fixed markdown with lint

2026-03-08 10:01:18 +01:00
parent 9ef04b59e9
commit 25ccdcb135
13 changed files with 301 additions and 269 deletions
@@ -1,13 +1,13 @@
 # AST: Comprehension
-Qui comprendiamo Astrocyte, sia BEH, che TUN e DEV

+Qui comprendiamo Astrocyte, sia BEH, che TUN e DEV

 ```Gen
 comprehension: AST

-	include:
-		- BEH-AST.md 
-		- TUN-AST.md
-		- DEV-AST.md
+ include:
+  - BEH-AST.md 
+  - TUN-AST.md
+  - DEV-AST.md
 
 ```
@@ -1,18 +1,20 @@
+# BEH-AST.md
+
 Qui comprendiamo:
+
 - BEH-AST: Astrocyte

-# BEH-AST: Container
-**Astrocyte**
+## BEH-AST: Container

 ```Gen
 container: BEH-AST

  expansion: 
-		- BEH-SYN ( fullness: indef, active: indef, emptiness: 0x ) 
+  - BEH-SYN ( fullness: indef, active: indef, emptiness: 0x ) 
 ```
+
 Modulated by: [[TUN-AST]]

-## Leakage: Context
+### Leakage: Context

-
-## ???: Episode
+### ???: Episode
@@ -1,3 +1,5 @@
+# DEV-AST.md
+
 Qui mettiamo la creazione o la distruzione di SYN. Il ragionamento qui e' tutto fa il network di Astocytes, tipo se c'e' abbastanza ATP o cose del genere.

 E' la creazione di nuove SYN che permette poi al TUN-AST di attivare la SYN, se c'e' la possibilita' fra PRE e POST.
@@ -1,49 +1,54 @@
+# TUN-AST.md
+
 Qui mettiamo l'attivazione/disattivazione di una SYN possibile, messa a disposizione dal DEV-AST.

 Il ragionamento e' fra la possibilita' di SYN, e le possibilita' di PRE e POST.

 La novita' e' lo SCOPE, nel quale avviene il ragionamento.

-# TUN-AST: Modulator
+## TUN-AST: Modulator
+
 ...

 ```Gen
 modulator: TUN-AST
-	contained_by: AREA1
+ contained_by: AREA1

-	modulates: BEH-AXO/expansion/BEH-PRE
+ modulates: BEH-AXO/expansion/BEH-PRE
        #

-	tub_modulation: # 
-		- prePossible ( N/BEH-AXO/BEH-PRE/possible )
-		- preActual ( N/BEH-AXO/BEH-PRE/actual )
-		- postPossible ( N/BEH-BD/BEH-POST/possible )
-		- postActual ( N/BEH-BD/BEH-POST/actual )
+ tub_modulation: # 
+  - prePossible ( N/BEH-AXO/BEH-PRE/possible )
+  - preActual ( N/BEH-AXO/BEH-PRE/actual )
+  - postPossible ( N/BEH-BD/BEH-POST/possible )
+  - postActual ( N/BEH-BD/BEH-POST/actual )
        - synPossible ( AST/BEH-AST/SYN/actual )
        - synActual ( AST/BEH-AST/SYN/actual )

-	tub_local:
-		- ??? (fullness: 50x, active: 0x, emptiness: 0x) 
-			# intricated with ???
+ tub_local:
+  - ??? (fullness: 50x, active: 0x, emptiness: 0x) 
+   # intricated with ???
 ```
+
 Forse con questi tub_modulation riesco a risolvere il problema dello SCOPE, perche' mi servono a mettere assieme scope diversi, quelli di PRE, POST e SYN.

-## ??: Context
+### ??: Context

 ....

 ```Gen
 context: ???

-	contained_by: TUN-AST
-	in_context: Fixed
-	rf: 60x
+ contained_by: TUN-AST
+ in_context: Fixed
+ rf: 60x

-	condition: ( ??? Empty ) # 
-		out_context: ???
+ condition: ( ??? Empty ) # 
+  out_context: ???
 ```

-## Activate: Episode
+### Activate: Episode
+
 ....

 ```Gen
@@ -54,6 +59,6 @@ episode: activate
  rf: ( active: 6x )

  hypothesis: NOT (?? empty)
-  	action: [??? decrease]
+   action: [??? decrease]
    trace: None
 ```
@@ -1,24 +1,29 @@
+# BEH-AXO.md
+
+## BEH-AXO: Container
+
 Qui comprendiamo:
+
 - BEH-AXO: Axon
 - BEH-PRE: Presynapse
 - BEH-VCGG: Voltage-Controlled Gated Channels

-# BEH-AXO: Container
 **Axon**: Axon does not contain specific behavior, here we comprehend it as a “cable” transporting the AP from SOMA to Presynapse. It expands BEH-PRE which can be Modulated (TUN).

 ```Gen
 container: BEH-AXO

  expansion: 
-		- BEH-PRE ( fullness: 50x, active: 20x, emptiness: 10x ) 
-			# modulated_by: TUN-SYN-AXO-PRE# possible/actual
+  - BEH-PRE ( fullness: 50x, active: 20x, emptiness: 10x ) 
+   # modulated_by: TUN-SYN-AXO-PRE# possible/actual
 ```

-# BEH-PRE: Container
+## BEH-PRE: Container

 **Presynapse:** We treat each presynapse as standalone. The vesicle reserve pool is a strictly private, local resource of each individual presynaptic bouton. What is shared between synapses on the same axon are signals (neuromodulators) and metabolic resources (energy), but not the synaptic vesicles themselves. This ensures both independent computation and cooperative metabolic support within the axonal branch.

 **Tubs:**
+
 - Ca2+: Calcium Ion entering the Presynapse when VCGG open. They are key to check the concentration, release vescicles and modulation
 - Rrp: Readily Releasable Pool
 The Readily Releasable Pool consists of the vesicles that are "docked" and "primed" at the active zone of the synapse.
@@ -40,6 +45,7 @@ Characteristics: This makes up the vast majority of the vesicles (up to 80% or 9

 **Behaviors**:
 L'idea e' che:
+
 - Fast
 -- i VCGG si aprano all'arrivo di un AP dal SOMA. Il numero dei VCGG presenti e' stato modulato (TUN) in una fase di non attivita' della presynapse
 -- I VCGG fanno entrare Ca2+ che ne aumenta la concentrazione
@@ -60,13 +66,13 @@ container: BEH-PRE

  tub_local:
    - Ca2+ ( fullness: 60x, active: 30x, emptiness: 0x )
-			#	modulated_by: DEV-PRE-CA2+FULL # Full
+   # modulated_by: DEV-PRE-CA2+FULL # Full

    - Rrp ( fullness: 30x, active: 15x, emptiness: 0x )
-			# modulated_by: DEV-PRE-RRP-FULL # Full
+   # modulated_by: DEV-PRE-RRP-FULL # Full

    - Rp ( fullness: 30x, active: 15x, emptiness: 0x )
-			# modulated_by: DEV-PRE-RRP-FULL # Full
+   # modulated_by: DEV-PRE-RRP-FULL # Full

    - TagRelease ( fullness: 1x, active: 0x, emptiness: 0x ) 

@@ -77,7 +83,8 @@ container: BEH-PRE
   
 ```

-## IntegrateCa2+: Context
+### IntegrateCa2+: Context
+
 Qui verifichiamo il livello di CA2+ nella presynapse. I comportamenti nella presinapsi dipendo tutti da questa concentrazione, sia quelli immediati di rilascio NT da vescicles che quelli di modulazione.

 ***Tens Milliseconds Time Scale***
@@ -90,16 +97,16 @@ context: IntegrateCa2+
  rf: ( active: 60x )

  condition: (Ca2+ empty) 
-		out_context: CaEmpty
+  out_context: CaEmpty

  condition: NOT (Ca2+ empty) AND NOT (Ca2+ full) 
-		out_context: CaMedium
+  out_context: CaMedium

  condition: (Ca2+ full) 
-		out_context: CaFull
+  out_context: CaFull
 ```

-## VescicleRelease: Episode
+### VescicleRelease: Episode

 Il rilascio di NT avviene solo se Ca+ FULLNESS? Ovviamente se ci sono Vesciche. O dipende da altro? Cioe’ cosi’ rilascerebbe tutte le vesciche se c’e’ fullness. Dovremmo mettere un tag, o una discesa improvvisa di Ca+ al release di una vescica. Perche’ potremmo avere il caso che i VGGC sia talmente tanti da far entrare tanto calcio da far si che la prima vescica consumi CA ma non abbastanza da andare sotto FULLNESS

@@ -120,12 +127,12 @@ episode: VescicleRelease
  rf: ( active: 6x )

  hypothesis: (Ca2+ full) AND NOT (Rrp empty)
-		action: [Rrp decrease, Nt increase, Ca2+ decrease, 
+  action: [Rrp decrease, Nt increase, Ca2+ decrease, 
                TagRelease increase]
-		trace: None
+  trace: None
 ```

-## Ca+ClearenceSlow: Episode
+### Ca+ClearenceSlow: Episode

 Svuotiamo a due velocita’. Il context (Check Ca+ concentration) e’ determinato a epoca piu’ lunga, tanto ci vuole qualche giro per fare entrare i primi Ca+  
 Le tracce lasciate servono alla modulazione
@@ -140,11 +147,12 @@ episode: Ca+ClearenceSlow
  rf: ( active: 6x )

  hypothesis: NOT (Ca+ empty) AND NOT (Ca+ full)
-  	action: [Ca+ decrease, CaTraces Increase]
+   action: [Ca+ decrease, CaTraces Increase]
    trace: None
 ```

-## Ca+ClearenceFast: Episode
+### Ca+ClearenceFast: Episode
+
 Qui l'idea oltre che a fare clearance e' anche quella di lasciare tracce su che livello di Ca2+ c'e' stato durante gli episodi. Un livello medio lascia meno tracce di un livello alto, e questo serve a ragionare sulla modulazione.

 Clearance mechanisms (in order of speed):
@@ -165,8 +173,8 @@ episode: Ca+ClearenceFast
  rf: ( active: 1x )

  condition: (Ca2+ full)
-		action: [Ca2+ decrease, CaTraces Increase]
-		trace: None
+  action: [Ca2+ decrease, CaTraces Increase]
+  trace: None
 ```

 ```Gen
@@ -178,25 +186,26 @@ episode: Ca+ClearenceMedium
  rf: ( active: 1x )

  hypothesis: NOT (Ca2+ full) AND NOT (Ca2+ empty)
-		action: [Ca2+ decrease, CaTraces Increase]
-		trace: None
+  action: [Ca2+ decrease, CaTraces Increase]
+  trace: None
 ```

-## STP - Pr Upregulation: Observable
+### STP - Pr Upregulation: Observable

 **Observed behavior**
 Upregulation (Facilitation): Residual Ca²⁺ from previous spikes increases P_r for next release

 ***Timing: > 10 ms***

-## STD - Pr Downregulation: Observable
+### STD - Pr Downregulation: Observable

 **Observed behavior**
 Downregulation (Depression): High-frequency firing depletes readily releasable vesicle pool, decreasing P_r

 ***Timing: > 10 ms***

-## VesciclesRecycling: Episode
+### VesciclesRecycling: Episode
+
 Dobbiamo capire se lasciare il recicling RecP oppure avere solo un Rp, almeno al primo giro di comprensione, per semplificare.

 Sequential steps:
@@ -217,12 +226,12 @@ episode: VesciclesRecycling
  in_context:
  rf: ( fullness: 10x, active: 5x, emptiness: 2x ) 
 # si parte con active, poi viene modulato
-#	modulated_by: DEV-PRE-VesciclesRecycling-RF
+# modulated_by: DEV-PRE-VesciclesRecycling-RF

  hypothesis:  
 ```

-## VescicleFromRPtoRRP-Slow: Episode
+### VescicleFromRPtoRRP-Slow: Episode

 Superpriming requires ATP for phosphorylation reactions and for molecular motors that move vesicles. If the reserve pool is depleted or ATP is low, the superpriming "conveyor belt" has nothing to feed into the RRP. (Astrocyte)

@@ -240,11 +249,11 @@ episode: VescicleFromRPtoRRP-Slow
  rf: ( active: 30x )

  hypothesis: NOT (RP empty)
-		action: [RP decrease, RRP increase]
-		trace: None 
+  action: [RP decrease, RRP increase]
+  trace: None 
 ```

-## VescicleFromRPtoRRP-Medium: Episode
+### VescicleFromRPtoRRP-Medium: Episode

 ***Seconds-Minutes Time Scale***

@@ -256,11 +265,11 @@ episode: VescicleFromRPtoRRP-Medium
  rf: ( active: 15x )

  hypothesis: NOT (RP empty) 
-		action: [RP decrease, RRP increease]
-		trace: None
+  action: [RP decrease, RRP increease]
+  trace: None
 ```

-## VescicleFromRPtoRRP-Fast: Episode
+### VescicleFromRPtoRRP-Fast: Episode

 ***Seconds-Minutes Time Scale***

@@ -275,7 +284,8 @@ episode: VescicleFromRPtoRRP-Fast
    action: [RP decrease, RRP increase]
    trace: None 
 ```
-## VesiclesFillingRP: Episode
+
+### VesiclesFillingRP: Episode

 Qui riempiamo le vesciche. Fino ad un numero massimo, che viene modulato in DEV

@@ -287,12 +297,12 @@ episode: VesiclesFillingRP

  in_context: AwayFromSpike
  rf: ( fullness: 100x, active: 60x, emptiness: 30x ) 
-#		modulated_by: DEV-PRE-VesiclesFillingRP-RF # RF
+#  modulated_by: DEV-PRE-VesiclesFillingRP-RF # RF

  hypothesis: 
 ```

-# BEH-PRE-VGCC: Container
+## BEH-PRE-VGCC: Container

 **Voltage Gated Ion Channels**: When an AP arrives from the SOMA, VCGG are opened and they let in CA2+ initiating the possible release of NT from the vescicles. In theory each RRP has its own VCGG nearby. We do not comprehend this, but consider VCGG shared between all the RPP of the presynapse (we impose a floor)

@@ -300,13 +310,13 @@ episode: VesiclesFillingRP
 container: BEH-PRE-VGCC

  tub_intricated:
-  	- Ca2+ ( contained_by: BEH-PRE )
+   - Ca2+ ( contained_by: BEH-PRE )

-	context_intricated:
-    - AP (	contained_by: BEH-SOMA )
+ context_intricated:
+    - AP ( contained_by: BEH-SOMA )
 ```

-## VgccOpen: Episode
+### VgccOpen: Episode

 Auto-inhibition? Ca²⁺ binding to calmodulin on VGCC. 5-50 ms

@@ -346,6 +356,6 @@ episode: VgccOpen
  rf: ( active: 1x )

 hypothesis: NOT (Ca2+ full)
-		action: [Ca2+ increase]
-		trace: None # Se Ca+FULLNESS, lascio tracce di overflow per modulazione DOWN, da capire UP
+  action: [Ca2+ increase]
+  trace: None # Se Ca+FULLNESS, lascio tracce di overflow per modulazione DOWN, da capire UP
 ```
@@ -1,67 +1,71 @@
+# BEH-AXO.md
+
 Qui comprendiamo:
+
 - BEH-BD: Dendritic Branch
 - BEH-POST: Postsynapsis
 - BEH-POST-AMPA: AMPA receptors (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors)

-# BEH-BD: Container
+## BEH-BD: Container
+
 **Dendritic Branch**: In questa prima fase, non consideriamo lo spike dendritico come comportamento. Questo limita molto il modello, perche' equipara tutte le Postsinapsi sui tre branch dendritici e non permette di fare in maniera che ad esempio due branch contestualizzino (base activity) e uno faccia scattare il threshold per lo spike somatico.
 Qui BEH-DB espande solo i BEH-POST, e' un cavo di collegamento come l'assone

 ```Gen
 Container: BEH-BD
 
-	expansion:
-		- BEH-POST ( fullness: 50x, active: 20x, emptiness: 10x ) 
-			# modulated_by: TUN-SYN-BD-POST possible/actual
+ expansion:
+  - BEH-POST ( fullness: 50x, active: 20x, emptiness: 10x ) 
+   # modulated_by: TUN-SYN-BD-POST possible/actual
 ```

-## BEH-POST: Container
+### BEH-POST: Container

 ```Gen
 container: BEH-POST

-	expansion: 
-		- BEH-POST-AMPA ( fullness: 10x, active: 5x, emptiness: 2x )
-			# modulated_by: TUN-POST-IC # possible/actual
+ expansion: 
+  - BEH-POST-AMPA ( fullness: 10x, active: 5x, emptiness: 2x )
+   # modulated_by: TUN-POST-IC # possible/actual

-	tub_local:
-		- Ca2+ ( fullness: 60x, active: 30x, emptiness: 0x )
-			#	modulated_by: DEV-POST-???-FULL # Full 
+ tub_local:
+  - Ca2+ ( fullness: 60x, active: 30x, emptiness: 0x )
+   # modulated_by: DEV-POST-???-FULL # Full 

-		- Nox ( fullness: 100x, active: 20x, emptiness: 0x ) # Nitric Oxide (NO):  A gas that diffuses freely.
+  - Nox ( fullness: 100x, active: 20x, emptiness: 0x ) # Nitric Oxide (NO):  A gas that diffuses freely.

-		- Ecb ( fullness: 100x, active: 20x, emptiness: 0x ) # Endocannabinoids (e.g., 2-AG)
+  - Ecb ( fullness: 100x, active: 20x, emptiness: 0x ) # Endocannabinoids (e.g., 2-AG)

-	tub_intricated:
-		- Nt ( contained_by: BEH-SYN )
-		- bAp (	contained_by: BEH-SOMA )
+ tub_intricated:
+  - Nt ( contained_by: BEH-SYN )
+  - bAp ( contained_by: BEH-SOMA )
 ```

-### Context
+#### Context

 ```Gen
 context: captureNt
-	contained_by: BEH-POST
+ contained_by: BEH-POST

-	in_context: Fixed
-	rf: ( active: 10x )
+ in_context: Fixed
+ rf: ( active: 10x )

-	condition: (Nt full) AND NOT (bAp)
-		out_context: NtCaptured
+ condition: (Nt full) AND NOT (bAp)
+  out_context: NtCaptured
 ```

-### Episode
+#### Episode

-### BEH-POST-AMPA: Container
+## BEH-POST-AMPA: Container

 ```Gen
 container: BEH-POST-AMPA

-	tub_intricated:
-		- Nt ( contained_by: BEH-SYN )
+ tub_intricated:
+  - Nt ( contained_by: BEH-SYN )

-	context_intricated:
-		- bAp (	contained_by: BEH-SOMA )
+ context_intricated:
+  - bAp ( contained_by: BEH-SOMA )
 ```

 #### AmpaOpen: Episode
@@ -80,8 +84,8 @@ episode: AmpaOpen
  rf: ( active: 1x )

 hypothesis: NOT (Ca2+ full)
-		action: [Ca2+ increase]
-		trace: None # Se Ca+FULLNESS, lascio tracce di overflow per modulazione DOWN, da capire UP
+  action: [Ca2+ increase]
+  trace: None # Se Ca+FULLNESS, lascio tracce di overflow per modulazione DOWN, da capire UP
 ```

 ### Depolarization by bAP
@@ -112,5 +116,3 @@ Da ricordare i Dendritic VCGG che si aprono facendo entrare Ca2+ all'arrivo di b
 ### Downregulation: Observable

 - Downregulation: AMPA desensitization acts as low-pass filter
-
-## 
@@ -7,8 +7,8 @@ Questo container serve solo ad espandere AXO, SOMA e DB.
 ```Gen
 container: BEH-N

-	expansion:
-  	- BEH-AXO ( active: 1x )
-  	- BEH-SOMA ( active: 1x )
-	- BEH-DB ( active: 3x )
+ expansion:
+   - BEH-AXO ( active: 1x )
+   - BEH-SOMA ( active: 1x )
+ - BEH-DB ( active: 3x )
 ```
@@ -4,11 +4,11 @@
 container: BEH-SOMA

  expansion: 
-		- BEH-SOMA-VCGG ( fullness: 50x, active: 20x, emptiness: 10x ) 
-			# modulated_by: TUN-SOMA-VCGG # possible/actual
+  - BEH-SOMA-VCGG ( fullness: 50x, active: 20x, emptiness: 10x ) 
+   # modulated_by: TUN-SOMA-VCGG # possible/actual

-	tub_intricated:
-		- SpikeTrainTraces ( contained_by: TUN-N )
+ tub_intricated:
+  - SpikeTrainTraces ( contained_by: TUN-N )
 ```

 ## Context
@@ -17,13 +17,13 @@ Qui mettiamo lo spike Dendritico. Sempre se vogliamo comprenderlo.

 ```Gen
 context: ???...
-	contained_by: BEH-SOMA
+ contained_by: BEH-SOMA

-	in_context: Fixed
-	rf: 60x
+ in_context: Fixed
+ rf: 60x

-	condition: 
-		activate: xxx
+ condition: 
+  activate: xxx
 ```

 ## Episode
@@ -36,8 +36,8 @@ episode: ??
  rf: ( active: 1x )

  hypothesis:  
-		action: 
-		trace: None
+  action: 
+  trace: None
 ```

 ## BEH-SOMA-VCGG: Container
@@ -57,8 +57,8 @@ episode: ??
  rf: ( active: 1x )

  hypothesis:  
-		action: 
-		trace: None
+  action: 
+  trace: None
 ```

 ##
@@ -52,23 +52,23 @@ modulator: DEV-RF

 ```Gen
 modulator: DEV-PRE-VesciclesRecycling-RF
-	contained_by: DEV-RF
+ contained_by: DEV-RF

-	modulates: BEH-PRE/episode/VesciclesRecycling
+ modulates: BEH-PRE/episode/VesciclesRecycling
 # each BEH-PRE is modulated!
 
-	tub_dev: 
-		- fulMod ( fullness: None, active: rf/fullness, emptiness: 0x )
-		- actMod ( fullness: None, active: rf/active, emptiness: 0x )
+ tub_dev: 
+  - fulMod ( fullness: None, active: rf/fullness, emptiness: 0x )
+  - actMod ( fullness: None, active: rf/active, emptiness: 0x )

 # qui stiamo modulando l'active di RF mantenendolo fra fullness e 
 # emptiness dichiarato in VesciclesRecycling
 
-	tub_local:
+ tub_local:

-	tub_intricated:
-		- Nox ( contained_by: BEH-POST )
-		- Ecb ( contained_by: BEH-POST )
+ tub_intricated:
+  - Nox ( contained_by: BEH-POST )
+  - Ecb ( contained_by: BEH-POST )
 ```

 #### Context
@@ -79,15 +79,15 @@ modulator: DEV-PRE-VesciclesRecycling-RF

 ```Gen
 modulator: DEV-PRE-VesiclesFillingRP-RF
-	contained_by: DEV-RF
+ contained_by: DEV-RF

-	modulates:
+ modulates:

-	tub_local:
+ tub_local:

-	tub_intricated:
-		- Nox ( contained_by: BEH-POST )
-		- Ecb ( contained_by: BEH-POST )
+ tub_intricated:
+  - Nox ( contained_by: BEH-POST )
+  - Ecb ( contained_by: BEH-POST )
 ```

 #### Context
@@ -98,15 +98,15 @@ modulator: DEV-PRE-VesiclesFillingRP-RF

 ```Gen
 modulator: DEV-PRE-LactateAtp-RF
-	contained_by: DEV-RF
+ contained_by: DEV-RF

-	modulates:
+ modulates:

-	tub_local:
+ tub_local:

-	tub_intricated:
-		- Nox ( contained_by: BEH-POST )
-		- Ecb ( contained_by: BEH-POST )
+ tub_intricated:
+  - Nox ( contained_by: BEH-POST )
+  - Ecb ( contained_by: BEH-POST )
 ```

 #### Context
@@ -126,21 +126,21 @@ modulator: DEV-FULL

 ```Gen
 modulator: DEV-PRE-CA2+-FULL
-	contained_by: DEV-FULL
+ contained_by: DEV-FULL

-	modulates: BEH-PRE/tub/Ca2+ # this is the tub whose "full" must be modulated
+ modulates: BEH-PRE/tub/Ca2+ # this is the tub whose "full" must be modulated
  
-	tub_dev: 
-			- fullMod ( fullness: 100x, active: Ca2+/fullness, emptiness: 50x ) # Ca2+Full "contains" a number of blocks equal to the current Full.
+ tub_dev: 
+   - fullMod ( fullness: 100x, active: Ca2+/fullness, emptiness: 50x ) # Ca2+Full "contains" a number of blocks equal to the current Full.
 # qui stiamo modulando la fullness di Ca2+, associandola ad
 # active di fullMod. Cambiando active di fullMod, 
 # si cambia la fullness di Ca2+

-	tub_local:
+ tub_local:

-	tub_intricated:
-		- Nox ( contained_by: BEH-POST )
-		- Ecb ( contained_by: BEH-POST )
+ tub_intricated:
+  - Nox ( contained_by: BEH-POST )
+  - Ecb ( contained_by: BEH-POST )
 ```

 #### Context
@@ -155,13 +155,13 @@ context: CheckPreTubCa2+
  rf: 60x

  condition: ( empty ) 
-		out_context: DecreaseFull
+  out_context: DecreaseFull

  condition: NOT ( empty ) AND NOT ( Ca2+ full ) 
-		out_context: Nothing
+  out_context: Nothing

  condition: ( full) 
-		out_context: IncreaseFull
+  out_context: IncreaseFull
 ```

 #### Episode
@@ -174,29 +174,29 @@ episode: VgccOpen
  rf: 1x

  hypothesis: NOT ( full ) AND NOT ( empty ) 
-		action: [ increase,  decrease]
-		trace: None
+  action: [ increase,  decrease]
+  trace: None
 ```

 ### DEV-PRE-RRP-FULL: Modulator

 ```Gen
 modulator: DEV-PRE-RRP-FULL
-	contained_by: DEV-FULL
+ contained_by: DEV-FULL

-	modulates: BEH-PRE/tub/Rrp # this is the tub whose "full" must be modulated
+ modulates: BEH-PRE/tub/Rrp # this is the tub whose "full" must be modulated
  
-	tub_dev: 
-			- fullMod ( fullness: 100x, active: Rrp/fullness, emptiness: 50x ) # RrpFull "contains" a number of blocks equal to the current Full.
+ tub_dev: 
+   - fullMod ( fullness: 100x, active: Rrp/fullness, emptiness: 50x ) # RrpFull "contains" a number of blocks equal to the current Full.
 # qui stiamo modulando la fullness di Rrp, associandola ad
 # active di fullMod. Cambiando active di fullMod, 
 # si cambia la fullness di Rrp

-	tub_local:
+ tub_local:

-	tub_intricated:
-		- Nox ( contained_by: BEH-POST )
-		- Ecb ( contained_by: BEH-POST )
+ tub_intricated:
+  - Nox ( contained_by: BEH-POST )
+  - Ecb ( contained_by: BEH-POST )
 ```

 #### Context
@@ -1,3 +1,5 @@
+# README.md
+
 Il neurone è il concetto che vogliamo comprendere. Partiamo dalla comprensione per espandere i concetti contenuti in N. L’espansione e’ anche di numerosita’ (ad esempio BEH-N espande 3 BEH-BD. Accanto all’espansione dei concetti aggiungiamo la modulabilita’ riferita a ciascun concetto (per quelli che scegliamo di voler modulare). In definitiva la comprensione risulta essere un’eterarchia e non una semplice gerarchia.

 ---
@@ -8,11 +8,11 @@ Il TUN contiene quei behavior di modulazione che non cambiano la somma (fullness

 ```Gen
 modulator: TUN-N
-	contained_by: N
+ contained_by: N

-	tub_local:
-		- SpikeTrainTraces (fullness: 50x, active: 0x, emptiness: 0x) 
-			# intricated with BEH-SOMA
+ tub_local:
+  - SpikeTrainTraces (fullness: 50x, active: 0x, emptiness: 0x) 
+   # intricated with BEH-SOMA
 ```

 ## IntegrateTunPossibility: Context
@@ -22,12 +22,12 @@ Qui controlliamo di essere lontani da uno spike train. Siamo in Day con BEH.
 ```Gen
 context: IntegrateTunPossibility

-	contained_by: TUN-N
-	in_context: Fixed
-	rf: 60x
+ contained_by: TUN-N
+ in_context: Fixed
+ rf: 60x

-	condition: ( SpikeTrainTraces Empty ) # Day
-		out_context: TunPossible
+ condition: ( SpikeTrainTraces Empty ) # Day
+  out_context: TunPossible
 ```

 ## TUN-SYN: Modulator
@@ -40,42 +40,42 @@ ATTENZIONE: Questo e POST e’ da cambiare, perche’ c’e’ il passaggio da T

 ```Gen
 modulator: TUN-SYN
-	contained_by: TUN-N
+ contained_by: TUN-N
 ```

 ### TUN-SYN-AXO-PRE: Modulator

 ```Gen
 modulator: TUN-SYN-AXO-PRE
-	contained_by: TUN-SYN 
+ contained_by: TUN-SYN 
 
-	modulates: BEH-AXO/expansion/BEH-PRE
+ modulates: BEH-AXO/expansion/BEH-PRE
 # qui stiamo modulando fullness e actual del tub BEH-PRE associandoli 
 # a tub_modulation prePos e PreAct. 

-	tub_modulation: # in TUN agiamo su fullness <-> active
-		- fulMod ( fullness: None, active: BEH-PRE/fullness, empty: 0x )  # riferimento a possible di BEH-PRE
-		- actMod ( fullness: None, active: BEH-PRE/active, empty: BEH-PRE/emptiness )  # riferimento a active di BEH-PRE
+ tub_modulation: # in TUN agiamo su fullness <-> active
+  - fulMod ( fullness: None, active: BEH-PRE/fullness, empty: 0x )  # riferimento a possible di BEH-PRE
+  - actMod ( fullness: None, active: BEH-PRE/active, empty: BEH-PRE/emptiness )  # riferimento a active di BEH-PRE

-	context_intricated:
-		- TunPossible (	contained_by: TUN-N )
+ context_intricated:
+  - TunPossible ( contained_by: TUN-N )

-	tub_local:
+ tub_local:

-	tub_intricated:
+ tub_intricated:
 ```

 #### Context

 ```Gen
 context: CheckTunSynAxoPrePossibility
-	contained_by: TUN-SYN-AXO-PRE
+ contained_by: TUN-SYN-AXO-PRE

-	in_context: TunPossible
-	rf: ( active: 60x )
+ in_context: TunPossible
+ rf: ( active: 60x )

-	condition:
-		out_context: 
+ condition:
+  out_context: 
 ```

 #### Episode
@@ -88,8 +88,8 @@ episode: TunSynAxoPre
  rf: 1x

  hypothesis: NOT () AND NOT ()
-		action: [ increase,  decrease]
-		trace: None
+  action: [ increase,  decrease]
+  trace: None
 ```

 ### TUN-SYN-BD-POST: Modulator
@@ -97,7 +97,7 @@ episode: TunSynAxoPre
 ```Gen
 modulator: TUN-SYN-BD-POST

-	contained_by: TUN-SYN
+ contained_by: TUN-SYN
 ...
 ```

@@ -114,7 +114,7 @@ Qui si modulano i canali ionici, sia quelli voltage (PRE/POST/SO/altro?) che que
 ```Gen
 modulator: TUN-CHAN

-	contained_by: TUN-N
+ contained_by: TUN-N
 ```

 ### TUN-PRE-VGCC: Modulator
@@ -122,24 +122,24 @@ modulator: TUN-CHAN
 ```Gen
 modulator: TUN-PRE-VGCC

-	contained_by: TUN-CHAN
+ contained_by: TUN-CHAN

-	modulates: BEH-PRE/expansion/BEH-PRE-VCGG
+ modulates: BEH-PRE/expansion/BEH-PRE-VCGG
  
-	tub_modulation: # in TUN agiamo su POS/ACT
-			- posMod ( fullness: None, active: BEH-PRE-VCGG/fullness, empty: 0x)  # riferimento a possible di BEH-PRE-VCGG
-			- actMod ( fullness: None, active: BEH-PRE-VCGG/active, empty: BEH-PRE-VCGG/emptiness)  # riferimento a active di BEH-PRE-VCGG
+ tub_modulation: # in TUN agiamo su POS/ACT
+   - posMod ( fullness: None, active: BEH-PRE-VCGG/fullness, empty: 0x)  # riferimento a possible di BEH-PRE-VCGG
+   - actMod ( fullness: None, active: BEH-PRE-VCGG/active, empty: BEH-PRE-VCGG/emptiness)  # riferimento a active di BEH-PRE-VCGG
 # qui stiamo modulando possible e actual di BEH-PRE-VCGG associandoli
 # a posMod e actMod. Non serve associare una fullness perche' 
 # la modulazione e' una pompa fra posMod e actMod e controlliamo
 # solo empty

-	context_intricated:
-		- TunPossible (	contained_by: TUN-N )
+ context_intricated:
+  - TunPossible ( contained_by: TUN-N )

-	tub_local:
+ tub_local:

-	tub_intricated:
+ tub_intricated:
 ```

 #### Context
@@ -152,7 +152,7 @@ context: Check
  rf: ( active: 60x )

  condition:  
-		out_context: TunPreVcgg
+  out_context: TunPreVcgg
 ```

 #### Episode
@@ -165,8 +165,8 @@ episode: Tun
  rf: ( active: x )

 hypothesis:  
-		action: 
-		trace: 
+  action: 
+  trace: 
 ```

 ### TUN-POST-AMPA: Modulator
@@ -174,20 +174,20 @@ episode: Tun
 ```Gen
 modulator: TUN-POST-AMPA

-	contained_by: TUN-CHAN
+ contained_by: TUN-CHAN

-	modulates: BEH-POST/expansion/BEH-POST-IC
+ modulates: BEH-POST/expansion/BEH-POST-IC

-		tub_modulation: # in TUN agiamo su POS/ACT
-			- posMod ( fullness: None, active: BEH-POST-IC/fullness, empty: 0x)  # riferimento a possible di BEH-PRE
-			- actMod ( fullness: None, active: BEH-POST-IC/active, empty: BEH-POST-IC/emptiness)  # riferimento a active di BEH-PRE
+  tub_modulation: # in TUN agiamo su POS/ACT
+   - posMod ( fullness: None, active: BEH-POST-IC/fullness, empty: 0x)  # riferimento a possible di BEH-PRE
+   - actMod ( fullness: None, active: BEH-POST-IC/active, empty: BEH-POST-IC/emptiness)  # riferimento a active di BEH-PRE

-	context_intricated:
-		- TunPossible (	contained_by: TUN-N )
+ context_intricated:
+  - TunPossible ( contained_by: TUN-N )

-	tub_local:
+ tub_local:

-	tub_intricated:
+ tub_intricated:
 ```

 #### Context
@@ -200,7 +200,7 @@ context: Check
  rf: ( active: 60x )

  condition:  
-		out_context: TunPostIc
+  out_context: TunPostIc
 ```

 #### Episode
@@ -213,8 +213,8 @@ episode: ?
  rf: ( active: x )

 hypothesis:  
-		action: 
-		trace: 
+  action: 
+  trace: 
 ```

 ### TUN-SOMA-VCGG: Modulator
@@ -222,21 +222,21 @@ episode: ?
 ```Gen
 modulator: TUN-SOMA-VCGG

-	contained_by: TUN-CHAN
+ contained_by: TUN-CHAN

-	modulates: BEH-SOMA/expansion/BEH-SOMA-VCGG
+ modulates: BEH-SOMA/expansion/BEH-SOMA-VCGG

-		expansion: BEH-SOMA-VCGG
-		tub_modulation: # in TUN agiamo su POS/ACT
-			- posMod ( fullness: None, active: BEH-SOMA-VCGG/fullness, empty: 0x)  # riferimento a possible di BEH-PRE
-			- actMod ( fullness: None, active: BEH-SOMA-VCGG/active, empty: BEH-SOMA-VCGG/emptiness)  # riferimento a active di BEH-PRE
+  expansion: BEH-SOMA-VCGG
+  tub_modulation: # in TUN agiamo su POS/ACT
+   - posMod ( fullness: None, active: BEH-SOMA-VCGG/fullness, empty: 0x)  # riferimento a possible di BEH-PRE
+   - actMod ( fullness: None, active: BEH-SOMA-VCGG/active, empty: BEH-SOMA-VCGG/emptiness)  # riferimento a active di BEH-PRE

-	context_intricated:
-		- TunPossible (	contained_by: TUN-N )
+ context_intricated:
+  - TunPossible ( contained_by: TUN-N )

-	tub_local:
+ tub_local:

-	tub_intricated:
+ tub_intricated:
 ```

 #### Context
@@ -249,7 +249,7 @@ context: Check
  rf: ( active: 60x )

  condition:  
-		out_context: TunSomaVcgg
+  out_context: TunSomaVcgg
 ```

 #### Episode
@@ -262,6 +262,6 @@ episode: ?
  rf: ( active: x )

 hypothesis:  
-		action: 
-		trace: 
+  action: 
+  trace: 
 ```
@@ -1,26 +1,32 @@
+# beh-WTA.md
+
 Qui comprendiamo:
+
 - BEH-WTA

-# BEH-WTA: Container
+## BEH-WTA: Container
+
 **Winner Take All**:

 ```Gen
 container: BEH-WTA

  expansion: 
-	INTERNAL-001:
-		- NEU-001.AXO -[AST-001]-> NEU-003.BD-001, NEU-004.BD-001
-		- NEU-002.AXO -[AST-001]-> NEU-003.BD-001
-	OUTGOING-001:
-		- NEU-003.AXO -[@]-> @.BD-001
-		- NEU-004.AXO -[@]-> @.BD-001
-	INCOMING-001:
-		- @.AXO -[@]-> NEU-001.BD-001, NEU-002.BD-001
-		- @.AXO -[@]-> NEU-004.BD-001, NEU-003.BD-001
+ INTERNAL-001:
+  - NEU-001.AXO -[AST-001]-> NEU-003.BD-001, NEU-004.BD-001
+  - NEU-002.AXO -[AST-001]-> NEU-003.BD-001
+ OUTGOING-001:
+  - NEU-003.AXO -[@]-> @.BD-001
+  - NEU-004.AXO -[@]-> @.BD-001
+ INCOMING-001:
+  - @.AXO -[@]-> NEU-001.BD-001, NEU-002.BD-001
+  - @.AXO -[@]-> NEU-004.BD-001, NEU-003.BD-001
 ```
+
 Questo e' il nuovo tipo di espansione che permette di specificare un "circuito" di possibilita'.
 A differenza di BD che espande PRE implicitamente e trattando PRE tutti allo stesso modo, ma comunque mantenendo la gerarchia, e la relazione, qui espandiamo esplicitamente.
 L'espansione:
+
 - dichiara N1 e N2
 - dichiara AST1
 - collega un N1 con un N2
@@ -29,10 +35,12 @@ L'espansione:

 In questo modo abbiamo allargato il concetto di espansione introducendo una sorta di spazialita', che dipende dalla relazione che viene imposta, e puo' essere verifica.
 Problemi da risolver:
+
 - posso permettere che una PRE e POST dello stesso N possano fare sinapsi.
 - vedere come intricare Neuroni fra organi e aree diverse, senza dover citare direttamente i Neurone e gli astrociti dell'altro argano o area. Questo credo sia risolvibile con una possibilita' di connnessione, tipo AST, ma che funziona per interOrgani, chiamabile NET.

 In questo caso potremmo specificare:
+
 - NEU-001.axon.terminal-1 -[excites:  ast=AST-001]-> AREA.Input-001

 E questo potrebbe rendere generale l'approccio.
@@ -1,12 +1,13 @@
 # WTA: Comprehension
+
 Qui comprendiamo un primo circuito Winner Take All, sia BEH, che TUN e DEV

 ```Gen
 comprehension: WTA

-	include:
-		- BEH-WTA.md 
-		- TUN-WTA.md
-		- DEV-WTA.md
+ include:
+  - BEH-WTA.md 
+  - TUN-WTA.md
+  - DEV-WTA.md
 
 ```