Merge branch 'master' of https://repo.splindex.net/ocrampal/organism
This commit is contained in:
@@ -5,9 +5,9 @@ Qui comprendiamo:
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- AXON: Axon
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## AXON: Container
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Modulation:
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- develops:
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- [PRESYNAPSE](presynapse.md)
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Intro:
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- is expanded by: [NEURON](neuron.md)
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- expands: [PRESYNAPSE](presynapse.md)
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The axon does not contain specific behavior.
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- 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:
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@@ -16,11 +16,9 @@ The axon does not contain specific behavior.
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```Gen
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AXON
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type: comprehension
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expansion:
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_presynapse: TUB [ comprehension: PRESYNAPSE, full: 50x, active: 0x, empty: 10x ]
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_@presynapse: TUB [ comprehension: PRESYNAPSE, full: 50x, active: 0x, empty: 10x ]
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# managed_by: EXCITATION or INHIBITION from winnertakeall
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```
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+100
-78
@@ -1,10 +1,14 @@
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---
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include_toc: true
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---
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# d-branch.md
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Qui comprendiamo:
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- D-BRANCH: Dendritic Branch
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## D-BRANCH: Container
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## D-BRANCH
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**Simplified behaviors**:
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@@ -23,24 +27,41 @@ Qui comprendiamo:
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(structural remodelling of spine neck geometry under LTP/LTD would live here if added later)
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---
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Intro:
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- is expanded by: [NEURON](neuron.md)
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- expands: [POSTSYNAPSE](posynapse.md)
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```Gen
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Container: D-BRANCH
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D-BRANCH
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type: comprehension
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include:
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BEH-POST.md
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include: posynapse.md
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expansion:
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- BEH-POST ( full: 50x, active: 0x, empty: 10x )
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# managed_by: BEH-EXH or BEH-INH from winnertakeall
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# developed_by: DEV-BD-BEH-POST-TUB from DEV-N
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_@postsynapse: TUB [ comprehension: POSTSYNAPSE, full: 50x, active: 0x, empty: 10x ]
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tub_local:
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- VPost ( full: 50x, active: 0x, empty: 10x )
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intrication:
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tub_intricated:
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- VDB ( contained_by: BEH-SOMA )
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# Scope
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!DAY: INTRICATION [ ref: &ORGANISM.!DAY ]
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!NIGHT: INTRICATION [ ref: &ORGANISM.!NIGHT ]
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# Context
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*VPostMax: CONTEXT []
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*VPostMedium: CONTEXT []
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*VPostLow: CONTEXT []
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# Tub
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_VDB: INTRICATION [ ref: &SOMA._VDB )
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instantiation:
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# Tub
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_VPost: TUB [ full: 50x, active: 0x, empty: 10x ]
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# Behaviour
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$: BEHAVIOUR [ behaviour: MAIN_DBRANCH ]
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```
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---
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@@ -51,85 +72,86 @@ Container: D-BRANCH
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---
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### ms: behaviors BD
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### MAIN_DBRANCH: !DAY
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#### CheckVPost:Context
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```Gen
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MAIN_DBRANCH
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type: behaviour
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within_scope: !DAY
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snippet:
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# *Fixed
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@: CONTEXTOR [ snippet: CheckVPost, rf: active 60x ]
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@: ACCUMULATOR [ snippet: VDBClearance, rf: active 2x ]
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# *VPostMax
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@: ACCUMULATOR [ snippet: VDBMax, rf: active 2x ]
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# *VPostMedium
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@: ACCUMULATOR [ snippet: VDBMed, rf: active 4x ]
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# *VPostLow
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@: ACCUMULATOR [ snippet: VDBMin, rf: active 8x ]
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```
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#### *Fixed
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##### CheckVPost
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Contestualizziamo in maniera Fixed?
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```Gen
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context: CheckVPost
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contained_by: D-BRANCH
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CheckVPost
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type: contextor
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in_context: Fixed
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rf: ( active: 60x )
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condition: (VPost fullness)
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out_context: VPostMax
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condition: (VPost mediumness)
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out_context: VPostMedium
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condition: (VPost emptiness)
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out_context: VPostLow
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in_context: *Fixed
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condition: _VPost fullness
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out_context: *VPostMax
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condition: _VPost mediumness
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out_context: *VPostMedium
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condition: _VPost emptiness
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out_context: *VPostLow
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```
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##### VDBMax: Episode
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```Gen
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episode: VDBMax
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contained_by: D-BRANCH
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in_context: VPostMax
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rf: ( active: 2x )
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hypothesis: NOT (VDB full)
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action: [VDB increase]
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trace:
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```
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##### VDBMed: Episode
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```Gen
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episode: VDBMed
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contained_by: D-BRANCH
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in_context: VPostMed
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rf: ( active: 2x )
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hypothesis: NOT (VDB full)
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action: [VDB increase]
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trace:
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```
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##### VDBLow: Episode
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```Gen
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episode: VDBLow
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contained_by: D-BRANCH
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in_context: VPostLow
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rf: ( active: 2x )
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hypothesis: NOT (VDB full)
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action: [VDB increase]
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trace:
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```
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#### VDBlearance: Episode
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##### VDBClearance
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Qui facciamo il clearance del VDB. Lo facciamo in questo modo perche' abbiamo semplificato quello che succede fra BD e SOMA.
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Qui posso aggiungere il flush, clearance veloce quando c'e' il bAP.
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```Gen
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episode: VDBClearance
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contained_by: D-BRANCH
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VDBClearance
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in_context: *Fixed
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in_context: Fixed
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rf: ( active: 2x )
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hypothesis: NOT (VDB empty)
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action: [VDB decrease]
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hypothesis: NOT _VDB empty
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action: [ _VDB decrease ]
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trace:
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```
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#### *VPostMax
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##### VDBMax
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```Gen
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VDBMax
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in_context: *VPostMax
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hypothesis: NOT _VDB full
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action: [ _VDB increase ]
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trace:
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```
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#### *VPostMedium
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##### VDBMed
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```Gen
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VDBMed
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in_context: *VPostMedium
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hypothesis: NOT _VDB full
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action: [ _VDB increase ]
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||||
trace:
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||||
```
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#### *VPostLow
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##### VDBLow
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```Gen
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in_context: *VPostLow
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||||
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||||
hypothesis: NOT _VDB full
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||||
action: [ _VDB increase ]
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trace:
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||||
```
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@@ -0,0 +1,71 @@
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---
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||||
include_toc: true
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||||
---
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||||
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||||
# post_ampa.md
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## POST-AMPA
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Intro:
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||||
- is expanded and tuned by: [POSTSYNAPSE](postsynapse.md)
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```Gen
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POST-AMPA
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type: comprehension
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||||
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||||
expansion:
|
||||
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intrication:
|
||||
# Scope
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!DAY: INTRICATION [ ref: &ORGANISM.!DAY ]
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!NIGHT: INTRICATION [ ref: &ORGANISM.!NIGHT ]
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# Context
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*bAP: INTRICATION [ ref: &SOMA.*bAP ]
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# Tub
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_NT: INTRICATION [ ref: &ASTROSYNAPSE._NT ]
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_Na: INTRICATION [ ref: &POSTSYNAPSE._Na ]
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instantiation:
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$: BEHAVIOUR [ behaviour: POST-AMPA-BHE ]
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||||
|
||||
```
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||||
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||||
### POST-AMPA: !DAY
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```Gen
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||||
POST-AMPA-BHE
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||||
type: behavior
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||||
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||||
within_scope: !DAY
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snippet:
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# NOT *bAP
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@: ACCUMULATOR [ snippet: NaInAMPAMax, rf: active 2x ]
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||||
@: ACCUMULATOR [ snippet: NaInAMPAMed, rf: active 4x ]
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||||
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||||
```
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#### NOT *bAP
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||||
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||||
##### NaInAMPAMax
|
||||
```Gen
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||||
NaInAMPAMax
|
||||
type: accumulator
|
||||
|
||||
in_context: NOT *bAP
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||||
hypothesis: _NT fullness
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||||
action: [ _Na increase ]
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||||
trace:
|
||||
```
|
||||
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||||
##### NaInAMPAMed
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||||
```Gen
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||||
NaInAMPAMed
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||||
type: accumulator
|
||||
|
||||
in_context: NOT *bAP
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||||
hypothesis: _NT mediumness
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action: [ _Na increase ]
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||||
trace:
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||||
```
|
||||
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||||
+31
-119
@@ -39,64 +39,31 @@ Qui comprendiamo:
|
||||
|
||||
---
|
||||
|
||||
**G expression**:
|
||||
|
||||
```Gen
|
||||
|
||||
*bAP
|
||||
POSTSYNAPSE (ms)
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||||
-- Ca Influx
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||||
CaNDMAEnterMax: ( active: 2x ) accumulator
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CaNDMAEnterMed: ( active: 4x ) accumulator
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||||
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NOT *bAP:
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||||
POSTSYNAPSE (ms)
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||||
-- Ca Influx
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||||
CaNDMAEnterMedNotBap: ( active: 4x ) accumulator
|
||||
CaNDMAEnterLow: ( active: 12x ) accumulator
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-- Ca Clearence
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CaClearance: ( active: 24x ) accumulator
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-- V Influx
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VPostMax: ( active: 4x ) accumulator ->VPost
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||||
VPostMed: ( active: 8x ) accumulator ->VPost
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||||
VPostLow: ( active: 16x ) accumulator ->VPost
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||||
-- V Clearence
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||||
VPostClearance: ( active: 18x ) accumulator ~->VPost
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||||
POST-AMPA (ms) ~ NT
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-- Na Influx
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||||
NaAMPAEnterMax: ( active: 2x ) accumulator ~NT
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||||
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
|
||||
|
||||
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
|
||||
|
||||
|
||||
|
||||
##### 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:
|
||||
```
|
||||
|
||||
@@ -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.
|
||||
|
||||
Reference in New Issue
Block a user