Update elements/neuron/soma.md

elements/neuron/soma.md

@@ -25,15 +25,19 @@ SOMA
     !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:
     
+    # Context  
+    *AP: CONTEXT []
+    *bAP: CONTEXT []
+    *VDBMax: CONTEXT []
+    *VDBMedium: CONTEXT []
+    *VDBLow: CONTEXT []
+    *NaSpill: CONTEXT []
+
     # Tub
     _VDB: TUB [ full: 60x, active: 30x, empty: 0x ]
     _Na: TUB [ full: 60x, active: 30x, empty: 0x ]
@@ -49,15 +53,10 @@ instantiation:
 ```
 
 **Tubs:**
-
 - **_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
-
 - **_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.
-
 - **_SomaRefractory**: tracce di refractory
 
 ### MAIN-SOMA: Container
@@ -68,9 +67,16 @@ MAIN-SOMA
   
   within_scope: !DAY
   
-
+  snippet:
+    # *Fixed
+    @: CONTEXTOR [ snippet: SomaSpike, rf: active 30x ]
+    @: ACCUMULATOR [ snippet: SomaRefractorySpill, rf: active 16x ]
+    @: ACCUMULATOR [ snippet: NASpill, rf: active 20x ]
+     # *AP
+    @: ACCUMULATOR [ snippet: ActiveAP, rf: active 8x ]
+    @: ACCUMULATOR [ snippet: ActiveAP, rf: active 8x ]
 ```
-#### any
+#### *Fixed
 
 ##### SOMA-Status: ( active: 60x ) contextor
 
@@ -79,22 +85,21 @@ As dendrites deliver current (VDB​), the soma acts like a capacitor. It "store
 This only applies if not ApCtx, or in other words, SOMA is not in refractory period.
 
 ```Gen
-SOMA-Status: ( active: 60x )
+SOMA-Status:
   type: contextor
-  contained_by: MAIN-SOMA
 
   in_context: any
-    condition: ( VDB fullness ) AND NOT AP_ctx
+    condition: _VDB fullness AND NOT AP_ctx
-      out_context: VDBMax_Ctx
+      out_context: *VDBMax
     condition: ( VDB mediumness ) AND NOT AP_ctx
-      out_context: VDBMedium_ctx 
+      out_context: *VDBMedium
-    condition: ( VDB emptiness ) AND NOT Ap_ctx
+    condition: _VDB emptiness AND NOT _Ap
-      out_context: VDBLow_ctx
+      out_context: *VDBLow
-    condition: NOT ( Na empty )
+    condition: NOT _Na empty
-      out_context: NaSpill_ctx
+      out_context: *NaSpill
 ```
 
-##### SomaSpike: ( active: 30x ) contextor
+##### SomaSpike
 
 Il fatto che mettiamo il check di AP separato dal check del Soma-Status, e' perche' vogliamo poter avere un RF specifico per AP, eventualmente tunabile.
 
@@ -103,34 +108,44 @@ Qui siamo nella fase effettiva di spike, non refractory che viene dopo. Fa da co
 La fullness di Na rappresenta il threshold e puo' essere modificato. La fullness di SomaRefractory rappresenta la lunghezza del refractory.
 
 ```Gen
-SomaSpike: ( active: 30x )
+SomaSpike
   type: contextor
-  contained_by: MAIN-SOMA
 
-  in_context: any
+  in_context: *Fixed
-    condition: ( Na fullness ) AND ( SomaRefractory emptiness )
+    condition: _Na fullness AND _SomaRefractory emptiness
-      out_context: AP_ctx
+      out_context: *AP
-      out_context: bAp_ctx
+      out_context: *bAp
 ```
 
-#### SomaRefractorySpill: ( active: 16x ) accumulator
+##### SomaRefractorySpill
 
 Lo spill deve essere piu' lento dell'increase che avviene in ActiveAP
 
 ```Gen
-SomaRefractorySpill: ( active: 16x )
+SomaRefractorySpill
   type: accumulator
-  contained_by: MAIN-SOMA
 
-  in_context: any
+  in_context: *Fixed
-    hypothesis: NOT ( SomaRefractory empty )
+    hypothesis: NOT _SomaRefractory empty
-      action: [ decrease SomaRefractory ]
+      action: [ decrease _SomaRefractory ]
       trace: 
 ```
 
-#### Ap_ctx
+##### NaSpill
 
-##### ActiveAP: ( active: 8x ) accumulator
+```Gen
+NaSpill
+  type: accumulator
+
+  in_context: *Fixed
+    hypothesis: NOT _Na empty
+      action: [ decrease _Na ]
+      trace:
+```
+
+#### *Ap
+
+##### ActiveAP
 
 Durante la fase effettiva di spike:
 
@@ -139,40 +154,21 @@ Durante la fase effettiva di spike:
 - riempiamo _Ca2 per le tracce medio termine di potenziamento/depotenziamento.
 
 ```Gen
-ActiveAP: ( active: 8x )
+ActiveAP
   type: accumulator
-  contained_by: MAIN-SOMA
 
-  in_context: Ap_ctx
+  in_context: *AP
-    hypothesis: NOT Na empty
+    hypothesis: NOT _Na empty
-      action: [ decrease Na ]
+      action: [ decrease _Na ] ## This is addition to the _NASpill
       trace: 
-
+    hypothesis: NOT _SomaRefractory full
-    hypothesis: NOT SomaRefractory full
       action: [ increase SomaRefractory ]
       trace: 
-
     hypothesis: NOT _Ca2 full
       action: [ increase _Ca2 ]
       trace: 
 ```
 
-#### NaSpill_ctx
-
-##### NaSpill: ( active: 8x ) accumulator
-
-Questo potrebbe non servire se eliminiamo tutti Na durante ActiveAP.
-
-```Gen
-NaSpill: ( active: 8x )
-  type: accumulator
-  contained_by: MAIN-SOMA
-
-  in_context: NaSpill_ctx
-    hypothesis: NOT ( Na emptiness )
-      action: [ decrease Na ]
-      trace:
-```
 
 ## SOMA_VGSC: Comprehension