high, medium and low. Andiamo a verificare se una di queste e' high per fare la modulazione
+- Abbiamo 3 tracce, high, medium and low. Andiamo a verificare una combinazione di queste per fare la modulazione
 - RF e' a 10, questo dovrebbe essere un RF di campionamento durante AP_ctx context che dovremmo assicurarci sia tipo 100. Il che implicherebbe 10 campionamenti.
+- The biological meaning is that a synapse that has just been through a burst is primed for fast recovery — the molecular machinery for vesicle docking is already engaged, calcium-dependent priming factors are still elevated, and the system is in a ready state. A synapse that has been silent for several seconds has cooled down and replenishes slowly.
+- So after one second of silence CaTrace has fallen to ~37% of its peak value, after two seconds to ~14%, after three seconds to ~5%. It asymptotes toward zero but never exactly reaches it. Between spikes, Ca2+ falls toward zero as the pumps clear it. The result is that CaTrace encodes not the instantaneous calcium level but the recent history of calcium activity — a smoothed, time-averaged measure of how active the synapse has been over the past one to two seconds.
+
 ---
 
 ```Gen
@@ -223,7 +223,7 @@ interacting: Ca2+TracesAccumulationLow
     trace: None
 ```
 
-##### Ca2+TracesAccumulationMedium: interacting
+#### Ca2+TracesAccumulationMedium: int: ms
 
 ```Gen
 interacting: Ca2+TracesAccumulationMedium
@@ -237,7 +237,7 @@ interacting: Ca2+TracesAccumulationMedium
     trace: None
 ```
 
-##### Ca2+TracesAccumulationHigh: interacting
+#### Ca2+TracesAccumulationHigh: int: ms
 
 
 ```Gen
@@ -254,11 +254,7 @@ interacting: Ca2+TracesAccumulationHigh
 
 ### NOT AP_ctx: PRESYNAPSE
 
-#### ms: NOT AP_ctx: PRESYNAPSE
+#### eCB clearance: int: ms
-
-#### sec: NOT AP_ctx: PRESYNAPSE
-
-##### eCB clearance: interacting
 
 eCB dipende da POST. Tende a modulare l'entrata di Ca2+ degli VGCC.
 
@@ -276,33 +272,7 @@ interacting: eCBClearance
     trace: None
 ```
 
-##### Ca2+TracesClearance: interacting
+#### RPShuttleLow: int: sec
-
-Qui non facciamo un flush di CaTraceX, riduciamo ogni mezzo secondo (context) di un RF di questo episodio.
-
-```Gen
-interacting: Ca2+TracesClearance
-  contained_by: PRESYNAPSE
-
-  in_context: NOT AP_ctx
-  rf: ( active: 30x ) # Slow
-
-  hypothesis: NOT (CaTraceHigh empty)
-    action: [CaTRaceHigh decrease]
-    trace: None
-
-  hypothesis: NOT (CaTraceMedium empty)
-    action: [CaTRaceMedium decrease]
-    trace: None
-
-  hypothesis: NOT (CaTraceLow empty)
-    action: [CaTRaceLow decrease]  hypothesis: NOT (CaTraceHigh empty)
-    action: [CaTRaceHigh decrease]
-    trace: None
-    trace: None
-```
-
-##### RPShuttleLow: interacting
 
 This happens in the seconds loop, once per second.
 
@@ -324,7 +294,7 @@ interacting: RPShuttleLow
     trace: None
 ```
 
-##### RPShuttleMedium: interacting
+#### RPShuttleMedium: int: sec
 
 The "Sub-Optimal" State. The machinery is working, but it's held back by partial limitations. This covers cases where the signal is steady but the "piston" isn't firing at full speed, or where a high vacancy in the RRP (emptiness) forces a low signal to work a bit harder.
 
@@ -345,7 +315,7 @@ interacting: RPShuttleMedium
     trace: None
 ```
 
-##### RPShuttleHigh: interacting
+#### RPShuttleHigh: int: sec
 
 The "High Performance" State. Multiple systems are optimized, but one is still at a "mediumness" level. This represents an active synapse that hasn't reached its absolute peak because either the supply is only 50% or the RRP isn't empty enough to create that "maximal vacuum" pull.
 
@@ -365,9 +335,7 @@ interacting: RPShuttleHigh
     trace: None
 ```
 
-#### min: NOT AP_ctx: PRESYNAPSE
+#### RefillRPGlutamine: int: min
-
-##### RefillRPGlutamine
 
 This happens in the minutes loop, once per minute, via the glutamine shuttle from the astrocyte. It is a two-step process across two cells.
 
@@ -397,14 +365,40 @@ Gln  — depletes over bursts,  refilled by glucose   (slowest, astrocyte-depend
 
 Each tier buys time for the one below it to respond. When all three are depleted simultaneously — which only happens under prolonged high-frequency firing with insufficient glucose — the synapse has no remaining buffer and goes silent until the minutes loop restores the Glutamine_pool.
 
-### VGCC-PRE-TUN: Tuner
+### TunPossible_ctx: PRESYNAPSE
+
+#### Ca2+TracesClearance: int: sec
+
+Qui facciamo un flush di CaTraceX.
+
+```Gen
+interacting: Ca2+TracesClearance
+  contained_by: PRESYNAPSE
+
+  in_context: NOT AP_ctx
+  rf: ( active: 30x ) # Slow
+
+  hypothesis: NOT (CaTraceHigh empty)
+    action: [CaTRaceHigh decrease]
+    trace: None
+
+  hypothesis: NOT (CaTraceMedium empty)
+    action: [CaTRaceMedium decrease]
+    trace: None
+
+  hypothesis: NOT (CaTraceLow empty)
+    action: [CaTRaceLow decrease]
+    trace: None
+```
+
+## VGCC-PRE-TUN: Tuner
 
 ```Gen
 tuner: VGCC-PRE-TUN
 
   # qui stiamo aggiungendo o eliminando VGCC-PRE. Fra un massimo full e minimo empty (empty puo' non essere 0)
 
-  contained_by: PRESYNAPSE
+  # contained_by: PRESYNAPSE non e' contenuto, si attacca.
 
   tunes: PRESYNAPSE/expansion/VCGG-PRE
 
@@ -419,7 +413,11 @@ tuner: VGCC-PRE-TUN
   tub_intricated:
 ```
 
-#### CheckVgccPreTun:contexting
+### TunPossible_ctx: VGCC-PRE-TUN
+
+#### CheckVgccPreTun: contexting: sec
+
+Qui controlliamo che ci siano le condizioni per aumentare o diminuire la quantita' di VGCC
 
 ```Gen
 contexting: CheckVgccPreTun
@@ -428,17 +426,34 @@ contexting: CheckVgccPreTun
   in_context: TunPossible_ctx
   rf: ( active: 60x )
 
-  condition:  
+  condition:  ( CaTraceHigh fullness )
-    out_context: TryTunPreVcgg_ctx
+    out_context: TryTunUpPreVcgg_ctx
+
+  condition:  ( CaTraceLow fullness )
+    out_context: TryTunDownPreVcgg_ctx
 ```
 
-#### PossibleVgccPreTun: interacting
+#### PossibleUpPreVgccTun: int: sec
 
 ```Gen
-interacting: PossibleVgccPreTun
+interacting: PossibleUpPreVgccTun
   contained_by: VGCC-PRE-TUN
 
-  in_context: TryTunPreVcgg_ctx
+  in_context: TryTunUpPreVcgg_ctx
+  rf: ( active: 10x )
+
+ hypothesis:  
+  action: 
+  trace: 
+```
+
+#### PossibleDownPreVgccTun: int: sec
+
+```Gen
+interacting: PossibleDownPreVgccTun
+  contained_by: VGCC-PRE-TUN
+
+  in_context: TryTunDownPreVcgg_ctx
   rf: ( active: 10x )
 
  hypothesis:  
@@ -465,9 +480,7 @@ container: VGCC-PRE
 
 Da rivedere le condizioni per aggiungere mGluR che ha come proxy NT concentration!!!!!
 
-#### ms: AP_ctx: VGCC-PRE
+#### Ca2+enterLow: int: ms
-
-##### Ca2+enterLow: interacting
 
 Here we comprehend the breaking activity on VGCC by: CDI, eCB and mGluR:
 
@@ -499,7 +512,7 @@ interacting: Ca2+enterLow
     trace: None
 ```
 
-##### Ca2+enterMedium: interacting
+#### Ca2+enterMedium: int: ms
 
 ```Gen
 interacting: Ca2+enterMedium
@@ -515,7 +528,7 @@ interacting: Ca2+enterMedium
     trace: None
 ```
 
-##### Ca2+enterHigh: interacting
+#### Ca2+enterHigh: int: ms
 
 ```Gen
 interacting: Ca2+enterHigh
@@ -532,9 +545,7 @@ interacting: Ca2+enterHigh
 
 ### NOT AP_ctx: VGCC-PRE
 
-#### ms: NOT AP_ctx: VGCC-PRE
+#### Ca2+ClearanceLow: int: ms
-
-##### Ca2+ClearanceLow: interacting
 
 Qui eliminiamo Ca2+. Il tempo che ci mette ad eliminare il Ca2+ dovrebbe essere minoe dell'inervallo fra un AP_ctx e un'altra. Siccome non comprendiamo per ora ATP, non c'e' accumulo di Ca2+ per mancanza di ATP (stanchezza).
 
@@ -560,7 +571,7 @@ interacting: Ca2+ClearanceLow
     trace: None
 ```
 
-##### Ca2+ClearanceHigh: interacting
+#### Ca2+ClearanceHigh: int: ms
 
 ```Gen
 interacting: Ca2+ClearanceHigh