Update elements/neuron/soma.md

elements/neuron/soma.md

@@ -19,8 +19,27 @@ SOMA
     _@SOMA_VGSC-M: TUB [ comprehension: SOMA_VGSC, full: 50x, active: 20x, empty: 10x ] 
     _@SOMA_VGSC-L: TUB [ comprehension: SOMA_VGSC, full: 50x, active: 20x, empty: 10x ] 
 
+  intrication:
+
+    # Scope
+    !DAY: INTRICATION [ ref: &ORGANISM.!DAY ]
+    !NIGHT: INTRICATION [ ref: &ORGANISM.!NIGHT ]
+
+    # Context  
+    *AP: INTRICATION [ ref: &SOMA.*AP ]
+    *TunePossible: INTRICATION [ ref: &... ] # To be defined...
+
+    # Tub
+    _SpikeTrainTraces: INTRICATION [ ref: &NEURON._SpikeTrainTraces ]
+
 instantiation:
     
+    # Tub
+    _VDB: TUB [ full: 60x, active: 30x, empty: 0x ]
+    _Na: TUB [ full: 60x, active: 30x, empty: 0x ]
+    _Ca2: TUB [ full: 60x, active: 30x, empty: 0x ]
+    _SomaRefractory: TUB [ full: 60x, active: 30x, empty: 0x ]
+
     # Behaviour
     $: BEHAVIOUR [ behaviour: MAIN-SOMA ]
     $: BEHAVIOUR [ behaviour: SOMA_VGSC_H_TUN ]
@@ -31,31 +50,25 @@ SOMA
 
 **Tubs:**
 
-- **VDB**: dendrites deliver current
+- **_VDB**: dendrites deliver current
 
-- **Na**: are a proxy for the Coulombs of charge building up on the somatic membrane. They are used to check threshold, but also to mimic Na+ and K+ pumping
+- **_Na**: are a proxy for the Coulombs of charge building up on the somatic membrane. They are used to check threshold, but also to mimic Na+ and K+ pumping
 
-- **Ca2+**: Medium term traces to guide tuning and Night development. It is a local trace, ATP is a global (Astrocyte)
+- **_Ca2**: Medium term traces to guide tuning and Night development. It is a local trace, ATP is a global (Astrocyte)
 
-- **SpikeTrainTraces**: sono le tracce che consentono al neurone di far partire il Tuning neuronale, quando e' lontano da uno spike-train, ovvero e' in riposo.
+- **_SpikeTrainTraces**: sono le tracce che consentono al neurone di far partire il Tuning neuronale, quando e' lontano da uno spike-train, ovvero e' in riposo.
 
-- **SomaRefractory**: tracce di refractory
+- **_SomaRefractory**: tracce di refractory
 
 ### MAIN-SOMA: Container
 
 ```Gen
 MAIN-SOMA
-  type: container
+  type: behaviour
-  activity_scope: !DAY
+  
+  within_scope: !DAY
   
-  tub_local:
-    - VDB
-    - Na
-    - Ca2+
-    - SomaRefractory
 
-  tub_intricated:  
-    - SpikeTrainTraces ( contained_in: DAY-N )
 ```
 #### any
 
@@ -123,7 +136,7 @@ Durante la fase effettiva di spike:
 
 - eliminiamo Na accumulati. Qui ad un RF molto maggiore che con NaSpill. In teoria qui dovremmo eliminare tutti gli Na e NaSpill potrebbe non servire.
 - riempiamo SomaRefractory per fase di refractory
-- riempiamo Ca2+ per le tracce medio termine di potenziamento/depotenziamento.
+- riempiamo _Ca2 per le tracce medio termine di potenziamento/depotenziamento.
 
 ```Gen
 ActiveAP: ( active: 8x )
@@ -139,8 +152,8 @@ ActiveAP: ( active: 8x )
       action: [ increase SomaRefractory ]
       trace: 
 
-    hypothesis: NOT Ca2+ full
+    hypothesis: NOT _Ca2 full
-      action: [ increase Ca2+ ]
+      action: [ increase _Ca2 ]
       trace: 
 ```