From 11651aa7bed534e7c397552ee97bea930907f1a5 Mon Sep 17 00:00:00 2001 From: Sergio Marchetti Date: Mon, 8 Jun 2026 02:28:14 +0200 Subject: [PATCH] Update elements/neuron/soma.md --- elements/neuron/soma.md | 104 ++++++++++++++++++++++++++-------------- 1 file changed, 68 insertions(+), 36 deletions(-) diff --git a/elements/neuron/soma.md b/elements/neuron/soma.md index 65a7e55..ca8b833 100644 --- a/elements/neuron/soma.md +++ b/elements/neuron/soma.md @@ -8,16 +8,14 @@ include_toc: true Expansions and modulations: - is expanded by: [NEURON](neuron.md) -- expands: SOMA_VGSC +- expands: VGCC_SOMA ```Gen SOMA type: comprehension expansion: - _@SOMA_VGSC-H: TUB [ comprehension: SOMA_VGSC, full: 50x, active: 20x, empty: 10x ] - _@SOMA_VGSC-M: TUB [ comprehension: SOMA_VGSC, full: 50x, active: 20x, empty: 10x ] - _@SOMA_VGSC-L: TUB [ comprehension: SOMA_VGSC, full: 50x, active: 20x, empty: 10x ] + _@VGCC_SOMA: TUB [ comprehension: VGCC_SOMA, full: 50x, active: 20x, empty: 10x ] intrication: @@ -46,10 +44,7 @@ instantiation: # Behaviour $: BEHAVIOUR [ behaviour: MAIN-SOMA ] - $: BEHAVIOUR [ behaviour: SOMA_VGSC_H_TUN ] - SOMA_VGSC_M_TUN [pass: &SOMA_VGSC_M] - SOMA_VGSC_L_TUN [pass: &SOMA_VGSC_L] - + $: BEHAVIOUR [ behaviour: VGCC_SOMA_TUN ] ``` **Tubs:** @@ -80,7 +75,7 @@ MAIN-SOMA ##### 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. +As dendrites deliver current (VDB​), the soma acts like a capacitor. It "stores" this charge in the form of membrane potential. This contextualizes VGCC_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. @@ -170,24 +165,60 @@ ActiveAP ``` -## SOMA_VGSC: Comprehension +## VGCC_SOMA Voltage Gated Sodium Channel: difficult to open (High) ```Gen -container: SOMA_VGSC-H +VGCC_SOMA + type: comprehension - tub_local: - VGSCRefractoryH ( full: 60x, active: 30x, empty: 0x ) + expansion: + + intrication: - tub_intricated: - Na ( contained_in: SOMA) + # Scope + !DAY: INTRICATION [ ref: &ORGANISM.!DAY ] + !NIGHT: INTRICATION [ ref: &ORGANISM.!NIGHT ] - context_intricated: - VDBMaxCtx ( contained_by: SOMA ) + # Context + + # Tub + _Na: INTRICATION [ ref: &SOMA._Na ] + + instantiation: + + # Context + *VDBMaxCtx: CONTEXT [] + *VDBMediumCtx: CONTEXT [] + *VDBMLowCtx: CONTEXT [] + + # Tub + _VGSCRefractoryH: TUB [ full: 60x, active: 30x, empty: 0x ) + _VGSCRefractoryM: TUB [ full: 60x, active: 30x, empty: 0x ) + _VGSCRefractoryL: TUB [ full: 60x, active: 30x, empty: 0x ) + + # Behaviour + $: BEHAVIOUR [ behaviour: VGCC_SOMA_BEH_H] + $: BEHAVIOUR [ behaviour: VGCC_SOMA_BEH_M] + $: BEHAVIOUR [ behaviour: VGCC_SOMA_BEH_L] + +``` +### VGCC_SOMA_BEH_H: !DAY + +```Gen +VGCC_SOMA_BEH_H + type: behaviour + + within_scope: !DAY + + snippets: + @: CONTEXTOR [ snippet: VGSC-H_Status, rf: active 60x ] + @: ACCUMULATOR [ snippet: NaEnterH, rf: active 1x ] + @: ACCUMULATOR [ snippet: VGSCRefractoryHSpill, rf: active 1x ] ``` -### sec: SOMA_VGSC-H +### sec: VGCC_SOMA-H #### VGSC-H_Status: ( active: 60x ) contextor @@ -196,7 +227,6 @@ Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di ```Gen VGSC-H_Status: ( active: 60x ) type: contextor - contained_by: SOMA_VGSC-H in_context: any condition: VDBMaxCtx AND ( VGSCRefractoryH emptiness ) @@ -214,7 +244,7 @@ Questo sopra è il commmento della versione precedente, ora la quantità di NA i ```Gen NaEnterH: ( active: 1x ) type: accumulator - contained_by: SOMA_VGSC-H + contained_by: VGCC_SOMA-H in_context: NaEnterH_ctx hypothesis: ( NOT Na full ) @@ -233,7 +263,7 @@ Lo Spill deve avere un rf maggiore dell'interacting che incrementa VGSCRefractor ```Gen VGSCRefractoryHSpill: ( active: 1x ) type: accumulator - contained_by: SOMA_VGSC-H + contained_by: VGCC_SOMA-H in_context: VGSCRefractoryHSpill_ctx hypothesis: NOT ( VGSCRefractoryH empty ) @@ -241,12 +271,14 @@ VGSCRefractoryHSpill: ( active: 1x ) trace: None ``` -## SOMA_VGSC-M: container + + +## VGCC_SOMA-M: container Voltage Gated Sodium Channel: less difficult to open (Medium) ```Gen -container: SOMA_VGSC-M +container: VGCC_SOMA-M tub_local: VGSCRefractoryM ( full: 60x, active: 30x, empty: 0x ) @@ -258,7 +290,7 @@ container: SOMA_VGSC-M VDBMedCtx ( contained_by: SOMA ) ``` -### sec: SOMA_VGSC-M +### sec: VGCC_SOMA-M #### VGSC-M_TPC: ( active: 60x ) contextor @@ -267,7 +299,7 @@ Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di ```Gen VGSC-M_Status: ( active: 60x ) type: contextor - contained_by: SOMA_VGSC-M + contained_by: VGCC_SOMA-M in_context: VDBMediumCtx OR VDBMaxCtx condition: ( VGSCRefractoryH emptiness ) @@ -282,7 +314,7 @@ Questo sopra è il commmento della versione precedente, ora la quantità di NA i ```Gen NaEnterM: ( active: 1x ) type: accumulator - contained_by: SOMA_VGSC-M + contained_by: VGCC_SOMA-M in_context: NaEnterM_ctx hypothesis: ( NOT Na full ) @@ -301,7 +333,7 @@ Lo Spill deve avere un rf maggiore dell'interacting che incrementa VGSCRefractor ```Gen VGSCRefractoryMSpill: ( active: 1x ) type: accumulator - contained_by: SOMA_VGSC-M + contained_by: VGCC_SOMA-M in_context: any hypothesis: NOT ( VGSCRefractoryM empty ) @@ -309,12 +341,12 @@ VGSCRefractoryMSpill: ( active: 1x ) trace: None ``` -## SOMA_VGSC_L: container +## VGCC_SOMA_L: container Voltage Gated Sodium Channel: easy to open (Low) ```Gen -container: SOMA_VGSC_L +container: VGCC_SOMA_L tub_local: VGSCRefractoryL ( full: 60x, active: 30x, empty: 0x ) @@ -326,7 +358,7 @@ container: SOMA_VGSC_L VDBLowCtx ( contained_by: SOMA ) ``` -### sec: SOMA_VGSC_L +### sec: VGCC_SOMA_L #### VGSC-L_TPC: ( active: 60x ) contextor @@ -335,7 +367,7 @@ Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di ```Gen VGSC-L_Status: ( active: 60x ) type: contextor - contained_by: SOMA_VGSC_L + contained_by: VGCC_SOMA_L in_context: VDBLowCtx OR VDBMediumCtx OR VDBMaxCtx condition: ( VGSCRefractoryH emptiness ) @@ -350,7 +382,7 @@ Questo sopra è il commmento della versione precedente, ora la quantità di NA i ```Gen NaEnterL: ( active: 1x ) type: accumulator - contained_by: SOMA_VGSC_L + contained_by: VGCC_SOMA_L in_context: NaEnterL_ctx hypothesis: ( NOT Na full ) @@ -379,14 +411,14 @@ VGSCRefractoryLSpill: ( active: 1x ) ``` -## SOMA_VGSC_TUN: Tuner +## VGCC_SOMA_TUN: Tuner ```Gen -SOMA_VGSC_TUN +VGCC_SOMA_TUN type: tuner contained_by: SOMA - tunes: SOMA/expansion/SOMA_VGSC + tunes: SOMA/expansion/VGCC_SOMA context_intricated: - TunPossible ( contained_by: DAY-N ) @@ -401,7 +433,7 @@ SOMA_VGSC_TUN ```Gen check_tpc: ( active: 60x ) type: contextor - contained_by: SOMA_VGSC-TUN + contained_by: VGCC_SOMA-TUN in_context: TunPossible condition: ??