Update 2 files

- /neuron/soma.md
- /neuron/somaSergio.md

neuron/somaSergio.md

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+# soma.md
+
+Qui comprendiamo:
+
+- SOMA: il soma
+- VGSC-SOMA-H: Na ion channels. Open only when VDB high
+- 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**:
+
+— ms:
+
+- Resting at -70 mV: Leak channels + pumps (keep at resting)
+- VDB Depolarization : ~1-2 ms: Na⁺ enters (some VGSCs open)
+- Opened VGSC and then remain closed for a refractory period
+- Spike if depolarized above threshold: to -50 mV
+- Ca2+ enter
+- Repolarization to -70 mV:  ~1-2 ms: K⁺ exits (VG K⁺ channels open) ← NOT pumps!
+- After-hyperpolarization: ~5-20 ms: K⁺ channels still open
+
+— secs:
+
+- Return to exact -70 mV: ~100-1000 ms: Na⁺/K⁺ pumps restore gradients
+- Ca2+ accumulation
+
+— mins:
+
+- VGSC modulation
+
+---
+
+**G expression**:
+
+— ms:
+
+- based on VDB, VGSC open and let Na+ in. VGSG then go into refractory
+- if Na fullness then ApCtx. Here the threshold is based only on the integration of Na+
+- increase SpikeTrainTraces (fast at spike)
+- increase Ca2+ traces
+- 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: ApCtx 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:**
+
+- **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.
+
+- **RefractorySoma**: tracce di refractory
+
+---
+
+```Gen
+container: SOMA
+
+  expansion: 
+    - VGSC-SOMA-H ( fullness: 50x, active: 20x, emptiness: 10x ) 
+      # modulated_by: VGSC-SOMA-H-TUN # possible/actual
+
+    - VGSC-SOMA-M ( fullness: 50x, active: 20x, emptiness: 10x ) 
+      # modulated_by: VGSC-SOMA-M-TUN # possible/actual
+
+    - VGSC-SOMA-L ( fullness: 50x, active: 20x, emptiness: 10x ) 
+      # modulated_by: VGSC-SOMA-L-TUN # possible/actual
+
+
+  tub_local:
+
+    - VDB
+
+    - Na
+
+    - Ca2+
+
+    - RefractorySoma
+
+  tub_intricated:  
+    - SpikeTrainTraces ( contained_in: DAY-N )
+```
+
+### ms: SOMA
+
+#### VDB-Concentration: check_tpc
+
+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 ApCtx, or in other words, SOMA is not in refractory period.
+
+```Gen
+check_tpc: VDB-Concentration
+  contained_by: SOMA
+
+  tpc: any
+  rf: ( active: 60x )
+
+  condition: (VDB fullness ) AND NOT ApCtx
+    out_tpc: VDBMaxCtx
+
+  condition: ( VDB mediumness ) AND NOT ApCtx
+    out_tpc: VDBMediumCtx 
+
+  condition: ( VDB emptiness ) AND NOT ApCtx
+    out_tpc: VDBLowCtx
+```
+
+#### SomaSpill: interacting
+
+```Gen
+interacting: SomaSpill
+  contained_by: SOMA
+
+  context: any
+  rf: ( active: 8x )
+
+  hypothesis: NOT NA emptiness
+    action: [ decrease NA ]
+    trace:
+```
+
+#### SomaSpike: check_tpc
+
+Qui siamo nella fase effettiva di spike, non refractory che viene dopo. Fa da contesto di durata fra un RF ed un altro.
+
+```Gen
+check_tpc: SomaSpike
+  contained_by: SOMA
+
+  context: fixed
+  rf: ( active: 60x )
+
+  condition: ( Na fullness ) AND ( RefractorySoma emptiness )
+    out_context: ApCtx
+    out_context: bApCtx
+```
+
+#### ApBeh: interacting
+
+Durante la fase effettiva di spike, eliminiamo Na accumulati, riempiamo RefractorySoma per fase di refractory e riempiamo Ca2+ per le tracce medio termine di potenziamento/depotenziamento.
+
+```Gen
+interacting: ApBeh
+  contained_by: SOMA
+
+  context: ApCtx
+  rf: ( active: 8x )
+
+  hypothesis: NOT Na empty
+    action: [ decrease Na ]
+    trace: 
+
+  hypothesis: NOT RefractorySoma full
+    action: [ increase RefractorySoma ]
+    trace: 
+
+  hypothesis: NOT Ca2+ full
+    action: [ increase Ca2+ ]
+    trace: 
+```
+
+#### RefractoryBeh: interacting
+
+```Gen
+interacting: RefractoryBeh
+  contained_by: SOMA
+
+  context: any
+  rf: ( active: 8x )
+
+  hypothesis: NOT RefractorySoma empty
+    action: [ decrease RefractorySoma ]
+    trace: 
+```
+
+### sec: SOMA
+
+### min: SOMA
+
+#### VGSC-SOMA-TUN: Tuner
+
+```Gen
+tuner: VGSC-SOMA-TUN
+
+ contained_by: SOMA
+
+ tunes: SOMA/expansion/VGSC-SOMA
+
+ context_intricated:
+  - TunPossible ( contained_by: DAY-N )
+
+ tub_local:
+
+ tub_intricated:
+```
+
+##### Check: check_tpc
+
+```Gen
+context: check_tpc
+  contained_by: VGSC-SOMA-TUN
+
+  context: TunPossible
+  rf: ( active: 60x )
+
+  condition:  
+  out_context: TunSomaVcgg
+```
+
+##### ?: interacting
+
+```Gen
+interacting: ?
+  contained_by: TUN-PRE-VGCC
+
+  context: TunSomaVcgg
+  rf: ( active: x )
+
+ hypothesis:  
+  action: 
+  trace: 
+```
+
+## VGSC-SOMA-H: container
+
+Voltage Gated Sodium Channel: difficult to open (High)
+
+```Gen
+container: VGSC-SOMA-H
+
+  tub_local:
+    Ready ( )
+
+  tub_intricated:
+    Na ( contained_in: SOMA)
+```
+
+### sec: VGSC-SOMA-H
+
+#### 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
+interacting: NaEnterH
+  contained_by: VGSC-H-SOMA
+
+  context: VDBMaxCtx AND ( NOT RefractoryH )
+  rf: ( active: 1x )
+
+  hypothesis: ( NOT Na fullness ) AND ( NOT ReadyH fullness )
+    action: [ Na increase, ReadyH increase ]
+    trace: None
+```
+
+##### CheckRefractoryH: check_tpc
+
+Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di Refractory. Questo perche' e' un era nella qualle avviene l'episodio.
+
+```Gen
+check_tpc: CheckRefractoryH
+  contained_by: VGSC-H-SOMA
+
+  context: NOT RefractoryH
+  rf: ( active: 60x )
+
+  condition: ( ReadyH fullness )
+    out_context: RefractoryH
+```
+
+##### RefractoryH: interacting
+
+Questo episodio deve girare varie volte nell'ambito del contesto di refractory che viene controllato ad un RF maggiore.
+
+```Gen
+interacting: RefractoryH
+  contained_by: VGSC-H-SOMA
+
+  context: RefractoryH
+  rf: ( active: 1x )
+
+  hypothesis: NOT ( ReadyH emptyness )  
+    action: [ ReadyH decrease ]
+    trace: None
+```
+
+## VGSC-SOMA-M: container
+
+Voltage Gated Sodium Channel: less difficult to open (Medium)
+
+```Gen
+container: VGSC-SOMA-M
+
+  tub_local:
+    Ready ( )
+
+  tub_intricated:
+    Na ( contained_in: SOMA)
+```
+
+### sec: VGSC-SOMA-M
+
+#### NaEnterM: interacting
+
+Se metto il controllo sulla (NOT Ready fullness) il VGSC puo' far entrare un numero di Na non superiore ad un massimo.
+
+```Gen
+interacting: NaEnterM
+  contained_by: VGSC-M-SOMA
+
+  context: (VDBMediumCtx OR VDBMaxCtx) AND ( NOT RefractoryM )
+  rf: ( active: 1x )
+
+  hypothesis: ( NOT Na fullness ) AND ( NOT ReadyM fullness )
+    action: [ Na increase, ReadyM increase ]
+    trace: None
+```
+
+##### CheckRefractoryM: check_tpc
+
+Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di Refractory. Questo perche' e' un era nella qualle avviene l'episodio.
+
+```Gen
+check_tpc: CheckRefractoryM
+  contained_by: VGSC-M-SOMA
+
+  context: NOT RefractoryM
+  rf: ( active: 60x )
+
+  condition: ( ReadyM fullness )
+    out_context: RefractoryM
+```
+
+##### RefractoryM: interacting
+
+Questo episodio deve girare varie volte nell'ambito del contesto di refractory che viene controllato ad un RF maggiore.
+
+```Gen
+interacting: RefractoryM
+  contained_by: VGSC-M-SOMA
+
+  context: RefractoryM
+  rf: ( active: 1x )
+
+  hypothesis: NOT ( ReadyM emptyness )  
+    action: [ ReadyM decrease ]
+    trace: None
+```
+
+## VGSC-SOMA-L: container
+
+Voltage Gated Sodium Channel: easy to open (Low)
+
+```Gen
+container: VGSC-SOMA-L
+
+  tub_local:
+    Ready ( )
+
+  tub_intricated:
+    Na ( contained_in: SOMA)
+```
+
+### sec: VGSC-SOMA-L
+
+#### NaEnterL: interacting
+
+Se metto il controllo sulla (NOT Ready fullness) il VGSC puo' far entrare un numero di Na non superiore ad un massimo.
+
+```Gen
+interacting: NaEnterL
+  contained_by: VGSC-L-SOMA
+
+  context: ( VDBLowCtx OR VDBMediumCtx OR VDBMaxCtx) AND ( NOT RefractoryL )
+  rf: ( active: 1x )
+
+  hypothesis: ( NOT Na fullness ) AND ( NOT ReadyL fullness )
+    action: [ Na increase, ReadyH increase ]
+    trace: None
+```
+
+##### CheckRefractoryL: check_tpc
+
+Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di Refractory. Questo perche' e' un era nella qualle avviene l'episodio.
+
+```Gen
+check_tpc: CheckRefractoryL
+  contained_by: VGSC-L-SOMA
+
+  context: NOT RefractoryL
+  rf: ( active: 60x )
+
+  condition: ( ReadyL fullness )
+    out_context: RefractoryL
+```
+
+##### RefractoryL: interacting
+
+Questo episodio deve girare varie volte nell'ambito del contesto di refractory che viene controllato ad un RF maggiore.
+
+```Gen
+interacting: RefractoryL
+  contained_by: VGSC-L-SOMA
+
+  context: RefractoryL
+  rf: ( active: 1x )
+
+  hypothesis: NOT ( ReadyL emptyness )  
+    action: [ ReadyL decrease ]
+    trace: None
+```
+