Update elements/neuron/soma.md

elements/neuron/soma.md

@@ -11,8 +11,6 @@ Qui comprendiamo:
 - VGSC-SOMA-M: Na ion channels. Open only when VDB medium
 - VGSC-SOMA-L: Na ion channels. Open only when VDB low
 
-## SOMA: container
-
 ---
 
 **Simplified verifiable behaviors**:
@@ -79,17 +77,32 @@ Qui comprendiamo:
 
 ---
 
+## SOMA: Comprehension
+
 ```Gen
-container: SOMA
+SOMA
+  type: comprehension
 
-  expansion: 
+  expand_comprehension: 
-    - VGSC-SOMA-H ( full: 50x, active: 20x, empty: 10x ) 
+    &VGSC-SOMA-H: VGSC-SOMA (full: 50x, active: 20x, empty: 10x) 
-      # modulated_by: VGSC-SOMA-H-TUN # possible/actual
+    &VGSC-SOMA-M: VGSC-SOMA (full: 50x, active: 20x, empty: 10x) 
-    - VGSC-SOMA-M ( full: 50x, active: 20x, empty: 10x ) 
+    &VGSC-SOMA-L: VGSC-SOMA (full: 50x, active: 20x, empty: 10x) 
-      # modulated_by: VGSC-SOMA-M-TUN # possible/actual
-    - VGSC-SOMA-L ( full: 50x, active: 20x, empty: 10x ) 
-      # modulated_by: VGSC-SOMA-L-TUN # possible/actual
 
+  instantiate_container:
+    SOMA-BEH []
+    VGSC-SOMA-H-TUN [pass: &VGSC-SOMA-H]
+    VGSC-SOMA-M-TUN [pass: &VGSC-SOMA-M]
+    VGSC-SOMA-L-TUN [pass: &VGSC-SOMA-L]
+  
+```
+
+### SOMA-BEH: Container
+
+```Gen
+SOMA-BEH
+  type: container
+  activity_scope: !DAY
+  
   tub_local:
     - VDB
     - Na
@@ -99,10 +112,9 @@ container: SOMA
   tub_intricated:  
     - SpikeTrainTraces ( contained_in: DAY-N )
 ```
+#### any
 
-### ms: SOMA
+##### SOMA-Status: ( active: 60x ) contextor
-
-#### SOMA-Status: ( active: 60x ) contextor
 
 As dendrites deliver current (VDB​), the soma acts like a capacitor. It "stores" this charge in the form of membrane potential. This contextualizes VGSC-SOMA to open ion channels that let Na+ ions in.
 
@@ -111,23 +123,20 @@ This only applies if not ApCtx, or in other words, SOMA is not in refractory per
 ```Gen
 SOMA-Status: ( active: 60x )
   type: contextor
-  contained_by: SOMA
+  contained_by: SOMA-BEH
 
   in_context: any
     condition: ( VDB fullness ) AND NOT AP_ctx
       out_context: VDBMax_Ctx
-
     condition: ( VDB mediumness ) AND NOT AP_ctx
       out_context: VDBMedium_ctx 
-
     condition: ( VDB emptiness ) AND NOT Ap_ctx
       out_context: VDBLow_ctx
-
     condition: NOT ( Na empty )
       out_context: NaSpill_ctx
 ```
 
-#### SomaSpike: ( active: 30x ) contextor
+##### SomaSpike: ( active: 30x ) contextor
 
 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.
 
@@ -138,7 +147,7 @@ La fullness di Na rappresenta il threshold e puo' essere modificato. La fullness
 ```Gen
 SomaSpike: ( active: 30x )
   type: contextor
-  contained_by: SOMA
+  contained_by: SOMA-BEH
 
   in_context: any
     condition: ( Na fullness ) AND ( SomaRefractory emptiness )
@@ -146,7 +155,24 @@ SomaSpike: ( active: 30x )
       out_context: bAp_ctx
 ```
 
-#### ActiveAP: ( active: 8x ) accumulator
+#### SomaRefractorySpill: ( active: 16x ) accumulator
+
+Lo spill deve essere piu' lento dell'increase che avviene in ActiveAP
+
+```Gen
+SomaRefractorySpill: ( active: 16x )
+  type: accumulator
+  contained_by: SOMA-BEH
+
+  in_context: any
+    hypothesis: NOT ( SomaRefractory empty )
+      action: [ decrease SomaRefractory ]
+      trace: 
+```
+
+#### Ap_ctx
+
+##### ActiveAP: ( active: 8x ) accumulator
 
 Durante la fase effettiva di spike:
 
@@ -157,7 +183,7 @@ Durante la fase effettiva di spike:
 ```Gen
 ActiveAP: ( active: 8x )
   type: accumulator
-  contained_by: SOMA
+  contained_by: SOMA-BEH
 
   in_context: Ap_ctx
     hypothesis: NOT Na empty
@@ -173,14 +199,16 @@ ActiveAP: ( active: 8x )
       trace: 
 ```
 
-#### NaSpill: ( active: 8x ) accumulator
+#### NaSpill_ctx
+
+##### NaSpill: ( active: 8x ) accumulator
 
 Questo potrebbe non servire se eliminiamo tutti Na durante ActiveAP.
 
 ```Gen
 NaSpill: ( active: 8x )
   type: accumulator
-  contained_by: SOMA
+  contained_by: SOMA-BEH
 
   in_context: NaSpill_ctx
     hypothesis: NOT ( Na emptiness )
@@ -188,24 +216,7 @@ NaSpill: ( active: 8x )
       trace:
 ```
 
-#### SomaRefractorySpill: ( active: 16x ) accumulator
+## VGSC-SOMA: Comprehension
-
-Lo spill deve essere piu' lento dell'increase che avviene in ActiveAP
-
-```Gen
-SomaRefractorySpill: ( active: 16x )
-  type: accumulator
-  contained_by: SOMA
-
-  in_context: any
-    hypothesis: NOT ( SomaRefractory empty )
-      action: [ decrease SomaRefractory ]
-      trace: 
-```
-
-### min: SOMA
-
-## VGSC-SOMA-H: container
 
 Voltage Gated Sodium Channel: difficult to open (High)