Update elements/neuron/soma.md

elements/neuron/soma.md

@@ -8,16 +8,14 @@ include_toc: true
 
 Expansions and modulations:
 - is expanded by: [NEURON](neuron.md)
-- expands: SOMA_VGSC
+- expands: VGCC_SOMA
 
 ```Gen
 SOMA
   type: comprehension
 
   expansion: 
-    _@SOMA_VGSC-H: TUB [ comprehension: SOMA_VGSC, full: 50x, active: 20x, empty: 10x ] 
+    _@VGCC_SOMA: TUB [ comprehension: VGCC_SOMA, full: 50x, active: 20x, empty: 10x ] 
-    _@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:
 
@@ -46,10 +44,7 @@ instantiation:
 
     # Behaviour
     $: BEHAVIOUR [ behaviour: MAIN-SOMA ]
-    $: BEHAVIOUR [ behaviour: SOMA_VGSC_H_TUN ]
+    $: BEHAVIOUR [ behaviour: VGCC_SOMA_TUN ]  
-    SOMA_VGSC_M_TUN [pass: &SOMA_VGSC_M]
-    SOMA_VGSC_L_TUN [pass: &SOMA_VGSC_L]
-  
 ```
 
 **Tubs:**
@@ -80,7 +75,7 @@ MAIN-SOMA
 
 ##### 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 SOMA_VGSC to open ion channels that let Na+ ions in.
+As dendrites deliver current (VDB​), the soma acts like a capacitor. It "stores" this charge in the form of membrane potential. This contextualizes VGCC_SOMA to open ion channels that let Na+ ions in.
 
 This only applies if not ApCtx, or in other words, SOMA is not in refractory period.
 
@@ -170,24 +165,60 @@ ActiveAP
 ```
 
 
-## SOMA_VGSC: Comprehension
+## VGCC_SOMA
 
 Voltage Gated Sodium Channel: difficult to open (High)
 
 ```Gen
-container: SOMA_VGSC-H
+VGCC_SOMA
+  type: comprehension
 
-  tub_local:
+  expansion:
-    VGSCRefractoryH ( full: 60x, active: 30x, empty: 0x )
+  
+  intrication:
 
-  tub_intricated:
+    # Scope
-    Na ( contained_in: SOMA)
+    !DAY: INTRICATION [ ref: &ORGANISM.!DAY ]
+    !NIGHT: INTRICATION [ ref: &ORGANISM.!NIGHT ]
 
-   context_intricated:
+    # Context  
-    VDBMaxCtx ( contained_by: SOMA )
+
+    # Tub
+    _Na: INTRICATION [ ref: &SOMA._Na ]
+  
+  instantiation:
+  
+    # Context
+    *VDBMaxCtx: CONTEXT []
+    *VDBMediumCtx: CONTEXT []
+    *VDBMLowCtx: CONTEXT []
+    
+    # Tub
+    _VGSCRefractoryH: TUB [ full: 60x, active: 30x, empty: 0x )
+    _VGSCRefractoryM: TUB [ full: 60x, active: 30x, empty: 0x )
+    _VGSCRefractoryL: TUB [ full: 60x, active: 30x, empty: 0x )
+
+    # Behaviour
+    $: BEHAVIOUR [ behaviour: VGCC_SOMA_BEH_H]
+    $: BEHAVIOUR [ behaviour: VGCC_SOMA_BEH_M]
+    $: BEHAVIOUR [ behaviour: VGCC_SOMA_BEH_L]
+    
+```
+### VGCC_SOMA_BEH_H: !DAY
+
+```Gen
+VGCC_SOMA_BEH_H
+  type: behaviour
+
+  within_scope: !DAY
+  
+  snippets:
+    @: CONTEXTOR [ snippet: VGSC-H_Status, rf: active 60x ]
+    @: ACCUMULATOR [ snippet: NaEnterH, rf: active 1x ]
+    @: ACCUMULATOR [ snippet: VGSCRefractoryHSpill, rf: active 1x ]
 ```
 
-### sec: SOMA_VGSC-H
+### sec: VGCC_SOMA-H
 
 #### VGSC-H_Status: ( active: 60x ) contextor
 
@@ -196,7 +227,6 @@ Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di
 ```Gen
 VGSC-H_Status: ( active: 60x )
   type: contextor
-  contained_by: SOMA_VGSC-H
 
   in_context: any
     condition: VDBMaxCtx AND ( VGSCRefractoryH emptiness ) 
@@ -214,7 +244,7 @@ Questo sopra è il commmento della versione precedente, ora la quantità di NA i
 ```Gen
 NaEnterH: ( active: 1x )
   type: accumulator
-  contained_by: SOMA_VGSC-H
+  contained_by: VGCC_SOMA-H
 
   in_context: NaEnterH_ctx
     hypothesis: ( NOT Na full )
@@ -233,7 +263,7 @@ Lo Spill deve avere un rf maggiore dell'interacting che incrementa VGSCRefractor
 ```Gen
 VGSCRefractoryHSpill: ( active: 1x )
   type: accumulator
-  contained_by: SOMA_VGSC-H
+  contained_by: VGCC_SOMA-H
 
   in_context: VGSCRefractoryHSpill_ctx
     hypothesis: NOT ( VGSCRefractoryH empty )  
@@ -241,12 +271,14 @@ VGSCRefractoryHSpill: ( active: 1x )
       trace: None
 ```
 
-## SOMA_VGSC-M: container
+
+
+## VGCC_SOMA-M: container
 
 Voltage Gated Sodium Channel: less difficult to open (Medium)
 
 ```Gen
-container: SOMA_VGSC-M
+container: VGCC_SOMA-M
 
   tub_local:
     VGSCRefractoryM ( full: 60x, active: 30x, empty: 0x )
@@ -258,7 +290,7 @@ container: SOMA_VGSC-M
     VDBMedCtx ( contained_by: SOMA ) 
 ```
 
-### sec: SOMA_VGSC-M
+### sec: VGCC_SOMA-M
 
 #### VGSC-M_TPC: ( active: 60x ) contextor
 
@@ -267,7 +299,7 @@ Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di
 ```Gen
 VGSC-M_Status: ( active: 60x )
   type: contextor
-  contained_by: SOMA_VGSC-M
+  contained_by: VGCC_SOMA-M
 
   in_context: VDBMediumCtx OR VDBMaxCtx
     condition: ( VGSCRefractoryH emptiness ) 
@@ -282,7 +314,7 @@ Questo sopra è il commmento della versione precedente, ora la quantità di NA i
 ```Gen
 NaEnterM: ( active: 1x )
   type: accumulator
-  contained_by: SOMA_VGSC-M
+  contained_by: VGCC_SOMA-M
 
   in_context: NaEnterM_ctx
     hypothesis: ( NOT Na full )
@@ -301,7 +333,7 @@ Lo Spill deve avere un rf maggiore dell'interacting che incrementa VGSCRefractor
 ```Gen
 VGSCRefractoryMSpill: ( active: 1x )
   type: accumulator
-  contained_by: SOMA_VGSC-M
+  contained_by: VGCC_SOMA-M
 
   in_context: any
     hypothesis: NOT ( VGSCRefractoryM empty )  
@@ -309,12 +341,12 @@ VGSCRefractoryMSpill: ( active: 1x )
       trace: None
 ```
 
-## SOMA_VGSC_L: container
+## VGCC_SOMA_L: container
 
 Voltage Gated Sodium Channel: easy to open (Low)
 
 ```Gen
-container: SOMA_VGSC_L
+container: VGCC_SOMA_L
 
   tub_local:
     VGSCRefractoryL ( full: 60x, active: 30x, empty: 0x )
@@ -326,7 +358,7 @@ container: SOMA_VGSC_L
     VDBLowCtx ( contained_by: SOMA ) 
 ```
 
-### sec: SOMA_VGSC_L
+### sec: VGCC_SOMA_L
 
 #### VGSC-L_TPC: ( active: 60x ) contextor
 
@@ -335,7 +367,7 @@ Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di
 ```Gen
 VGSC-L_Status: ( active: 60x )
   type: contextor
-  contained_by: SOMA_VGSC_L
+  contained_by: VGCC_SOMA_L
 
   in_context: VDBLowCtx OR VDBMediumCtx OR VDBMaxCtx
     condition: ( VGSCRefractoryH emptiness ) 
@@ -350,7 +382,7 @@ Questo sopra è il commmento della versione precedente, ora la quantità di NA i
 ```Gen
 NaEnterL: ( active: 1x )
   type: accumulator
-  contained_by: SOMA_VGSC_L
+  contained_by: VGCC_SOMA_L
 
   in_context: NaEnterL_ctx
     hypothesis: ( NOT Na full )
@@ -379,14 +411,14 @@ VGSCRefractoryLSpill: ( active: 1x )
 ```
 
 
-## SOMA_VGSC_TUN: Tuner
+## VGCC_SOMA_TUN: Tuner
 
 ```Gen
-SOMA_VGSC_TUN
+VGCC_SOMA_TUN
  type: tuner
  contained_by: SOMA
 
- tunes: SOMA/expansion/SOMA_VGSC
+ tunes: SOMA/expansion/VGCC_SOMA
 
  context_intricated:
   - TunPossible ( contained_by: DAY-N )
@@ -401,7 +433,7 @@ SOMA_VGSC_TUN
 ```Gen
 check_tpc: ( active: 60x )
   type: contextor
-  contained_by: SOMA_VGSC-TUN
+  contained_by: VGCC_SOMA-TUN
 
   in_context: TunPossible
       condition:  ??