SOMA
  type: comprehension

  expand_comprehension: 
    &SOMA_VGSC-H: SOMA_VGSC (full: 50x, active: 20x, empty: 10x) 
    &SOMA_VGSC-M: SOMA_VGSC (full: 50x, active: 20x, empty: 10x) 
    &SOMA_VGSC_L: SOMA_VGSC (full: 50x, active: 20x, empty: 10x) 

  instantiate_container:
    MAIN-SOMA []
    SOMA_VGSC_H_TUN [pass: &SOMA_VGSC_H]
    SOMA_VGSC_M_TUN [pass: &SOMA_VGSC_M]
    SOMA_VGSC_L_TUN [pass: &SOMA_VGSC_L]

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

MAIN-SOMA
  type: container
  activity_scope: !DAY
  
  tub_local:
    - VDB
    - Na
    - Ca2+
    - SomaRefractory

  tub_intricated:  
    - SpikeTrainTraces ( contained_in: DAY-N )

any

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.

This only applies if not ApCtx, or in other words, SOMA is not in refractory period.

SOMA-Status: ( active: 60x )
  type: contextor
  contained_by: MAIN-SOMA

  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

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.

Qui siamo nella fase effettiva di spike, non refractory che viene dopo. Fa da contesto di durata fra un RF ed un altro.

La fullness di Na rappresenta il threshold e puo' essere modificato. La fullness di SomaRefractory rappresenta la lunghezza del refractory.

SomaSpike: ( active: 30x )
  type: contextor
  contained_by: MAIN-SOMA

  in_context: any
    condition: ( Na fullness ) AND ( SomaRefractory emptiness )
      out_context: AP_ctx
      out_context: bAp_ctx

SomaRefractorySpill: ( active: 16x ) accumulator

Lo spill deve essere piu' lento dell'increase che avviene in ActiveAP

SomaRefractorySpill: ( active: 16x )
  type: accumulator
  contained_by: MAIN-SOMA

  in_context: any
    hypothesis: NOT ( SomaRefractory empty )
      action: [ decrease SomaRefractory ]
      trace:

Ap_ctx

ActiveAP: ( active: 8x ) accumulator

Durante la fase effettiva di spike:

eliminiamo Na accumulati. Qui ad un RF molto maggiore che con NaSpill. In teoria qui dovremmo eliminare tutti gli Na e NaSpill potrebbe non servire.
riempiamo SomaRefractory per fase di refractory
riempiamo Ca2+ per le tracce medio termine di potenziamento/depotenziamento.

ActiveAP: ( active: 8x )
  type: accumulator
  contained_by: MAIN-SOMA

  in_context: Ap_ctx
    hypothesis: NOT Na empty
      action: [ decrease Na ]
      trace: 

    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.

NaSpill: ( active: 8x )
  type: accumulator
  contained_by: MAIN-SOMA

  in_context: NaSpill_ctx
    hypothesis: NOT ( Na emptiness )
      action: [ decrease Na ]
      trace:

SOMA_VGSC: Comprehension

Voltage Gated Sodium Channel: difficult to open (High)

container: SOMA_VGSC-H

  tub_local:
    VGSCRefractoryH ( full: 60x, active: 30x, empty: 0x )

  tub_intricated:
    Na ( contained_in: SOMA)

   context_intricated:
    VDBMaxCtx ( contained_by: SOMA )

sec: SOMA_VGSC-H

VGSC-H_Status: ( active: 60x ) contextor

Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di VGSCRefractory. Questo perche' e' un era nella quale avviene l'episodio.

VGSC-H_Status: ( active: 60x )
  type: contextor
  contained_by: SOMA_VGSC-H

  in_context: any
    condition: VDBMaxCtx AND ( VGSCRefractoryH emptiness ) 
      out_context: NaEnterH_Ctx

    condition: ( VGSCRefractoryH mediumness ) OR ( VGSCRefractoryH fullness )
      out_context: VGSCRefractoryHSpill_ctx

NaEnterH: ( active: 1x ) accumulator

Se metto il controllo sulla (NOT Ready fullness) il VGSC puo' far entrare un numero di Na non superiore ad un massimo. Questo sopra è il commmento della versione precedente, ora la quantità di NA increase dipende dal rf di VGSC-H_TPC dato che li c'è la condition sulla presenza delle traccie di refractory

NaEnterH: ( active: 1x )
  type: accumulator
  contained_by: SOMA_VGSC-H

  in_context: NaEnterH_ctx
    hypothesis: ( NOT Na full )
      action: [ Na increase]
      trace: None

    hypothesis: ( NOT VGSCRefractoryH full )
      action: [ VGSCRefractoryH increase ]
      trace: None

VGSCRefractoryHSpill: ( active: 1x ) accumulator

Lo Spill deve avere un rf maggiore dell'interacting che incrementa VGSCRefractoryH (interactor precedente)

VGSCRefractoryHSpill: ( active: 1x )
  type: accumulator
  contained_by: SOMA_VGSC-H

  in_context: VGSCRefractoryHSpill_ctx
    hypothesis: NOT ( VGSCRefractoryH empty )  
      action: [ VGSCRefractoryH decrease ]
      trace: None

SOMA_VGSC-M: container

Voltage Gated Sodium Channel: less difficult to open (Medium)

container: SOMA_VGSC-M

  tub_local:
    VGSCRefractoryM ( full: 60x, active: 30x, empty: 0x )

  tub_intricated:
    Na ( contained_in: SOMA)

  context_intricated:
    VDBMedCtx ( contained_by: SOMA )

sec: SOMA_VGSC-M

VGSC-M_TPC: ( active: 60x ) contextor

Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di VGSCRefractory. Questo perche' e' un era nella quale avviene l'episodio.

VGSC-M_Status: ( active: 60x )
  type: contextor
  contained_by: SOMA_VGSC-M

  in_context: VDBMediumCtx OR VDBMaxCtx
    condition: ( VGSCRefractoryH emptiness ) 
      out_context: NaEnterM_Ctx

NaEnterM: ( active: 1x ) accumulator

NaEnterM: ( active: 1x )
  type: accumulator
  contained_by: SOMA_VGSC-M

  in_context: NaEnterM_ctx
    hypothesis: ( NOT Na full )
      action: [ Na increase]
      trace: None

    hypothesis: ( NOT VGSCRefractoryM full )
      action: [ VGSCRefractoryH increase ]
      trace: None

VGSCRefractoryMSpill: ( active: 1x ) accumulator

Lo Spill deve avere un rf maggiore dell'interacting che incrementa VGSCRefractoryH (interactor precedente)

VGSCRefractoryMSpill: ( active: 1x )
  type: accumulator
  contained_by: SOMA_VGSC-M

  in_context: any
    hypothesis: NOT ( VGSCRefractoryM empty )  
      action: [ VGSCRefractoryM decrease ]
      trace: None

SOMA_VGSC_L: container

Voltage Gated Sodium Channel: easy to open (Low)

container: SOMA_VGSC_L

  tub_local:
    VGSCRefractoryL ( full: 60x, active: 30x, empty: 0x )

  tub_intricated:
    Na ( contained_in: SOMA)

  context_intricated:
    VDBLowCtx ( contained_by: SOMA )

sec: SOMA_VGSC_L

VGSC-L_TPC: ( active: 60x ) contextor

Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di VGSCRefractory. Questo perche' e' un era nella qualle avviene l'episodio.

VGSC-L_Status: ( active: 60x )
  type: contextor
  contained_by: SOMA_VGSC_L

  in_context: VDBLowCtx OR VDBMediumCtx OR VDBMaxCtx
    condition: ( VGSCRefractoryH emptiness ) 
      out_context: NaEnterL_ctx

NaEnterL: ( active: 1x ) accumulator

NaEnterL: ( active: 1x )
  type: accumulator
  contained_by: SOMA_VGSC_L

  in_context: NaEnterL_ctx
    hypothesis: ( NOT Na full )
      action: [ Na increase]
      trace: None

    hypothesis: ( NOT VGSCRefractoryL full )
      action: [ VGSCRefractoryL increase ]
      trace: None

VGSCRefractoryLSpill: ( active: 1x ) accumulator

Lo Spill deve avere un rf maggiore dell'interacting che incrementa VGSCRefractoryH (interactor precedente)

VGSCRefractoryLSpill: ( active: 1x )
  type: accumulator
  
  contained_by: VGSC-L-SOMA

  in_context: any
    hypothesis: NOT ( VGSCRefractoryL empty )  
      action: [ VGSCRefractoryL decrease ]
      trace: None

SOMA_VGSC_TUN: Tuner

SOMA_VGSC_TUN
 type: tuner
 contained_by: SOMA

 tunes: SOMA/expansion/SOMA_VGSC

 context_intricated:
  - TunPossible ( contained_by: DAY-N )

 tub_local:

 tub_intricated:

check_tpc: ( active: 60x ) contextor

check_tpc: ( active: 60x )
  type: contextor
  contained_by: SOMA_VGSC-TUN

  in_context: TunPossible
      condition:  ??
        out_context: TunSomaVcgg

?: ( active: x ) accumulator

?: ( active: x )
  type: accumulator
  contained_by: TUN-PRE-VGCC

  in_context: TunSomaVcgg
     hypothesis:  
      action: 
      trace:

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soma.md

SOMA: Comprehension

MAIN-SOMA: Container

any

SOMA-Status: ( active: 60x ) contextor

SomaSpike: ( active: 30x ) contextor

SomaRefractorySpill: ( active: 16x ) accumulator

Ap_ctx

ActiveAP: ( active: 8x ) accumulator

NaSpill_ctx

NaSpill: ( active: 8x ) accumulator

SOMA_VGSC: Comprehension

sec: SOMA_VGSC-H

VGSC-H_Status: ( active: 60x ) contextor

NaEnterH: ( active: 1x ) accumulator

VGSCRefractoryHSpill: ( active: 1x ) accumulator

SOMA_VGSC-M: container

sec: SOMA_VGSC-M

VGSC-M_TPC: ( active: 60x ) contextor

NaEnterM: ( active: 1x ) accumulator

VGSCRefractoryMSpill: ( active: 1x ) accumulator

SOMA_VGSC_L: container

sec: SOMA_VGSC_L

VGSC-L_TPC: ( active: 60x ) contextor

NaEnterL: ( active: 1x ) accumulator

VGSCRefractoryLSpill: ( active: 1x ) accumulator

SOMA_VGSC_TUN: Tuner

check_tpc: ( active: 60x ) contextor

?: ( active: x ) accumulator

10 KiB

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