change interacting

neuron/soma.md

@@ -38,22 +38,27 @@ Qui comprendiamo:
 
 — ms:
 
-- Here the threshold is based only on the integration of Na+
-- The threshold is tuned during the spiketrain. Low threshold at rest, to increase sensitivity, threshold increase during spike to increase discrimination
+- based on VDB, VGSC open and let Na+ in. VGSG then go into refractory
+- if Na fullness then AP. Here the threshold is based only on the integration of Na+
 - increase SpikeTrainTraces (fast at spike)
 - increase Ca2+ traces
-
-- fast pump which decreases Na+, we do not model K+
-
-- must figure out how to deal with deoplarization
+- decrease Na: fast pump which decreases Na+, we do not model K+
+-- there is a tug of war between Na entering and exiting. Na can reach fullness only if VDB increases fast (derivative)
+- there are 2 context: AP and RefractorySoma imlemented with timers and tunable
 - decrease SpikeTraintraces slow, only if away from spiketrain this is empty
 
+- Tune:
+-- The threshold is tuned during the spiketrain. Low threshold at rest, to increase sensitivity, threshold increase during spike to increase discrimination
+
 — secs:
 
 - SpikeTrainTraces
 
 — mins:
 
+- Tune:
+-- refractory lenght
+
 ---
 
 **Tubs:**
@@ -100,17 +105,17 @@ container: SOMA
 
 ### ms: SOMA
 
-#### CheckVDB: Context
+#### CheckVDB: Interacting
 
 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.
 
 This only applies if not AP, or in other words, SOMA is not in refractory period.
 
 ```Gen
-context: CheckVDB
+interacting: CheckVDB
   contained_by: SOMA
 
-  in_context: Fixed
+  context: Fixed
   rf: ( active: 60x )
 
   condition: (VDB fullness ) AND NOT AP
@@ -123,47 +128,54 @@ context: CheckVDB
     out_context: VDBLow
 ```
 
-#### CheckSomaSpike: Context
+#### CheckSomaSpike: Interacting
 
-The initiation and duration of a spike
+Qui siamo nella fase effettiva di spike, non refractory che viene dopo. Fa da contesto di durata fra un RF ed un altro.
 
 ```Gen
-context: CheckSomaSpike
+interacting: CheckSomaSpike
   contained_by: SOMA
 
-  in_context: Fixed
+  context: Fixed
   rf: ( active: 60x )
 
-  condition: ( Na fullness OR APRefractory )
+  condition: ( Na fullness ) AND ( NOT SomaRefractory )
     out_context: AP
     out_context: bAP
 ```
 
-#### SomaSpike: Episode
+#### APInteracting: Interacting
+
+Durante la fase effettiva di spike, eliminiamo Na accumulati e riempiamo per fase di refractory
 
 ```Gen
-episode: SomaSpike
+interacting: APInteracting
   contained_by: SOMA
 
-  in_context: AP
+  context: AP
   rf: ( active: 8x )
 
- hypothesis: 
-  action: 
+ hypothesis: NOT Na empty
+  action: [ decrease Na ]
   trace: 
+
+hypothesis: NOT RefractorySoma full
+  action: [ increase RefractorySoma ]
+  trace: 
+
 ```
 
-#### ClearNa: Episode
+#### ClearRefractorySoma: Interacting
 
 ```Gen
-episode: ClearNa
+interacting: ClearRefractorySoma
   contained_by: SOMA
 
-  in_context: Fixed
+  context: Fixed
   rf: ( active: 8x )
 
- hypothesis: 
-  action: 
+ hypothesis: NOT RefractorySoma empty
+  action: [ decrease RefractorySoma ]
   trace: 
 ```
 
@@ -194,20 +206,20 @@ tuner: VGSC-SOMA-TUN
 context: Check
   contained_by: VGSC-SOMA-TUN
 
-  in_context: TunPossible
+  context: TunPossible
   rf: ( active: 60x )
 
   condition:  
   out_context: TunSomaVcgg
 ```
 
-##### ?: Episode
+##### ?: Interacting
 
 ```Gen
-episode: ?
+interacting: ?
   contained_by: TUN-PRE-VGCC
 
-  in_context: TunSomaVcgg
+  context: TunSomaVcgg
   rf: ( active: x )
 
  hypothesis:  
@@ -231,15 +243,15 @@ container: VGSC-SOMA-H
 
 ### sec: VGSC-SOMA-H
 
-#### NaEnterH: Episode
+#### NaEnterH: Interacting
 
 Se metto il controllo sulla (NOT Ready fullness) il VGSC puo' far entrare un numero di Na non superiore ad un massimo.
 
 ```Gen
-episode: NaEnterH
+interacting: NaEnterH
   contained_by: VGSC-H-SOMA
 
-  in_context: VDBMax AND ( NOT RefractoryH )
+  context: VDBMax AND ( NOT RefractoryH )
   rf: ( active: 1x )
 
   hypothesis: ( NOT Na fullness ) AND ( NOT ReadyH fullness )
@@ -255,22 +267,22 @@ Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di
 context: CheckRefractoryH
   contained_by: VGSC-H-SOMA
 
-  in_context: NOT RefractoryH
+  context: NOT RefractoryH
   rf: ( active: 60x )
 
   condition: ( ReadyH fullness )
     out_context: RefractoryH
 ```
 
-##### RefractoryH: Episode
+##### RefractoryH: Interacting
 
 Questo episodio deve girare varie volte nell'ambito del contesto di refractory che viene controllato ad un RF maggiore.
 
 ```Gen
-episode: RefractoryH
+interacting: RefractoryH
   contained_by: VGSC-H-SOMA
 
-  in_context: RefractoryH
+  context: RefractoryH
   rf: ( active: 1x )
 
   hypothesis: NOT ( Ready emptyness )  
@@ -289,13 +301,13 @@ container: VGSC-SOMA-M
 
 ### sec: VGSC-SOMA-M
 
-#### Episode2
+#### Interacting2
 
 ```Gen
-episode: ??
+interacting: ??
   contained_by: VGSC-M-SOMA
 
-  in_context: xxx
+  context: xxx
   rf: ( active: 1x )
 
   hypothesis:  
@@ -314,13 +326,13 @@ container: VGSC-SOMA-M
 
 ### sec: VGSC-SOMA-L
 
-#### Episode3
+#### Interacting3
 
 ```Gen
-episode: ??
+interacting: ??
   contained_by: VGSC-L-SOMA
 
-  in_context: xxx
+  context: xxx
   rf: ( active: 1x )
 
   hypothesis: