From 5b786c27266a9ffb38aab4453869cbdb01c78eb1 Mon Sep 17 00:00:00 2001 From: Sergio Marchetti Date: Sun, 31 May 2026 22:55:19 +0200 Subject: [PATCH 1/8] Update elements/neuron/post_ampa.md --- elements/neuron/post_ampa.md | 67 ++++++++++++++++++++++++++++++++++++ 1 file changed, 67 insertions(+) diff --git a/elements/neuron/post_ampa.md b/elements/neuron/post_ampa.md index e69de29..5fdc271 100644 --- a/elements/neuron/post_ampa.md +++ b/elements/neuron/post_ampa.md @@ -0,0 +1,67 @@ +--- +include_toc: true +--- + +# post_ampa.md + +## POST-AMPA: Comprehension +```Gen +POST-AMPA + type: comprehension + + expansion: + + intrication: + # Scope + !DAY: INTRICATION [ ref: &ORGANISM.!DAY ] + !NIGHT: INTRICATION [ ref: &ORGANISM.!NIGHT ] + + # Context + *bAP: INTRICATION [ ref: &SOMA.*bAP ] + + # Tub + _NT: INTRICATION [ ref: &ASTROSYNAPSE._NT ] + _Na: INTRICATION [ ref: &POSTSYNAPSE._Na ] + + instantiation: + $: BEHAVIOUR [ behaviour: POST-AMPA-BHE ] + +``` + +### POST-AMPA: Behaviour +```Gen +POST-AMPA-BHE: !DAY + type: behavior + + within_scope: !DAY + + snippet: + # NOT *bAP + @: ACCUMULATOR [ snippet: NaInAMPAMax, rf: active 2x ] + @: ACCUMULATOR [ snippet: NaInAMPAMed, rf: active 4x ] + +``` + +#### NOT *bAP + +##### NaInAMPAMax: ( active: 2x ) accumulator +```Gen +NaInAMPAMax + type: accumulator + + in_context: NOT *bAP + hypothesis: _NT fullness + action: [ _Na increase ] + trace: +``` + +##### NaInAMPAMed: ( active: 4x ) accumulator +```Gen +NaInAMPAMed + type: accumulator + + in_context: NOT *bAP + hypothesis: _NT mediumness + action: [ _Na increase ] + trace: +``` From c84c70e964e508d19524bbbddfb22d2da0ea0bb5 Mon Sep 17 00:00:00 2001 From: Sergio Marchetti Date: Sun, 31 May 2026 23:06:17 +0200 Subject: [PATCH 2/8] Update elements/neuron/postsynapse.md --- elements/neuron/postsynapse.md | 142 +++++++-------------------------- 1 file changed, 27 insertions(+), 115 deletions(-) diff --git a/elements/neuron/postsynapse.md b/elements/neuron/postsynapse.md index 65f657d..5cc44b2 100644 --- a/elements/neuron/postsynapse.md +++ b/elements/neuron/postsynapse.md @@ -39,47 +39,6 @@ Qui comprendiamo: --- -**G expression**: - -```Gen - -*bAP - POSTSYNAPSE (ms) - -- Ca Influx - CaNDMAEnterMax: ( active: 2x ) accumulator - CaNDMAEnterMed: ( active: 4x ) accumulator - -NOT *bAP: - POSTSYNAPSE (ms) - -- Ca Influx - CaNDMAEnterMedNotBap: ( active: 4x ) accumulator - CaNDMAEnterLow: ( active: 12x ) accumulator - -- Ca Clearence - CaClearance: ( active: 24x ) accumulator - -- V Influx - VPostMax: ( active: 4x ) accumulator ->VPost - VPostMed: ( active: 8x ) accumulator ->VPost - VPostLow: ( active: 16x ) accumulator ->VPost - -- V Clearence - VPostClearance: ( active: 18x ) accumulator ~->VPost - POST-AMPA (ms) ~ NT - -- Na Influx - NaAMPAEnterMax: ( active: 2x ) accumulator ~NT - NaAMPAEnterMed: ( active: 4x ) accumulator ~NT - POST-NA-CLEAR (ms) - -- Na Clearence - NaClearanceHigh: ( active: 4x ) accumulator - NaClearanceLow: ( active: 16x ) accumulator - -TunPossible_ctx - TUN-POST-AMPA (sec) - CheckTunPostAmpa: ( active: 60x ) contexting - TryTunUpPostAmpa_ctx - PossibleUpPostAmpaTun: ( active: 10x ) accumulator - TryTunDownPostAmpa_ctx - PossibleDownPostAmpaTun: ( active: 10x ) accumulator -``` - **Tubs:** - **Na**: Ioni entranti tramite AMPA receptors @@ -91,11 +50,19 @@ TunPossible_ctx --- -## POSTSYNAPSE: Comprehension +Intro: + - is expanded and developed by: [D_BRANCH](d-branch.md) + - is tuned by: ORGANISM, organs, modules + - expands and tunes: [POST-AMPA](post_ampa.md) + - develops [_posMod](??), [_actMod](??) + +## POSTSYNAPSE ```Gen POSTSYNAPSE - type: comprehension + type: comprehension + + include: post_ampa.md expansion: _@PostAmpaAll: TUB [ comprehension: POST-AMPA, full: 10x, active: 5x, empty: 2x ] @@ -131,7 +98,7 @@ POSTSYNAPSE ``` -### MAIN_POST: Behaviour +### MAIN_POST: !DAY ``` MAIN_POST type: behaviour @@ -161,7 +128,7 @@ MAIN_POST ![post-ltp-ltd.png](.attachments/post-ltp-ltd.png) -##### CaNDMAEnterMax: ( active: 2x ) accumulator +##### CaNDMAEnterMax ```Gen CaNDMAEnterMax @@ -175,7 +142,7 @@ CaNDMAEnterMax trace: ``` -##### CaNDMAEnterMed: ( active: 4x ) accumulator +##### CaNDMAEnterMed ```Gen CaNDMAEnterMed @@ -190,7 +157,7 @@ CaNDMAEnterMed #### NOT *bAP -##### CaNDMAEnterLow: ( active: 12x ) accumulator +##### CaNDMAEnterLow ```Gen CaNDMAEnterLow @@ -203,7 +170,7 @@ CaNDMAEnterLow trace: ``` -##### CaNDMAEnterMedNotBap: ( active: 4x ) accumulator +##### CaNDMAEnterMedNotBap ```Gen CaNDMAEnterMedNotBap @@ -216,7 +183,7 @@ CaNDMAEnterMedNotBap trace: ``` -##### CaClearance: ( active: 24x ) accumulator +##### CaClearance ```Gen CaClearance # Low @@ -229,7 +196,7 @@ CaClearance # Low trace: None ``` -##### VPostMax: ( active: 4x ) accumulator +##### VPostMax ```Gen VPostMa type: accumulator @@ -241,7 +208,7 @@ VPostMa trace: None ``` -##### VPostMed: ( active: 8x ) accumulator +##### VPostMed ```Gen VPostMed type: accumulator @@ -253,7 +220,7 @@ VPostMed trace: None ``` -##### VPostMin: ( active: 16x ) accumulator +##### VPostMin ```Gen VPostMin type: accumulator @@ -266,7 +233,7 @@ VPostMin ``` Il VPost clearance lo facciamo qui nel container dove creaiamo anche i VPost, perche' altrimenti, se lo facessimo in DB, perderemmo l'aspetto temporale della contribuzione dei singoli POST. -##### VPostClearance: ( active: 18x ) accumulator +##### VPostClearance ```Gen VPostClearance type: accumulator @@ -280,7 +247,7 @@ VPostClearance Il NA clearance lo mettiamo qui come sniplet, perche' gli AMPA creano, e questi pompano fuori. Qui non e' un problema di perdere l'integrazione temporale, perche' gli AMPA sono tutti uguali nel loro behavior. Abbiamo messo gli AMPA come container perche' cosi' possiamo modularne la numerosita'. -##### NaClearanceHigh: ( active: 4x ) accumulator +##### NaClearanceHigh ```Gen NaClearanceHigh type: accumulator @@ -292,7 +259,7 @@ NaClearanceHigh trace: None ``` -##### NaClearanceLow: ( active: 16x ) accumulator +##### NaClearanceLow ```Gen NaClearanceLow type: accumulator @@ -304,7 +271,7 @@ NaClearanceLow trace: None ``` -### TUN-POST-AMPA: Behaviour +### TUN-POST-AMPA: !DAY ```Gen TUN-POST-AMPA type: behaviour @@ -323,9 +290,9 @@ TUN-POST-AMPA ``` -#### TunPossible_ctx +#### *TunPossible -##### CheckTunPostAmpa: ( active: 60x ) contextor +##### CheckTunPostAmpa ```Gen CheckTunPostAmpa type: contextor @@ -338,7 +305,7 @@ CheckTunPostAmpa out_context: *TryTunDownPostAmpa ``` -##### PossibleUpPostAmpaTun: ( active: 10x ) accumulator +##### PossibleUpPostAmpaTun ```Gen PossibleUpPostAmpaTun: ( active: 10x ) type: accumulator @@ -349,7 +316,7 @@ PossibleUpPostAmpaTun: ( active: 10x ) trace: ``` -##### PossibleDownPostAmpaTun: ( active: 10x ) accumulator +##### PossibleDownPostAmpaTun ```Gen PossibleDownPostAmpaTun type: accumulator @@ -359,58 +326,3 @@ PossibleDownPostAmpaTun action: trace: ``` - -## POST-AMPA: Comprehension -```Gen -POST-AMPA - type: comprehension - - expansion: - - intrication: - # Tub - _NT: INTRICATION [ ref: &ASTROSYNAPSE._NT ] - _Na: INTRICATION [ ref: &POSTSYNAPSE._Na ] - - instantiation: - $: BEHAVIOUR [ behaviour: POST-AMPA-BHE ] - -``` - -### POST-AMPA: Behaviour -```Gen -POST-AMPA-BHE - type: behavior - - within_scope: !DAY - - snippet: - # NOT *bAP - @: ACCUMULATOR [ snippet: NaAMPAEnterMax, rf: active 2x ] - @: ACCUMULATOR [ snippet: NaAMPAEnterMed, rf: active 4x ] - -``` - -#### NOT *bAP - -##### NaAMPAEnterMax: ( active: 2x ) accumulator -```Gen -NaAMPAEnterMax - type: accumulator - - in_context: NOT *bAP - hypothesis: _NT fullness - action: [ _Na increase ] - trace: -``` - -##### NaAMPAEnterMed: ( active: 4x ) accumulator -```Gen -NaAMPAEnterMed - type: accumulator - - in_context: NOT *bAP - hypothesis: _NT mediumness - action: [ _Na increase ] - trace: -``` From edc387f906ab8d314ad1cc9bb70a17d5654f45a3 Mon Sep 17 00:00:00 2001 From: Sergio Marchetti Date: Sun, 31 May 2026 23:10:08 +0200 Subject: [PATCH 3/8] Update elements/neuron/post_ampa.md --- elements/neuron/post_ampa.md | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/elements/neuron/post_ampa.md b/elements/neuron/post_ampa.md index 5fdc271..9f6d952 100644 --- a/elements/neuron/post_ampa.md +++ b/elements/neuron/post_ampa.md @@ -4,7 +4,11 @@ include_toc: true # post_ampa.md -## POST-AMPA: Comprehension +## POST-AMPA + +Intro: + - is expanded and tuned by: [POSTSYNAPSE](postsynapse.md) + ```Gen POST-AMPA type: comprehension @@ -28,9 +32,9 @@ POST-AMPA ``` -### POST-AMPA: Behaviour +### POST-AMPA: !DAY ```Gen -POST-AMPA-BHE: !DAY +POST-AMPA-BHE type: behavior within_scope: !DAY @@ -44,7 +48,7 @@ POST-AMPA-BHE: !DAY #### NOT *bAP -##### NaInAMPAMax: ( active: 2x ) accumulator +##### NaInAMPAMax ```Gen NaInAMPAMax type: accumulator @@ -55,7 +59,7 @@ NaInAMPAMax trace: ``` -##### NaInAMPAMed: ( active: 4x ) accumulator +##### NaInAMPAMed ```Gen NaInAMPAMed type: accumulator From 67812f6318d43894546dab46b646cc150b19d429 Mon Sep 17 00:00:00 2001 From: Sergio Marchetti Date: Sun, 31 May 2026 23:11:24 +0200 Subject: [PATCH 4/8] Update elements/neuron/pre_vgcc.md --- elements/neuron/pre_vgcc.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/elements/neuron/pre_vgcc.md b/elements/neuron/pre_vgcc.md index 2bbc51f..e13eb8b 100644 --- a/elements/neuron/pre_vgcc.md +++ b/elements/neuron/pre_vgcc.md @@ -6,7 +6,7 @@ include_toc: true ## PRE_VGCC -- modulation: +Intro: - is expanded and tuned by: [PRESYNAPSE](presynapse.md) Voltage-Controlled Gated Channels: Qui per ora non gestiamo l'evoluzione della depolarizzazione. Alla scomparsa dell'AP, i VGCC smettono di funzionare. From d6a5f80a8d831c2155832d903bf353878ce13bce Mon Sep 17 00:00:00 2001 From: Sergio Marchetti Date: Sun, 31 May 2026 23:13:38 +0200 Subject: [PATCH 5/8] Update elements/neuron/postsynapse.md --- elements/neuron/postsynapse.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/elements/neuron/postsynapse.md b/elements/neuron/postsynapse.md index 5cc44b2..ec470f5 100644 --- a/elements/neuron/postsynapse.md +++ b/elements/neuron/postsynapse.md @@ -41,12 +41,12 @@ Qui comprendiamo: **Tubs:** -- **Na**: Ioni entranti tramite AMPA receptors -- **NT**: +- **_Na**: Ioni entranti tramite AMPA receptors +- **_NT**: Neuro Trasmettitori - **_Ca2**: Ioni entranti tramite NMDA -- **VPost**: il voltage che viene sentito in DB -- **eCB**: -- **Nox**:? +- **_VPost**: il voltage che viene sentito in DB +- **_eCB**: +- **_Nox**:? --- From 2e2ae5b1050e1f70e94d79b72bc45a2fd975afd4 Mon Sep 17 00:00:00 2001 From: Sergio Marchetti Date: Sun, 31 May 2026 23:59:12 +0200 Subject: [PATCH 6/8] Update elements/neuron/axon.md --- elements/neuron/axon.md | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/elements/neuron/axon.md b/elements/neuron/axon.md index 7031829..80363b6 100644 --- a/elements/neuron/axon.md +++ b/elements/neuron/axon.md @@ -5,9 +5,9 @@ Qui comprendiamo: - AXON: Axon ## AXON: Container -Modulation: -- develops: - - [PRESYNAPSE](presynapse.md) +Intro: +- is expanded by: [NEURON](neuron.md) +- expands: [PRESYNAPSE](presynapse.md) The axon does not contain specific behavior. - We might add balancing of ATP within PRE later. Here we comprehend it as a “cable” transporting the AP from SOMA to Presynapse. It expands PRESYNAPSE which: @@ -16,11 +16,9 @@ The axon does not contain specific behavior. ```Gen AXON - type: comprehension expansion: - _presynapse: TUB [ comprehension: PRESYNAPSE, full: 50x, active: 0x, empty: 10x ] # managed_by: EXCITATION or INHIBITION from winnertakeall ``` From 85d8f0bb99b4a35af0ca3779463b164751fbabfa Mon Sep 17 00:00:00 2001 From: Sergio Marchetti Date: Mon, 1 Jun 2026 00:06:11 +0200 Subject: [PATCH 7/8] Update elements/neuron/axon.md --- elements/neuron/axon.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/elements/neuron/axon.md b/elements/neuron/axon.md index 80363b6..304ab1f 100644 --- a/elements/neuron/axon.md +++ b/elements/neuron/axon.md @@ -19,6 +19,6 @@ AXON type: comprehension expansion: - _presynapse: TUB [ comprehension: PRESYNAPSE, full: 50x, active: 0x, empty: 10x ] + _@presynapse: TUB [ comprehension: PRESYNAPSE, full: 50x, active: 0x, empty: 10x ] # managed_by: EXCITATION or INHIBITION from winnertakeall ``` From a2804b032060b22ab942101de4fd1bc3abe58843 Mon Sep 17 00:00:00 2001 From: Sergio Marchetti Date: Mon, 1 Jun 2026 00:38:44 +0200 Subject: [PATCH 8/8] Update elements/neuron/d-branch.md --- elements/neuron/d-branch.md | 184 ++++++++++++++++++++---------------- 1 file changed, 103 insertions(+), 81 deletions(-) diff --git a/elements/neuron/d-branch.md b/elements/neuron/d-branch.md index b35d1c1..08c11d9 100644 --- a/elements/neuron/d-branch.md +++ b/elements/neuron/d-branch.md @@ -1,10 +1,14 @@ +--- +include_toc: true +--- + # d-branch.md Qui comprendiamo: - D-BRANCH: Dendritic Branch -## D-BRANCH: Container +## D-BRANCH **Simplified behaviors**: @@ -23,24 +27,41 @@ Qui comprendiamo: (structural remodelling of spine neck geometry under LTP/LTD would live here if added later) --- +Intro: +- is expanded by: [NEURON](neuron.md) +- expands: [POSTSYNAPSE](posynapse.md) ```Gen -Container: D-BRANCH - - include: - BEH-POST.md +D-BRANCH + type: comprehension + include: posynapse.md + expansion: - - BEH-POST ( full: 50x, active: 0x, empty: 10x ) - # managed_by: BEH-EXH or BEH-INH from winnertakeall - # developed_by: DEV-BD-BEH-POST-TUB from DEV-N + _@postsynapse: TUB [ comprehension: POSTSYNAPSE, full: 50x, active: 0x, empty: 10x ] - tub_local: - - VPost ( full: 50x, active: 0x, empty: 10x ) + intrication: - tub_intricated: - - VDB ( contained_by: BEH-SOMA ) + # Scope + !DAY: INTRICATION [ ref: &ORGANISM.!DAY ] + !NIGHT: INTRICATION [ ref: &ORGANISM.!NIGHT ] + # Context + *VPostMax: CONTEXT [] + *VPostMedium: CONTEXT [] + *VPostLow: CONTEXT [] + + # Tub + _VDB: INTRICATION [ ref: &SOMA._VDB ) + + + instantiation: + + # Tub + _VPost: TUB [ full: 50x, active: 0x, empty: 10x ] + + # Behaviour + $: BEHAVIOUR [ behaviour: MAIN_DBRANCH ] ``` --- @@ -51,85 +72,86 @@ Container: D-BRANCH --- -### ms: behaviors BD +### MAIN_DBRANCH: !DAY -#### CheckVPost:Context +```Gen +MAIN_DBRANCH + type: behaviour + + within_scope: !DAY + + snippet: + # *Fixed + @: CONTEXTOR [ snippet: CheckVPost, rf: active 60x ] + @: ACCUMULATOR [ snippet: VDBClearance, rf: active 2x ] + # *VPostMax + @: ACCUMULATOR [ snippet: VDBMax, rf: active 2x ] + # *VPostMedium + @: ACCUMULATOR [ snippet: VDBMed, rf: active 4x ] + # *VPostLow + @: ACCUMULATOR [ snippet: VDBMin, rf: active 8x ] + +``` +#### *Fixed + +##### CheckVPost Contestualizziamo in maniera Fixed? ```Gen -context: CheckVPost - contained_by: D-BRANCH - - in_context: Fixed - rf: ( active: 60x ) - - condition: (VPost fullness) - out_context: VPostMax - - condition: (VPost mediumness) - out_context: VPostMedium - - condition: (VPost emptiness) - out_context: VPostLow +CheckVPost + type: contextor + + in_context: *Fixed + condition: _VPost fullness + out_context: *VPostMax + condition: _VPost mediumness + out_context: *VPostMedium + condition: _VPost emptiness + out_context: *VPostLow ``` -##### VDBMax: Episode - -```Gen -episode: VDBMax - contained_by: D-BRANCH - - in_context: VPostMax - rf: ( active: 2x ) - - hypothesis: NOT (VDB full) - action: [VDB increase] - trace: -``` - -##### VDBMed: Episode - -```Gen -episode: VDBMed - contained_by: D-BRANCH - - in_context: VPostMed - rf: ( active: 2x ) - - hypothesis: NOT (VDB full) - action: [VDB increase] - trace: -``` - -##### VDBLow: Episode - -```Gen -episode: VDBLow - contained_by: D-BRANCH - - in_context: VPostLow - rf: ( active: 2x ) - - hypothesis: NOT (VDB full) - action: [VDB increase] - trace: -``` - -#### VDBlearance: Episode - +##### VDBClearance Qui facciamo il clearance del VDB. Lo facciamo in questo modo perche' abbiamo semplificato quello che succede fra BD e SOMA. - Qui posso aggiungere il flush, clearance veloce quando c'e' il bAP. ```Gen -episode: VDBClearance - contained_by: D-BRANCH +VDBClearance + in_context: *Fixed - in_context: Fixed - rf: ( active: 2x ) - - hypothesis: NOT (VDB empty) - action: [VDB decrease] - trace: + hypothesis: NOT _VDB empty + action: [ _VDB decrease ] + trace: +``` +#### *VPostMax +##### VDBMax + +```Gen +VDBMax + in_context: *VPostMax + + hypothesis: NOT _VDB full + action: [ _VDB increase ] + trace: +``` +#### *VPostMedium +##### VDBMed + +```Gen +VDBMed + in_context: *VPostMedium + + hypothesis: NOT _VDB full + action: [ _VDB increase ] + trace: +``` +#### *VPostLow +##### VDBLow + +```Gen + in_context: *VPostLow + + hypothesis: NOT _VDB full + action: [ _VDB increase ] + trace: ```