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fixed markdown with lint

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2026-03-08 10:01:18 +01:00
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astrocyte/AST.md
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# AST: Comprehension # AST: Comprehension
Qui comprendiamo Astrocyte, sia BEH, che TUN e DEV
Qui comprendiamo Astrocyte, sia BEH, che TUN e DEV
```Gen ```Gen
comprehension: AST comprehension: AST
include: include:
- BEH-AST.md - BEH-AST.md
- TUN-AST.md - TUN-AST.md
- DEV-AST.md - DEV-AST.md
``` ```
astrocyte/BEH-AST.md
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# BEH-AST.md
Qui comprendiamo: Qui comprendiamo:
- BEH-AST: Astrocyte - BEH-AST: Astrocyte
# BEH-AST: Container ## BEH-AST: Container
**Astrocyte**
```Gen ```Gen
container: BEH-AST container: BEH-AST
expansion: expansion:
- BEH-SYN ( fullness: indef, active: indef, emptiness: 0x ) - BEH-SYN ( fullness: indef, active: indef, emptiness: 0x )
``` ```
Modulated by: [[TUN-AST]] Modulated by: [[TUN-AST]]
## Leakage: Context ### Leakage: Context
### ???: Episode
## ???: Episode
astrocyte/DEV-AST.md
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# DEV-AST.md
Qui mettiamo la creazione o la distruzione di SYN. Il ragionamento qui e' tutto fa il network di Astocytes, tipo se c'e' abbastanza ATP o cose del genere. Qui mettiamo la creazione o la distruzione di SYN. Il ragionamento qui e' tutto fa il network di Astocytes, tipo se c'e' abbastanza ATP o cose del genere.
E' la creazione di nuove SYN che permette poi al TUN-AST di attivare la SYN, se c'e' la possibilita' fra PRE e POST. E' la creazione di nuove SYN che permette poi al TUN-AST di attivare la SYN, se c'e' la possibilita' fra PRE e POST.
astrocyte/TUN-AST.md
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# TUN-AST.md
Qui mettiamo l'attivazione/disattivazione di una SYN possibile, messa a disposizione dal DEV-AST. Qui mettiamo l'attivazione/disattivazione di una SYN possibile, messa a disposizione dal DEV-AST.
Il ragionamento e' fra la possibilita' di SYN, e le possibilita' di PRE e POST. Il ragionamento e' fra la possibilita' di SYN, e le possibilita' di PRE e POST.
La novita' e' lo SCOPE, nel quale avviene il ragionamento. La novita' e' lo SCOPE, nel quale avviene il ragionamento.
# TUN-AST: Modulator ## TUN-AST: Modulator
... ...
```Gen ```Gen
modulator: TUN-AST modulator: TUN-AST
contained_by: AREA1 contained_by: AREA1
modulates: BEH-AXO/expansion/BEH-PRE modulates: BEH-AXO/expansion/BEH-PRE
# #
tub_modulation: # tub_modulation: #
- prePossible ( N/BEH-AXO/BEH-PRE/possible ) - prePossible ( N/BEH-AXO/BEH-PRE/possible )
- preActual ( N/BEH-AXO/BEH-PRE/actual ) - preActual ( N/BEH-AXO/BEH-PRE/actual )
- postPossible ( N/BEH-BD/BEH-POST/possible ) - postPossible ( N/BEH-BD/BEH-POST/possible )
- postActual ( N/BEH-BD/BEH-POST/actual ) - postActual ( N/BEH-BD/BEH-POST/actual )
- synPossible ( AST/BEH-AST/SYN/actual ) - synPossible ( AST/BEH-AST/SYN/actual )
- synActual ( AST/BEH-AST/SYN/actual ) - synActual ( AST/BEH-AST/SYN/actual )
tub_local: tub_local:
- ??? (fullness: 50x, active: 0x, emptiness: 0x) - ??? (fullness: 50x, active: 0x, emptiness: 0x)
# intricated with ??? # intricated with ???
``` ```
Forse con questi tub_modulation riesco a risolvere il problema dello SCOPE, perche' mi servono a mettere assieme scope diversi, quelli di PRE, POST e SYN. Forse con questi tub_modulation riesco a risolvere il problema dello SCOPE, perche' mi servono a mettere assieme scope diversi, quelli di PRE, POST e SYN.
## ??: Context ### ??: Context
.... ....
```Gen ```Gen
context: ??? context: ???
contained_by: TUN-AST contained_by: TUN-AST
in_context: Fixed in_context: Fixed
rf: 60x rf: 60x
condition: ( ??? Empty ) # condition: ( ??? Empty ) #
out_context: ??? out_context: ???
``` ```
## Activate: Episode ### Activate: Episode
.... ....
```Gen ```Gen
@@ -54,6 +59,6 @@ episode: activate
rf: ( active: 6x ) rf: ( active: 6x )
hypothesis: NOT (?? empty) hypothesis: NOT (?? empty)
action: [??? decrease] action: [??? decrease]
trace: None trace: None
``` ```
neuron/BEH-AXO.md
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# BEH-AXO.md
## BEH-AXO: Container
Qui comprendiamo: Qui comprendiamo:
- BEH-AXO: Axon - BEH-AXO: Axon
- BEH-PRE: Presynapse - BEH-PRE: Presynapse
- BEH-VCGG: Voltage-Controlled Gated Channels - BEH-VCGG: Voltage-Controlled Gated Channels
# BEH-AXO: Container
**Axon**: Axon does not contain specific behavior, here we comprehend it as a “cable” transporting the AP from SOMA to Presynapse. It expands BEH-PRE which can be Modulated (TUN). **Axon**: Axon does not contain specific behavior, here we comprehend it as a “cable” transporting the AP from SOMA to Presynapse. It expands BEH-PRE which can be Modulated (TUN).
```Gen ```Gen
container: BEH-AXO container: BEH-AXO
expansion: expansion:
- BEH-PRE ( fullness: 50x, active: 20x, emptiness: 10x ) - BEH-PRE ( fullness: 50x, active: 20x, emptiness: 10x )
# modulated_by: TUN-SYN-AXO-PRE# possible/actual # modulated_by: TUN-SYN-AXO-PRE# possible/actual
``` ```
# BEH-PRE: Container ## BEH-PRE: Container
**Presynapse:** We treat each presynapse as standalone. The vesicle reserve pool is a strictly private, local resource of each individual presynaptic bouton. What is shared between synapses on the same axon are signals (neuromodulators) and metabolic resources (energy), but not the synaptic vesicles themselves. This ensures both independent computation and cooperative metabolic support within the axonal branch. **Presynapse:** We treat each presynapse as standalone. The vesicle reserve pool is a strictly private, local resource of each individual presynaptic bouton. What is shared between synapses on the same axon are signals (neuromodulators) and metabolic resources (energy), but not the synaptic vesicles themselves. This ensures both independent computation and cooperative metabolic support within the axonal branch.
**Tubs:** **Tubs:**
- Ca2+: Calcium Ion entering the Presynapse when VCGG open. They are key to check the concentration, release vescicles and modulation - Ca2+: Calcium Ion entering the Presynapse when VCGG open. They are key to check the concentration, release vescicles and modulation
- Rrp: Readily Releasable Pool - Rrp: Readily Releasable Pool
The Readily Releasable Pool consists of the vesicles that are "docked" and "primed" at the active zone of the synapse. The Readily Releasable Pool consists of the vesicles that are "docked" and "primed" at the active zone of the synapse.
@@ -40,6 +45,7 @@ Characteristics: This makes up the vast majority of the vesicles (up to 80% or 9
**Behaviors**: **Behaviors**:
L'idea e' che: L'idea e' che:
- Fast - Fast
-- i VCGG si aprano all'arrivo di un AP dal SOMA. Il numero dei VCGG presenti e' stato modulato (TUN) in una fase di non attivita' della presynapse -- i VCGG si aprano all'arrivo di un AP dal SOMA. Il numero dei VCGG presenti e' stato modulato (TUN) in una fase di non attivita' della presynapse
-- I VCGG fanno entrare Ca2+ che ne aumenta la concentrazione -- I VCGG fanno entrare Ca2+ che ne aumenta la concentrazione
@@ -60,13 +66,13 @@ container: BEH-PRE
tub_local: tub_local:
- Ca2+ ( fullness: 60x, active: 30x, emptiness: 0x ) - Ca2+ ( fullness: 60x, active: 30x, emptiness: 0x )
# modulated_by: DEV-PRE-CA2+FULL # Full # modulated_by: DEV-PRE-CA2+FULL # Full
- Rrp ( fullness: 30x, active: 15x, emptiness: 0x ) - Rrp ( fullness: 30x, active: 15x, emptiness: 0x )
# modulated_by: DEV-PRE-RRP-FULL # Full # modulated_by: DEV-PRE-RRP-FULL # Full
- Rp ( fullness: 30x, active: 15x, emptiness: 0x ) - Rp ( fullness: 30x, active: 15x, emptiness: 0x )
# modulated_by: DEV-PRE-RRP-FULL # Full # modulated_by: DEV-PRE-RRP-FULL # Full
- TagRelease ( fullness: 1x, active: 0x, emptiness: 0x ) - TagRelease ( fullness: 1x, active: 0x, emptiness: 0x )
@@ -77,7 +83,8 @@ container: BEH-PRE
``` ```
## IntegrateCa2+: Context ### IntegrateCa2+: Context
Qui verifichiamo il livello di CA2+ nella presynapse. I comportamenti nella presinapsi dipendo tutti da questa concentrazione, sia quelli immediati di rilascio NT da vescicles che quelli di modulazione. Qui verifichiamo il livello di CA2+ nella presynapse. I comportamenti nella presinapsi dipendo tutti da questa concentrazione, sia quelli immediati di rilascio NT da vescicles che quelli di modulazione.
***Tens Milliseconds Time Scale*** ***Tens Milliseconds Time Scale***
@@ -90,16 +97,16 @@ context: IntegrateCa2+
rf: ( active: 60x ) rf: ( active: 60x )
condition: (Ca2+ empty) condition: (Ca2+ empty)
out_context: CaEmpty out_context: CaEmpty
condition: NOT (Ca2+ empty) AND NOT (Ca2+ full) condition: NOT (Ca2+ empty) AND NOT (Ca2+ full)
out_context: CaMedium out_context: CaMedium
condition: (Ca2+ full) condition: (Ca2+ full)
out_context: CaFull out_context: CaFull
``` ```
## VescicleRelease: Episode ### VescicleRelease: Episode
Il rilascio di NT avviene solo se Ca+ FULLNESS? Ovviamente se ci sono Vesciche. O dipende da altro? Cioe’ cosi’ rilascerebbe tutte le vesciche se c’e’ fullness. Dovremmo mettere un tag, o una discesa improvvisa di Ca+ al release di una vescica. Perche’ potremmo avere il caso che i VGGC sia talmente tanti da far entrare tanto calcio da far si che la prima vescica consumi CA ma non abbastanza da andare sotto FULLNESS Il rilascio di NT avviene solo se Ca+ FULLNESS? Ovviamente se ci sono Vesciche. O dipende da altro? Cioe’ cosi’ rilascerebbe tutte le vesciche se c’e’ fullness. Dovremmo mettere un tag, o una discesa improvvisa di Ca+ al release di una vescica. Perche’ potremmo avere il caso che i VGGC sia talmente tanti da far entrare tanto calcio da far si che la prima vescica consumi CA ma non abbastanza da andare sotto FULLNESS
@@ -120,12 +127,12 @@ episode: VescicleRelease
rf: ( active: 6x ) rf: ( active: 6x )
hypothesis: (Ca2+ full) AND NOT (Rrp empty) hypothesis: (Ca2+ full) AND NOT (Rrp empty)
action: [Rrp decrease, Nt increase, Ca2+ decrease, action: [Rrp decrease, Nt increase, Ca2+ decrease,
TagRelease increase] TagRelease increase]
trace: None trace: None
``` ```
## Ca+ClearenceSlow: Episode ### Ca+ClearenceSlow: Episode
Svuotiamo a due velocita’. Il context (Check Ca+ concentration) e’ determinato a epoca piu’ lunga, tanto ci vuole qualche giro per fare entrare i primi Ca+ Svuotiamo a due velocita’. Il context (Check Ca+ concentration) e’ determinato a epoca piu’ lunga, tanto ci vuole qualche giro per fare entrare i primi Ca+
Le tracce lasciate servono alla modulazione Le tracce lasciate servono alla modulazione
@@ -140,11 +147,12 @@ episode: Ca+ClearenceSlow
rf: ( active: 6x ) rf: ( active: 6x )
hypothesis: NOT (Ca+ empty) AND NOT (Ca+ full) hypothesis: NOT (Ca+ empty) AND NOT (Ca+ full)
action: [Ca+ decrease, CaTraces Increase] action: [Ca+ decrease, CaTraces Increase]
trace: None trace: None
``` ```
## Ca+ClearenceFast: Episode ### Ca+ClearenceFast: Episode
Qui l'idea oltre che a fare clearance e' anche quella di lasciare tracce su che livello di Ca2+ c'e' stato durante gli episodi. Un livello medio lascia meno tracce di un livello alto, e questo serve a ragionare sulla modulazione. Qui l'idea oltre che a fare clearance e' anche quella di lasciare tracce su che livello di Ca2+ c'e' stato durante gli episodi. Un livello medio lascia meno tracce di un livello alto, e questo serve a ragionare sulla modulazione.
Clearance mechanisms (in order of speed): Clearance mechanisms (in order of speed):
@@ -165,8 +173,8 @@ episode: Ca+ClearenceFast
rf: ( active: 1x ) rf: ( active: 1x )
condition: (Ca2+ full) condition: (Ca2+ full)
action: [Ca2+ decrease, CaTraces Increase] action: [Ca2+ decrease, CaTraces Increase]
trace: None trace: None
``` ```
```Gen ```Gen
@@ -178,25 +186,26 @@ episode: Ca+ClearenceMedium
rf: ( active: 1x ) rf: ( active: 1x )
hypothesis: NOT (Ca2+ full) AND NOT (Ca2+ empty) hypothesis: NOT (Ca2+ full) AND NOT (Ca2+ empty)
action: [Ca2+ decrease, CaTraces Increase] action: [Ca2+ decrease, CaTraces Increase]
trace: None trace: None
``` ```
## STP - Pr Upregulation: Observable ### STP - Pr Upregulation: Observable
**Observed behavior** **Observed behavior**
Upregulation (Facilitation): Residual Ca²⁺ from previous spikes increases P_r for next release Upregulation (Facilitation): Residual Ca²⁺ from previous spikes increases P_r for next release
***Timing: > 10 ms*** ***Timing: > 10 ms***
## STD - Pr Downregulation: Observable ### STD - Pr Downregulation: Observable
**Observed behavior** **Observed behavior**
Downregulation (Depression): High-frequency firing depletes readily releasable vesicle pool, decreasing P_r Downregulation (Depression): High-frequency firing depletes readily releasable vesicle pool, decreasing P_r
***Timing: > 10 ms*** ***Timing: > 10 ms***
## VesciclesRecycling: Episode ### VesciclesRecycling: Episode
Dobbiamo capire se lasciare il recicling RecP oppure avere solo un Rp, almeno al primo giro di comprensione, per semplificare. Dobbiamo capire se lasciare il recicling RecP oppure avere solo un Rp, almeno al primo giro di comprensione, per semplificare.
Sequential steps: Sequential steps:
@@ -217,12 +226,12 @@ episode: VesciclesRecycling
in_context: in_context:
rf: ( fullness: 10x, active: 5x, emptiness: 2x ) rf: ( fullness: 10x, active: 5x, emptiness: 2x )
# si parte con active, poi viene modulato # si parte con active, poi viene modulato
# modulated_by: DEV-PRE-VesciclesRecycling-RF # modulated_by: DEV-PRE-VesciclesRecycling-RF
hypothesis: hypothesis:
``` ```
## VescicleFromRPtoRRP-Slow: Episode ### VescicleFromRPtoRRP-Slow: Episode
Superpriming requires ATP for phosphorylation reactions and for molecular motors that move vesicles. If the reserve pool is depleted or ATP is low, the superpriming "conveyor belt" has nothing to feed into the RRP. (Astrocyte) Superpriming requires ATP for phosphorylation reactions and for molecular motors that move vesicles. If the reserve pool is depleted or ATP is low, the superpriming "conveyor belt" has nothing to feed into the RRP. (Astrocyte)
@@ -240,11 +249,11 @@ episode: VescicleFromRPtoRRP-Slow
rf: ( active: 30x ) rf: ( active: 30x )
hypothesis: NOT (RP empty) hypothesis: NOT (RP empty)
action: [RP decrease, RRP increase] action: [RP decrease, RRP increase]
trace: None trace: None
``` ```
## VescicleFromRPtoRRP-Medium: Episode ### VescicleFromRPtoRRP-Medium: Episode
***Seconds-Minutes Time Scale*** ***Seconds-Minutes Time Scale***
@@ -256,11 +265,11 @@ episode: VescicleFromRPtoRRP-Medium
rf: ( active: 15x ) rf: ( active: 15x )
hypothesis: NOT (RP empty) hypothesis: NOT (RP empty)
action: [RP decrease, RRP increease] action: [RP decrease, RRP increease]
trace: None trace: None
``` ```
## VescicleFromRPtoRRP-Fast: Episode ### VescicleFromRPtoRRP-Fast: Episode
***Seconds-Minutes Time Scale*** ***Seconds-Minutes Time Scale***
@@ -275,7 +284,8 @@ episode: VescicleFromRPtoRRP-Fast
action: [RP decrease, RRP increase] action: [RP decrease, RRP increase]
trace: None trace: None
``` ```
## VesiclesFillingRP: Episode
### VesiclesFillingRP: Episode
Qui riempiamo le vesciche. Fino ad un numero massimo, che viene modulato in DEV Qui riempiamo le vesciche. Fino ad un numero massimo, che viene modulato in DEV
@@ -287,12 +297,12 @@ episode: VesiclesFillingRP
in_context: AwayFromSpike in_context: AwayFromSpike
rf: ( fullness: 100x, active: 60x, emptiness: 30x ) rf: ( fullness: 100x, active: 60x, emptiness: 30x )
# modulated_by: DEV-PRE-VesiclesFillingRP-RF # RF # modulated_by: DEV-PRE-VesiclesFillingRP-RF # RF
hypothesis: hypothesis:
``` ```
# BEH-PRE-VGCC: Container ## BEH-PRE-VGCC: Container
**Voltage Gated Ion Channels**: When an AP arrives from the SOMA, VCGG are opened and they let in CA2+ initiating the possible release of NT from the vescicles. In theory each RRP has its own VCGG nearby. We do not comprehend this, but consider VCGG shared between all the RPP of the presynapse (we impose a floor) **Voltage Gated Ion Channels**: When an AP arrives from the SOMA, VCGG are opened and they let in CA2+ initiating the possible release of NT from the vescicles. In theory each RRP has its own VCGG nearby. We do not comprehend this, but consider VCGG shared between all the RPP of the presynapse (we impose a floor)
@@ -300,13 +310,13 @@ episode: VesiclesFillingRP
container: BEH-PRE-VGCC container: BEH-PRE-VGCC
tub_intricated: tub_intricated:
- Ca2+ ( contained_by: BEH-PRE ) - Ca2+ ( contained_by: BEH-PRE )
context_intricated: context_intricated:
- AP ( contained_by: BEH-SOMA ) - AP ( contained_by: BEH-SOMA )
``` ```
## VgccOpen: Episode ### VgccOpen: Episode
Auto-inhibition? Ca²⁺ binding to calmodulin on VGCC. 5-50 ms Auto-inhibition? Ca²⁺ binding to calmodulin on VGCC. 5-50 ms
@@ -346,6 +356,6 @@ episode: VgccOpen
rf: ( active: 1x ) rf: ( active: 1x )
hypothesis: NOT (Ca2+ full) hypothesis: NOT (Ca2+ full)
action: [Ca2+ increase] action: [Ca2+ increase]
trace: None # Se Ca+FULLNESS, lascio tracce di overflow per modulazione DOWN, da capire UP trace: None # Se Ca+FULLNESS, lascio tracce di overflow per modulazione DOWN, da capire UP
``` ```
neuron/BEH-BD.md
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@@ -1,67 +1,71 @@
# BEH-AXO.md
Qui comprendiamo: Qui comprendiamo:
- BEH-BD: Dendritic Branch - BEH-BD: Dendritic Branch
- BEH-POST: Postsynapsis - BEH-POST: Postsynapsis
- BEH-POST-AMPA: AMPA receptors (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors) - BEH-POST-AMPA: AMPA receptors (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors)
# BEH-BD: Container ## BEH-BD: Container
**Dendritic Branch**: In questa prima fase, non consideriamo lo spike dendritico come comportamento. Questo limita molto il modello, perche' equipara tutte le Postsinapsi sui tre branch dendritici e non permette di fare in maniera che ad esempio due branch contestualizzino (base activity) e uno faccia scattare il threshold per lo spike somatico. **Dendritic Branch**: In questa prima fase, non consideriamo lo spike dendritico come comportamento. Questo limita molto il modello, perche' equipara tutte le Postsinapsi sui tre branch dendritici e non permette di fare in maniera che ad esempio due branch contestualizzino (base activity) e uno faccia scattare il threshold per lo spike somatico.
Qui BEH-DB espande solo i BEH-POST, e' un cavo di collegamento come l'assone Qui BEH-DB espande solo i BEH-POST, e' un cavo di collegamento come l'assone
```Gen ```Gen
Container: BEH-BD Container: BEH-BD
expansion: expansion:
- BEH-POST ( fullness: 50x, active: 20x, emptiness: 10x ) - BEH-POST ( fullness: 50x, active: 20x, emptiness: 10x )
# modulated_by: TUN-SYN-BD-POST possible/actual # modulated_by: TUN-SYN-BD-POST possible/actual
``` ```
## BEH-POST: Container ### BEH-POST: Container
```Gen ```Gen
container: BEH-POST container: BEH-POST
expansion: expansion:
- BEH-POST-AMPA ( fullness: 10x, active: 5x, emptiness: 2x ) - BEH-POST-AMPA ( fullness: 10x, active: 5x, emptiness: 2x )
# modulated_by: TUN-POST-IC # possible/actual # modulated_by: TUN-POST-IC # possible/actual
tub_local: tub_local:
- Ca2+ ( fullness: 60x, active: 30x, emptiness: 0x ) - Ca2+ ( fullness: 60x, active: 30x, emptiness: 0x )
# modulated_by: DEV-POST-???-FULL # Full # modulated_by: DEV-POST-???-FULL # Full
- Nox ( fullness: 100x, active: 20x, emptiness: 0x ) # Nitric Oxide (NO): A gas that diffuses freely. - Nox ( fullness: 100x, active: 20x, emptiness: 0x ) # Nitric Oxide (NO): A gas that diffuses freely.
- Ecb ( fullness: 100x, active: 20x, emptiness: 0x ) # Endocannabinoids (e.g., 2-AG) - Ecb ( fullness: 100x, active: 20x, emptiness: 0x ) # Endocannabinoids (e.g., 2-AG)
tub_intricated: tub_intricated:
- Nt ( contained_by: BEH-SYN ) - Nt ( contained_by: BEH-SYN )
- bAp ( contained_by: BEH-SOMA ) - bAp ( contained_by: BEH-SOMA )
``` ```
### Context #### Context
```Gen ```Gen
context: captureNt context: captureNt
contained_by: BEH-POST contained_by: BEH-POST
in_context: Fixed in_context: Fixed
rf: ( active: 10x ) rf: ( active: 10x )
condition: (Nt full) AND NOT (bAp) condition: (Nt full) AND NOT (bAp)
out_context: NtCaptured out_context: NtCaptured
``` ```
### Episode #### Episode
### BEH-POST-AMPA: Container ## BEH-POST-AMPA: Container
```Gen ```Gen
container: BEH-POST-AMPA container: BEH-POST-AMPA
tub_intricated: tub_intricated:
- Nt ( contained_by: BEH-SYN ) - Nt ( contained_by: BEH-SYN )
context_intricated: context_intricated:
- bAp ( contained_by: BEH-SOMA ) - bAp ( contained_by: BEH-SOMA )
``` ```
#### AmpaOpen: Episode #### AmpaOpen: Episode
@@ -80,8 +84,8 @@ episode: AmpaOpen
rf: ( active: 1x ) rf: ( active: 1x )
hypothesis: NOT (Ca2+ full) hypothesis: NOT (Ca2+ full)
action: [Ca2+ increase] action: [Ca2+ increase]
trace: None # Se Ca+FULLNESS, lascio tracce di overflow per modulazione DOWN, da capire UP trace: None # Se Ca+FULLNESS, lascio tracce di overflow per modulazione DOWN, da capire UP
``` ```
### Depolarization by bAP ### Depolarization by bAP
@@ -112,5 +116,3 @@ Da ricordare i Dendritic VCGG che si aprono facendo entrare Ca2+ all'arrivo di b
### Downregulation: Observable ### Downregulation: Observable
- Downregulation: AMPA desensitization acts as low-pass filter - Downregulation: AMPA desensitization acts as low-pass filter
##
neuron/BEH-N.md
+4 -4
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@@ -7,8 +7,8 @@ Questo container serve solo ad espandere AXO, SOMA e DB.
```Gen ```Gen
container: BEH-N container: BEH-N
expansion: expansion:
- BEH-AXO ( active: 1x ) - BEH-AXO ( active: 1x )
- BEH-SOMA ( active: 1x ) - BEH-SOMA ( active: 1x )
- BEH-DB ( active: 3x ) - BEH-DB ( active: 3x )
``` ```
neuron/BEH-SOMA.md
+13 -13
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@@ -4,11 +4,11 @@
container: BEH-SOMA container: BEH-SOMA
expansion: expansion:
- BEH-SOMA-VCGG ( fullness: 50x, active: 20x, emptiness: 10x ) - BEH-SOMA-VCGG ( fullness: 50x, active: 20x, emptiness: 10x )
# modulated_by: TUN-SOMA-VCGG # possible/actual # modulated_by: TUN-SOMA-VCGG # possible/actual
tub_intricated: tub_intricated:
- SpikeTrainTraces ( contained_by: TUN-N ) - SpikeTrainTraces ( contained_by: TUN-N )
``` ```
## Context ## Context
@@ -17,13 +17,13 @@ Qui mettiamo lo spike Dendritico. Sempre se vogliamo comprenderlo.
```Gen ```Gen
context: ???... context: ???...
contained_by: BEH-SOMA contained_by: BEH-SOMA
in_context: Fixed in_context: Fixed
rf: 60x rf: 60x
condition: condition:
activate: xxx activate: xxx
``` ```
## Episode ## Episode
@@ -36,8 +36,8 @@ episode: ??
rf: ( active: 1x ) rf: ( active: 1x )
hypothesis: hypothesis:
action: action:
trace: None trace: None
``` ```
## BEH-SOMA-VCGG: Container ## BEH-SOMA-VCGG: Container
@@ -57,8 +57,8 @@ episode: ??
rf: ( active: 1x ) rf: ( active: 1x )
hypothesis: hypothesis:
action: action:
trace: None trace: None
``` ```
## ##
neuron/DEV-N.md
+42 -42
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@@ -52,23 +52,23 @@ modulator: DEV-RF
```Gen ```Gen
modulator: DEV-PRE-VesciclesRecycling-RF modulator: DEV-PRE-VesciclesRecycling-RF
contained_by: DEV-RF contained_by: DEV-RF
modulates: BEH-PRE/episode/VesciclesRecycling modulates: BEH-PRE/episode/VesciclesRecycling
# each BEH-PRE is modulated! # each BEH-PRE is modulated!
tub_dev: tub_dev:
- fulMod ( fullness: None, active: rf/fullness, emptiness: 0x ) - fulMod ( fullness: None, active: rf/fullness, emptiness: 0x )
- actMod ( fullness: None, active: rf/active, emptiness: 0x ) - actMod ( fullness: None, active: rf/active, emptiness: 0x )
# qui stiamo modulando l'active di RF mantenendolo fra fullness e # qui stiamo modulando l'active di RF mantenendolo fra fullness e
# emptiness dichiarato in VesciclesRecycling # emptiness dichiarato in VesciclesRecycling
tub_local: tub_local:
tub_intricated: tub_intricated:
- Nox ( contained_by: BEH-POST ) - Nox ( contained_by: BEH-POST )
- Ecb ( contained_by: BEH-POST ) - Ecb ( contained_by: BEH-POST )
``` ```
#### Context #### Context
@@ -79,15 +79,15 @@ modulator: DEV-PRE-VesciclesRecycling-RF
```Gen ```Gen
modulator: DEV-PRE-VesiclesFillingRP-RF modulator: DEV-PRE-VesiclesFillingRP-RF
contained_by: DEV-RF contained_by: DEV-RF
modulates: modulates:
tub_local: tub_local:
tub_intricated: tub_intricated:
- Nox ( contained_by: BEH-POST ) - Nox ( contained_by: BEH-POST )
- Ecb ( contained_by: BEH-POST ) - Ecb ( contained_by: BEH-POST )
``` ```
#### Context #### Context
@@ -98,15 +98,15 @@ modulator: DEV-PRE-VesiclesFillingRP-RF
```Gen ```Gen
modulator: DEV-PRE-LactateAtp-RF modulator: DEV-PRE-LactateAtp-RF
contained_by: DEV-RF contained_by: DEV-RF
modulates: modulates:
tub_local: tub_local:
tub_intricated: tub_intricated:
- Nox ( contained_by: BEH-POST ) - Nox ( contained_by: BEH-POST )
- Ecb ( contained_by: BEH-POST ) - Ecb ( contained_by: BEH-POST )
``` ```
#### Context #### Context
@@ -126,21 +126,21 @@ modulator: DEV-FULL
```Gen ```Gen
modulator: DEV-PRE-CA2+-FULL modulator: DEV-PRE-CA2+-FULL
contained_by: DEV-FULL contained_by: DEV-FULL
modulates: BEH-PRE/tub/Ca2+ # this is the tub whose "full" must be modulated modulates: BEH-PRE/tub/Ca2+ # this is the tub whose "full" must be modulated
tub_dev: tub_dev:
- fullMod ( fullness: 100x, active: Ca2+/fullness, emptiness: 50x ) # Ca2+Full "contains" a number of blocks equal to the current Full. - fullMod ( fullness: 100x, active: Ca2+/fullness, emptiness: 50x ) # Ca2+Full "contains" a number of blocks equal to the current Full.
# qui stiamo modulando la fullness di Ca2+, associandola ad # qui stiamo modulando la fullness di Ca2+, associandola ad
# active di fullMod. Cambiando active di fullMod, # active di fullMod. Cambiando active di fullMod,
# si cambia la fullness di Ca2+ # si cambia la fullness di Ca2+
tub_local: tub_local:
tub_intricated: tub_intricated:
- Nox ( contained_by: BEH-POST ) - Nox ( contained_by: BEH-POST )
- Ecb ( contained_by: BEH-POST ) - Ecb ( contained_by: BEH-POST )
``` ```
#### Context #### Context
@@ -155,13 +155,13 @@ context: CheckPreTubCa2+
rf: 60x rf: 60x
condition: ( empty ) condition: ( empty )
out_context: DecreaseFull out_context: DecreaseFull
condition: NOT ( empty ) AND NOT ( Ca2+ full ) condition: NOT ( empty ) AND NOT ( Ca2+ full )
out_context: Nothing out_context: Nothing
condition: ( full) condition: ( full)
out_context: IncreaseFull out_context: IncreaseFull
``` ```
#### Episode #### Episode
@@ -174,29 +174,29 @@ episode: VgccOpen
rf: 1x rf: 1x
hypothesis: NOT ( full ) AND NOT ( empty ) hypothesis: NOT ( full ) AND NOT ( empty )
action: [ increase, decrease] action: [ increase, decrease]
trace: None trace: None
``` ```
### DEV-PRE-RRP-FULL: Modulator ### DEV-PRE-RRP-FULL: Modulator
```Gen ```Gen
modulator: DEV-PRE-RRP-FULL modulator: DEV-PRE-RRP-FULL
contained_by: DEV-FULL contained_by: DEV-FULL
modulates: BEH-PRE/tub/Rrp # this is the tub whose "full" must be modulated modulates: BEH-PRE/tub/Rrp # this is the tub whose "full" must be modulated
tub_dev: tub_dev:
- fullMod ( fullness: 100x, active: Rrp/fullness, emptiness: 50x ) # RrpFull "contains" a number of blocks equal to the current Full. - fullMod ( fullness: 100x, active: Rrp/fullness, emptiness: 50x ) # RrpFull "contains" a number of blocks equal to the current Full.
# qui stiamo modulando la fullness di Rrp, associandola ad # qui stiamo modulando la fullness di Rrp, associandola ad
# active di fullMod. Cambiando active di fullMod, # active di fullMod. Cambiando active di fullMod,
# si cambia la fullness di Rrp # si cambia la fullness di Rrp
tub_local: tub_local:
tub_intricated: tub_intricated:
- Nox ( contained_by: BEH-POST ) - Nox ( contained_by: BEH-POST )
- Ecb ( contained_by: BEH-POST ) - Ecb ( contained_by: BEH-POST )
``` ```
#### Context #### Context
neuron/README.md
+2
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@@ -1,3 +1,5 @@
# README.md
Il neurone è il concetto che vogliamo comprendere. Partiamo dalla comprensione per espandere i concetti contenuti in N. L’espansione e’ anche di numerosita’ (ad esempio BEH-N espande 3 BEH-BD. Accanto all’espansione dei concetti aggiungiamo la modulabilita’ riferita a ciascun concetto (per quelli che scegliamo di voler modulare). In definitiva la comprensione risulta essere un’eterarchia e non una semplice gerarchia. Il neurone è il concetto che vogliamo comprendere. Partiamo dalla comprensione per espandere i concetti contenuti in N. L’espansione e’ anche di numerosita’ (ad esempio BEH-N espande 3 BEH-BD. Accanto all’espansione dei concetti aggiungiamo la modulabilita’ riferita a ciascun concetto (per quelli che scegliamo di voler modulare). In definitiva la comprensione risulta essere un’eterarchia e non una semplice gerarchia.
--- ---
neuron/TUN-N.md
+65 -65
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@@ -8,11 +8,11 @@ Il TUN contiene quei behavior di modulazione che non cambiano la somma (fullness
```Gen ```Gen
modulator: TUN-N modulator: TUN-N
contained_by: N contained_by: N
tub_local: tub_local:
- SpikeTrainTraces (fullness: 50x, active: 0x, emptiness: 0x) - SpikeTrainTraces (fullness: 50x, active: 0x, emptiness: 0x)
# intricated with BEH-SOMA # intricated with BEH-SOMA
``` ```
## IntegrateTunPossibility: Context ## IntegrateTunPossibility: Context
@@ -22,12 +22,12 @@ Qui controlliamo di essere lontani da uno spike train. Siamo in Day con BEH.
```Gen ```Gen
context: IntegrateTunPossibility context: IntegrateTunPossibility
contained_by: TUN-N contained_by: TUN-N
in_context: Fixed in_context: Fixed
rf: 60x rf: 60x
condition: ( SpikeTrainTraces Empty ) # Day condition: ( SpikeTrainTraces Empty ) # Day
out_context: TunPossible out_context: TunPossible
``` ```
## TUN-SYN: Modulator ## TUN-SYN: Modulator
@@ -40,42 +40,42 @@ ATTENZIONE: Questo e POST e’ da cambiare, perche’ c’e’ il passaggio da T
```Gen ```Gen
modulator: TUN-SYN modulator: TUN-SYN
contained_by: TUN-N contained_by: TUN-N
``` ```
### TUN-SYN-AXO-PRE: Modulator ### TUN-SYN-AXO-PRE: Modulator
```Gen ```Gen
modulator: TUN-SYN-AXO-PRE modulator: TUN-SYN-AXO-PRE
contained_by: TUN-SYN contained_by: TUN-SYN
modulates: BEH-AXO/expansion/BEH-PRE modulates: BEH-AXO/expansion/BEH-PRE
# qui stiamo modulando fullness e actual del tub BEH-PRE associandoli # qui stiamo modulando fullness e actual del tub BEH-PRE associandoli
# a tub_modulation prePos e PreAct. # a tub_modulation prePos e PreAct.
tub_modulation: # in TUN agiamo su fullness <-> active tub_modulation: # in TUN agiamo su fullness <-> active
- fulMod ( fullness: None, active: BEH-PRE/fullness, empty: 0x ) # riferimento a possible di BEH-PRE - fulMod ( fullness: None, active: BEH-PRE/fullness, empty: 0x ) # riferimento a possible di BEH-PRE
- actMod ( fullness: None, active: BEH-PRE/active, empty: BEH-PRE/emptiness ) # riferimento a active di BEH-PRE - actMod ( fullness: None, active: BEH-PRE/active, empty: BEH-PRE/emptiness ) # riferimento a active di BEH-PRE
context_intricated: context_intricated:
- TunPossible ( contained_by: TUN-N ) - TunPossible ( contained_by: TUN-N )
tub_local: tub_local:
tub_intricated: tub_intricated:
``` ```
#### Context #### Context
```Gen ```Gen
context: CheckTunSynAxoPrePossibility context: CheckTunSynAxoPrePossibility
contained_by: TUN-SYN-AXO-PRE contained_by: TUN-SYN-AXO-PRE
in_context: TunPossible in_context: TunPossible
rf: ( active: 60x ) rf: ( active: 60x )
condition: condition:
out_context: out_context:
``` ```
#### Episode #### Episode
@@ -88,8 +88,8 @@ episode: TunSynAxoPre
rf: 1x rf: 1x
hypothesis: NOT () AND NOT () hypothesis: NOT () AND NOT ()
action: [ increase, decrease] action: [ increase, decrease]
trace: None trace: None
``` ```
### TUN-SYN-BD-POST: Modulator ### TUN-SYN-BD-POST: Modulator
@@ -97,7 +97,7 @@ episode: TunSynAxoPre
```Gen ```Gen
modulator: TUN-SYN-BD-POST modulator: TUN-SYN-BD-POST
contained_by: TUN-SYN contained_by: TUN-SYN
... ...
``` ```
@@ -114,7 +114,7 @@ Qui si modulano i canali ionici, sia quelli voltage (PRE/POST/SO/altro?) che que
```Gen ```Gen
modulator: TUN-CHAN modulator: TUN-CHAN
contained_by: TUN-N contained_by: TUN-N
``` ```
### TUN-PRE-VGCC: Modulator ### TUN-PRE-VGCC: Modulator
@@ -122,24 +122,24 @@ modulator: TUN-CHAN
```Gen ```Gen
modulator: TUN-PRE-VGCC modulator: TUN-PRE-VGCC
contained_by: TUN-CHAN contained_by: TUN-CHAN
modulates: BEH-PRE/expansion/BEH-PRE-VCGG modulates: BEH-PRE/expansion/BEH-PRE-VCGG
tub_modulation: # in TUN agiamo su POS/ACT tub_modulation: # in TUN agiamo su POS/ACT
- posMod ( fullness: None, active: BEH-PRE-VCGG/fullness, empty: 0x) # riferimento a possible di BEH-PRE-VCGG - posMod ( fullness: None, active: BEH-PRE-VCGG/fullness, empty: 0x) # riferimento a possible di BEH-PRE-VCGG
- actMod ( fullness: None, active: BEH-PRE-VCGG/active, empty: BEH-PRE-VCGG/emptiness) # riferimento a active di BEH-PRE-VCGG - actMod ( fullness: None, active: BEH-PRE-VCGG/active, empty: BEH-PRE-VCGG/emptiness) # riferimento a active di BEH-PRE-VCGG
# qui stiamo modulando possible e actual di BEH-PRE-VCGG associandoli # qui stiamo modulando possible e actual di BEH-PRE-VCGG associandoli
# a posMod e actMod. Non serve associare una fullness perche' # a posMod e actMod. Non serve associare una fullness perche'
# la modulazione e' una pompa fra posMod e actMod e controlliamo # la modulazione e' una pompa fra posMod e actMod e controlliamo
# solo empty # solo empty
context_intricated: context_intricated:
- TunPossible ( contained_by: TUN-N ) - TunPossible ( contained_by: TUN-N )
tub_local: tub_local:
tub_intricated: tub_intricated:
``` ```
#### Context #### Context
@@ -152,7 +152,7 @@ context: Check
rf: ( active: 60x ) rf: ( active: 60x )
condition: condition:
out_context: TunPreVcgg out_context: TunPreVcgg
``` ```
#### Episode #### Episode
@@ -165,8 +165,8 @@ episode: Tun
rf: ( active: x ) rf: ( active: x )
hypothesis: hypothesis:
action: action:
trace: trace:
``` ```
### TUN-POST-AMPA: Modulator ### TUN-POST-AMPA: Modulator
@@ -174,20 +174,20 @@ episode: Tun
```Gen ```Gen
modulator: TUN-POST-AMPA modulator: TUN-POST-AMPA
contained_by: TUN-CHAN contained_by: TUN-CHAN
modulates: BEH-POST/expansion/BEH-POST-IC modulates: BEH-POST/expansion/BEH-POST-IC
tub_modulation: # in TUN agiamo su POS/ACT tub_modulation: # in TUN agiamo su POS/ACT
- posMod ( fullness: None, active: BEH-POST-IC/fullness, empty: 0x) # riferimento a possible di BEH-PRE - posMod ( fullness: None, active: BEH-POST-IC/fullness, empty: 0x) # riferimento a possible di BEH-PRE
- actMod ( fullness: None, active: BEH-POST-IC/active, empty: BEH-POST-IC/emptiness) # riferimento a active di BEH-PRE - actMod ( fullness: None, active: BEH-POST-IC/active, empty: BEH-POST-IC/emptiness) # riferimento a active di BEH-PRE
context_intricated: context_intricated:
- TunPossible ( contained_by: TUN-N ) - TunPossible ( contained_by: TUN-N )
tub_local: tub_local:
tub_intricated: tub_intricated:
``` ```
#### Context #### Context
@@ -200,7 +200,7 @@ context: Check
rf: ( active: 60x ) rf: ( active: 60x )
condition: condition:
out_context: TunPostIc out_context: TunPostIc
``` ```
#### Episode #### Episode
@@ -213,8 +213,8 @@ episode: ?
rf: ( active: x ) rf: ( active: x )
hypothesis: hypothesis:
action: action:
trace: trace:
``` ```
### TUN-SOMA-VCGG: Modulator ### TUN-SOMA-VCGG: Modulator
@@ -222,21 +222,21 @@ episode: ?
```Gen ```Gen
modulator: TUN-SOMA-VCGG modulator: TUN-SOMA-VCGG
contained_by: TUN-CHAN contained_by: TUN-CHAN
modulates: BEH-SOMA/expansion/BEH-SOMA-VCGG modulates: BEH-SOMA/expansion/BEH-SOMA-VCGG
expansion: BEH-SOMA-VCGG expansion: BEH-SOMA-VCGG
tub_modulation: # in TUN agiamo su POS/ACT tub_modulation: # in TUN agiamo su POS/ACT
- posMod ( fullness: None, active: BEH-SOMA-VCGG/fullness, empty: 0x) # riferimento a possible di BEH-PRE - 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 - actMod ( fullness: None, active: BEH-SOMA-VCGG/active, empty: BEH-SOMA-VCGG/emptiness) # riferimento a active di BEH-PRE
context_intricated: context_intricated:
- TunPossible ( contained_by: TUN-N ) - TunPossible ( contained_by: TUN-N )
tub_local: tub_local:
tub_intricated: tub_intricated:
``` ```
#### Context #### Context
@@ -249,7 +249,7 @@ context: Check
rf: ( active: 60x ) rf: ( active: 60x )
condition: condition:
out_context: TunSomaVcgg out_context: TunSomaVcgg
``` ```
#### Episode #### Episode
@@ -262,6 +262,6 @@ episode: ?
rf: ( active: x ) rf: ( active: x )
hypothesis: hypothesis:
action: action:
trace: trace:
``` ```
winnertakeall/BEH-WTA.md
+18 -10
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@@ -1,26 +1,32 @@
# beh-WTA.md
Qui comprendiamo: Qui comprendiamo:
- BEH-WTA - BEH-WTA
# BEH-WTA: Container ## BEH-WTA: Container
**Winner Take All**: **Winner Take All**:
```Gen ```Gen
container: BEH-WTA container: BEH-WTA
expansion: expansion:
INTERNAL-001: INTERNAL-001:
- NEU-001.AXO -[AST-001]-> NEU-003.BD-001, NEU-004.BD-001 - NEU-001.AXO -[AST-001]-> NEU-003.BD-001, NEU-004.BD-001
- NEU-002.AXO -[AST-001]-> NEU-003.BD-001 - NEU-002.AXO -[AST-001]-> NEU-003.BD-001
OUTGOING-001: OUTGOING-001:
- NEU-003.AXO -[@]-> @.BD-001 - NEU-003.AXO -[@]-> @.BD-001
- NEU-004.AXO -[@]-> @.BD-001 - NEU-004.AXO -[@]-> @.BD-001
INCOMING-001: INCOMING-001:
- @.AXO -[@]-> NEU-001.BD-001, NEU-002.BD-001 - @.AXO -[@]-> NEU-001.BD-001, NEU-002.BD-001
- @.AXO -[@]-> NEU-004.BD-001, NEU-003.BD-001 - @.AXO -[@]-> NEU-004.BD-001, NEU-003.BD-001
``` ```
Questo e' il nuovo tipo di espansione che permette di specificare un "circuito" di possibilita'. Questo e' il nuovo tipo di espansione che permette di specificare un "circuito" di possibilita'.
A differenza di BD che espande PRE implicitamente e trattando PRE tutti allo stesso modo, ma comunque mantenendo la gerarchia, e la relazione, qui espandiamo esplicitamente. A differenza di BD che espande PRE implicitamente e trattando PRE tutti allo stesso modo, ma comunque mantenendo la gerarchia, e la relazione, qui espandiamo esplicitamente.
L'espansione: L'espansione:
- dichiara N1 e N2 - dichiara N1 e N2
- dichiara AST1 - dichiara AST1
- collega un N1 con un N2 - collega un N1 con un N2
@@ -29,10 +35,12 @@ L'espansione:
In questo modo abbiamo allargato il concetto di espansione introducendo una sorta di spazialita', che dipende dalla relazione che viene imposta, e puo' essere verifica. In questo modo abbiamo allargato il concetto di espansione introducendo una sorta di spazialita', che dipende dalla relazione che viene imposta, e puo' essere verifica.
Problemi da risolver: Problemi da risolver:
- posso permettere che una PRE e POST dello stesso N possano fare sinapsi. - posso permettere che una PRE e POST dello stesso N possano fare sinapsi.
- vedere come intricare Neuroni fra organi e aree diverse, senza dover citare direttamente i Neurone e gli astrociti dell'altro argano o area. Questo credo sia risolvibile con una possibilita' di connnessione, tipo AST, ma che funziona per interOrgani, chiamabile NET. - vedere come intricare Neuroni fra organi e aree diverse, senza dover citare direttamente i Neurone e gli astrociti dell'altro argano o area. Questo credo sia risolvibile con una possibilita' di connnessione, tipo AST, ma che funziona per interOrgani, chiamabile NET.
In questo caso potremmo specificare: In questo caso potremmo specificare:
- NEU-001.axon.terminal-1 -[excites: ast=AST-001]-> AREA.Input-001 - NEU-001.axon.terminal-1 -[excites: ast=AST-001]-> AREA.Input-001
E questo potrebbe rendere generale l'approccio. E questo potrebbe rendere generale l'approccio.
winnertakeall/WTA.md
+5 -4
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@@ -1,12 +1,13 @@
# WTA: Comprehension # WTA: Comprehension
Qui comprendiamo un primo circuito Winner Take All, sia BEH, che TUN e DEV Qui comprendiamo un primo circuito Winner Take All, sia BEH, che TUN e DEV
```Gen ```Gen
comprehension: WTA comprehension: WTA
include: include:
- BEH-WTA.md - BEH-WTA.md
- TUN-WTA.md - TUN-WTA.md
- DEV-WTA.md - DEV-WTA.md
``` ```