From 79bdd9dbedf5158ab55c593588408ca96ad8e25a Mon Sep 17 00:00:00 2001
From: ocrampal <ocrampal@ocrampal.com>
Date: Wed, 15 Apr 2026 12:13:52 +0200
Subject: [PATCH] varie

---
 neuron/soma.md | 42 +++++++++++++++++++++++++-----------------
 1 file changed, 25 insertions(+), 17 deletions(-)

diff --git a/neuron/soma.md b/neuron/soma.md
index cf74a8c..ba6ab79 100644
--- a/neuron/soma.md
+++ b/neuron/soma.md
@@ -11,17 +11,26 @@ Qui comprendiamo:
 — ms:
 
 - Resting at -70 mV: Leak channels + pumps (keep at resting)
+-- ?
 - VDB Depolarization : ~1-2 ms: Na⁺ enters (some VGSCs open)
 - Opened VGSC remain closed for a refractory period
  Spike if depolarized above threshold: to -50 mV
+ -- 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
+ -- increase SpikeTrainTraces (fast at spike)
+ -- increase Ca2+ traces
 - Repolarization to -70 mV:  ~1-2 ms: K⁺ exits (VG K⁺ channels open) ← NOT pumps!
+-- fast pump which decreases Na+, we do not model K+
 - After-hyperpolarization: ~5-20 ms: K⁺ channels still open
+-- must figure out how to deal with deoplarization
+-- decrease SpikeTraintraces slow, only if away from spiketrain this is empty
 
 — seconds:
 
 - Return to exact -70 mV: ~100-1000 ms: Na⁺/K⁺ pumps restore gradients
+-- slow pump
 - Ca2+ accumulation: SpikeTrainTraces
-
+-- ?
 — mins:
 
 - VGSC modulation
@@ -32,12 +41,14 @@ Qui comprendiamo:
 
 - **VDB**: dendrites deliver current
 
-- **VSOMA**: are a proxy for the Coulombs of charge building up on the somatic membrane.
+- **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
 
 - **AP**:
 
 - **bAP**:
 
+- **Ca2+**: Medium term traces to guide tuning and Night development
+
 - **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.
 
 ---
@@ -46,21 +57,23 @@ Qui comprendiamo:
 container: BEH-SOMA
 
   expansion: 
-    - BEH-SOMA-VGSC ( fullness: 50x, active: 20x, emptiness: 10x ) 
+    - VGSC-SOMA ( fullness: 50x, active: 20x, emptiness: 10x ) 
       # modulated_by: TUN-SOMA-VCGG # possible/actual
 
   tub_local:
 
     - VDB
 
-    - VSOMA
+    - Na
 
     - AP
 
     - bAP
 
-  tub_intricated:
-    - SpikeTrainTraces ( contained_by: TUN-N )
+    - Ca2+
+
+  tub_intricated:  
+    - SpikeTrainTraces ( contained_in: DAY-N )
 ```
 
 ### ms: behaviors SOMA
@@ -165,16 +178,11 @@ episode: ClearVSOMA
 #### TUN-SOMA-VCGG: Tuner
 
 ```Gen
-tuner: TUN-SOMA-VCGG
+tuner: VGSC-SOMA-TUN
 
- contained_by: BEH-SOMA
+ contained_by: SOMA
 
- tunes: 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
+ tunes: SOMA/expansion/VGSC-SOMA
 
  context_intricated:
   - TunPossible ( contained_by: DAY-N )
@@ -211,12 +219,12 @@ episode: ?
   trace: 
 ```
 
-## BEH-SOMA-VGSC: Container
+## VGSC-SOMA: Container
 
 Voltage Gated Sodium Channel
 
 ```Gen
-container: BEH-SOMA-VGSC
+container: VGSC-SOMA
 
 ```
 
@@ -226,7 +234,7 @@ container: BEH-SOMA-VGSC
 
 ```Gen
 episode: ??
-  contained_by: BEH-SOMA-VGSC
+  contained_by: VGSC-SOMA
 
   in_context: xxx
   rf: ( active: 1x )