diff --git a/elements/neuron/axon.md b/elements/neuron/axon.md index 7031829..304ab1f 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 ] + _@presynapse: TUB [ comprehension: PRESYNAPSE, full: 50x, active: 0x, empty: 10x ] # managed_by: EXCITATION or INHIBITION from winnertakeall ``` 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: ``` diff --git a/elements/neuron/post_ampa.md b/elements/neuron/post_ampa.md index e69de29..9f6d952 100644 --- a/elements/neuron/post_ampa.md +++ b/elements/neuron/post_ampa.md @@ -0,0 +1,71 @@ +--- +include_toc: true +--- + +# post_ampa.md + +## POST-AMPA + +Intro: + - is expanded and tuned by: [POSTSYNAPSE](postsynapse.md) + +```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: !DAY +```Gen +POST-AMPA-BHE + type: behavior + + within_scope: !DAY + + snippet: + # NOT *bAP + @: ACCUMULATOR [ snippet: NaInAMPAMax, rf: active 2x ] + @: ACCUMULATOR [ snippet: NaInAMPAMed, rf: active 4x ] + +``` + +#### NOT *bAP + +##### NaInAMPAMax +```Gen +NaInAMPAMax + type: accumulator + + in_context: NOT *bAP + hypothesis: _NT fullness + action: [ _Na increase ] + trace: +``` + +##### NaInAMPAMed +```Gen +NaInAMPAMed + type: accumulator + + in_context: NOT *bAP + hypothesis: _NT mediumness + action: [ _Na increase ] + trace: +``` diff --git a/elements/neuron/postsynapse.md b/elements/neuron/postsynapse.md index 65f657d..ec470f5 100644 --- a/elements/neuron/postsynapse.md +++ b/elements/neuron/postsynapse.md @@ -39,63 +39,30 @@ 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 -- **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**:? --- -## 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: -``` 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.