diff --git a/astrocyte/AST.md b/astrocyte/AST.md index ff78ceb..3c28a5c 100644 --- a/astrocyte/AST.md +++ b/astrocyte/AST.md @@ -1,13 +1,13 @@ # AST: Comprehension -Qui comprendiamo Astrocyte, sia BEH, che TUN e DEV +Qui comprendiamo Astrocyte, sia BEH, che TUN e DEV ```Gen comprehension: AST - include: - - BEH-AST.md - - TUN-AST.md - - DEV-AST.md + include: + - BEH-AST.md + - TUN-AST.md + - DEV-AST.md -``` \ No newline at end of file +``` diff --git a/astrocyte/BEH-AST.md b/astrocyte/BEH-AST.md index 699f2ca..cf2203f 100644 --- a/astrocyte/BEH-AST.md +++ b/astrocyte/BEH-AST.md @@ -1,18 +1,20 @@ +# BEH-AST.md + Qui comprendiamo: + - BEH-AST: Astrocyte -# BEH-AST: Container -**Astrocyte** +## BEH-AST: Container ```Gen container: BEH-AST expansion: - - BEH-SYN ( fullness: indef, active: indef, emptiness: 0x ) + - BEH-SYN ( fullness: indef, active: indef, emptiness: 0x ) ``` + Modulated by: [[TUN-AST]] -## Leakage: Context +### Leakage: Context - -## ???: Episode +### ???: Episode diff --git a/astrocyte/DEV-AST.md b/astrocyte/DEV-AST.md index b27243a..7c7a514 100644 --- a/astrocyte/DEV-AST.md +++ b/astrocyte/DEV-AST.md @@ -1,3 +1,5 @@ -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. +# DEV-AST.md -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. \ No newline at end of file +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. diff --git a/astrocyte/TUN-AST.md b/astrocyte/TUN-AST.md index 4779902..69d4f67 100644 --- a/astrocyte/TUN-AST.md +++ b/astrocyte/TUN-AST.md @@ -1,49 +1,54 @@ -Qui mettiamo l'attivazione/disattivazione di una SYN possibile, messa a disposizione dal DEV-AST. +# TUN-AST.md + +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. La novita' e' lo SCOPE, nel quale avviene il ragionamento. -# TUN-AST: Modulator +## TUN-AST: Modulator + ... ```Gen modulator: TUN-AST - contained_by: AREA1 + contained_by: AREA1 - modulates: BEH-AXO/expansion/BEH-PRE + modulates: BEH-AXO/expansion/BEH-PRE # - tub_modulation: # - - prePossible ( N/BEH-AXO/BEH-PRE/possible ) - - preActual ( N/BEH-AXO/BEH-PRE/actual ) - - postPossible ( N/BEH-BD/BEH-POST/possible ) - - postActual ( N/BEH-BD/BEH-POST/actual ) + tub_modulation: # + - prePossible ( N/BEH-AXO/BEH-PRE/possible ) + - preActual ( N/BEH-AXO/BEH-PRE/actual ) + - postPossible ( N/BEH-BD/BEH-POST/possible ) + - postActual ( N/BEH-BD/BEH-POST/actual ) - synPossible ( AST/BEH-AST/SYN/actual ) - synActual ( AST/BEH-AST/SYN/actual ) - tub_local: - - ??? (fullness: 50x, active: 0x, emptiness: 0x) - # intricated with ??? + tub_local: + - ??? (fullness: 50x, active: 0x, emptiness: 0x) + # 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. -## ??: Context +### ??: Context .... ```Gen context: ??? - contained_by: TUN-AST - in_context: Fixed - rf: 60x + contained_by: TUN-AST + in_context: Fixed + rf: 60x - condition: ( ??? Empty ) # - out_context: ??? + condition: ( ??? Empty ) # + out_context: ??? ``` -## Activate: Episode +### Activate: Episode + .... ```Gen @@ -54,6 +59,6 @@ episode: activate rf: ( active: 6x ) hypothesis: NOT (?? empty) - action: [??? decrease] + action: [??? decrease] trace: None ``` diff --git a/neuron/BEH-AXO.md b/neuron/BEH-AXO.md index 7865169..d36eb43 100644 --- a/neuron/BEH-AXO.md +++ b/neuron/BEH-AXO.md @@ -1,24 +1,29 @@ +# BEH-AXO.md + +## BEH-AXO: Container + Qui comprendiamo: + - BEH-AXO: Axon - BEH-PRE: Presynapse - 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). ```Gen container: BEH-AXO expansion: - - BEH-PRE ( fullness: 50x, active: 20x, emptiness: 10x ) - # modulated_by: TUN-SYN-AXO-PRE# possible/actual + - BEH-PRE ( fullness: 50x, active: 20x, emptiness: 10x ) + # 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. **Tubs:** + - Ca2+: Calcium Ion entering the Presynapse when VCGG open. They are key to check the concentration, release vescicles and modulation - Rrp: Readily Releasable Pool 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**: L'idea e' che: + - 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 fanno entrare Ca2+ che ne aumenta la concentrazione @@ -60,13 +66,13 @@ container: BEH-PRE tub_local: - 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 ) - # modulated_by: DEV-PRE-RRP-FULL # Full + # modulated_by: DEV-PRE-RRP-FULL # Full - 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 ) @@ -74,10 +80,11 @@ container: BEH-PRE tub_intricated: - Nt ( contained_by: BEH-SYN ) # intricated name (from BEH-SYN) - + ``` -## 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. ***Tens Milliseconds Time Scale*** @@ -90,16 +97,16 @@ context: IntegrateCa2+ rf: ( active: 60x ) condition: (Ca2+ empty) - out_context: CaEmpty + out_context: CaEmpty condition: NOT (Ca2+ empty) AND NOT (Ca2+ full) - out_context: CaMedium + out_context: CaMedium 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 @@ -120,12 +127,12 @@ episode: VescicleRelease rf: ( active: 6x ) hypothesis: (Ca2+ full) AND NOT (Rrp empty) - action: [Rrp decrease, Nt increase, Ca2+ decrease, + action: [Rrp decrease, Nt increase, Ca2+ decrease, 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+ Le tracce lasciate servono alla modulazione @@ -140,11 +147,12 @@ episode: Ca+ClearenceSlow rf: ( active: 6x ) hypothesis: NOT (Ca+ empty) AND NOT (Ca+ full) - action: [Ca+ decrease, CaTraces Increase] + action: [Ca+ decrease, CaTraces Increase] 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. Clearance mechanisms (in order of speed): @@ -165,8 +173,8 @@ episode: Ca+ClearenceFast rf: ( active: 1x ) condition: (Ca2+ full) - action: [Ca2+ decrease, CaTraces Increase] - trace: None + action: [Ca2+ decrease, CaTraces Increase] + trace: None ``` ```Gen @@ -178,25 +186,26 @@ episode: Ca+ClearenceMedium rf: ( active: 1x ) hypothesis: NOT (Ca2+ full) AND NOT (Ca2+ empty) - action: [Ca2+ decrease, CaTraces Increase] - trace: None + action: [Ca2+ decrease, CaTraces Increase] + trace: None ``` -## STP - Pr Upregulation: Observable +### STP - Pr Upregulation: Observable **Observed behavior** Upregulation (Facilitation): Residual Ca²⁺ from previous spikes increases P_r for next release ***Timing: > 10 ms*** -## STD - Pr Downregulation: Observable +### STD - Pr Downregulation: Observable **Observed behavior** Downregulation (Depression): High-frequency firing depletes readily releasable vesicle pool, decreasing P_r ***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. Sequential steps: @@ -217,12 +226,12 @@ episode: VesciclesRecycling in_context: rf: ( fullness: 10x, active: 5x, emptiness: 2x ) # si parte con active, poi viene modulato -# modulated_by: DEV-PRE-VesciclesRecycling-RF +# modulated_by: DEV-PRE-VesciclesRecycling-RF 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) @@ -240,11 +249,11 @@ episode: VescicleFromRPtoRRP-Slow rf: ( active: 30x ) hypothesis: NOT (RP empty) - action: [RP decrease, RRP increase] - trace: None + action: [RP decrease, RRP increase] + trace: None ``` -## VescicleFromRPtoRRP-Medium: Episode +### VescicleFromRPtoRRP-Medium: Episode ***Seconds-Minutes Time Scale*** @@ -256,11 +265,11 @@ episode: VescicleFromRPtoRRP-Medium rf: ( active: 15x ) hypothesis: NOT (RP empty) - action: [RP decrease, RRP increease] - trace: None + action: [RP decrease, RRP increease] + trace: None ``` -## VescicleFromRPtoRRP-Fast: Episode +### VescicleFromRPtoRRP-Fast: Episode ***Seconds-Minutes Time Scale*** @@ -275,7 +284,8 @@ episode: VescicleFromRPtoRRP-Fast action: [RP decrease, RRP increase] trace: None ``` -## VesiclesFillingRP: Episode + +### VesiclesFillingRP: Episode Qui riempiamo le vesciche. Fino ad un numero massimo, che viene modulato in DEV @@ -287,12 +297,12 @@ episode: VesiclesFillingRP in_context: AwayFromSpike rf: ( fullness: 100x, active: 60x, emptiness: 30x ) -# modulated_by: DEV-PRE-VesiclesFillingRP-RF # RF +# modulated_by: DEV-PRE-VesiclesFillingRP-RF # RF 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) @@ -300,13 +310,13 @@ episode: VesiclesFillingRP container: BEH-PRE-VGCC tub_intricated: - - Ca2+ ( contained_by: BEH-PRE ) + - Ca2+ ( contained_by: BEH-PRE ) - context_intricated: - - AP ( contained_by: BEH-SOMA ) + context_intricated: + - AP ( contained_by: BEH-SOMA ) ``` -## VgccOpen: Episode +### VgccOpen: Episode Auto-inhibition? Ca²⁺ binding to calmodulin on VGCC. 5-50 ms @@ -346,6 +356,6 @@ episode: VgccOpen rf: ( active: 1x ) hypothesis: NOT (Ca2+ full) - action: [Ca2+ increase] - trace: None # Se Ca+FULLNESS, lascio tracce di overflow per modulazione DOWN, da capire UP + action: [Ca2+ increase] + trace: None # Se Ca+FULLNESS, lascio tracce di overflow per modulazione DOWN, da capire UP ``` diff --git a/neuron/BEH-BD.md b/neuron/BEH-BD.md index 4a167db..4fc3387 100644 --- a/neuron/BEH-BD.md +++ b/neuron/BEH-BD.md @@ -1,67 +1,71 @@ +# BEH-AXO.md + Qui comprendiamo: + - BEH-BD: Dendritic Branch - BEH-POST: Postsynapsis - 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. Qui BEH-DB espande solo i BEH-POST, e' un cavo di collegamento come l'assone ```Gen Container: BEH-BD - - expansion: - - BEH-POST ( fullness: 50x, active: 20x, emptiness: 10x ) - # modulated_by: TUN-SYN-BD-POST possible/actual + + expansion: + - BEH-POST ( fullness: 50x, active: 20x, emptiness: 10x ) + # modulated_by: TUN-SYN-BD-POST possible/actual ``` -## BEH-POST: Container +### BEH-POST: Container ```Gen container: BEH-POST - expansion: - - BEH-POST-AMPA ( fullness: 10x, active: 5x, emptiness: 2x ) - # modulated_by: TUN-POST-IC # possible/actual + expansion: + - BEH-POST-AMPA ( fullness: 10x, active: 5x, emptiness: 2x ) + # modulated_by: TUN-POST-IC # possible/actual - tub_local: - - Ca2+ ( fullness: 60x, active: 30x, emptiness: 0x ) - # modulated_by: DEV-POST-???-FULL # Full + tub_local: + - Ca2+ ( fullness: 60x, active: 30x, emptiness: 0x ) + # 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: - - Nt ( contained_by: BEH-SYN ) - - bAp ( contained_by: BEH-SOMA ) + tub_intricated: + - Nt ( contained_by: BEH-SYN ) + - bAp ( contained_by: BEH-SOMA ) ``` -### Context +#### Context ```Gen context: captureNt - contained_by: BEH-POST + contained_by: BEH-POST - in_context: Fixed - rf: ( active: 10x ) + in_context: Fixed + rf: ( active: 10x ) - condition: (Nt full) AND NOT (bAp) - out_context: NtCaptured + condition: (Nt full) AND NOT (bAp) + out_context: NtCaptured ``` -### Episode +#### Episode -### BEH-POST-AMPA: Container +## BEH-POST-AMPA: Container ```Gen container: BEH-POST-AMPA - tub_intricated: - - Nt ( contained_by: BEH-SYN ) + tub_intricated: + - Nt ( contained_by: BEH-SYN ) - context_intricated: - - bAp ( contained_by: BEH-SOMA ) + context_intricated: + - bAp ( contained_by: BEH-SOMA ) ``` #### AmpaOpen: Episode @@ -80,13 +84,13 @@ episode: AmpaOpen rf: ( active: 1x ) hypothesis: NOT (Ca2+ full) - action: [Ca2+ increase] - trace: None # Se Ca+FULLNESS, lascio tracce di overflow per modulazione DOWN, da capire UP + action: [Ca2+ increase] + trace: None # Se Ca+FULLNESS, lascio tracce di overflow per modulazione DOWN, da capire UP ``` ### Depolarization by bAP -Da ricordare i Dendritic VCGG che si aprono facendo entrare Ca2+ all'arrivo di bAP. In teoria abbiamo 3 Ion Channel. +Da ricordare i Dendritic VCGG che si aprono facendo entrare Ca2+ all'arrivo di bAP. In teoria abbiamo 3 Ion Channel. - Timing: > 1 ms - InContext: bAP backpropagating action potential @@ -112,5 +116,3 @@ Da ricordare i Dendritic VCGG che si aprono facendo entrare Ca2+ all'arrivo di b ### Downregulation: Observable - Downregulation: AMPA desensitization acts as low-pass filter - -## \ No newline at end of file diff --git a/neuron/BEH-N.md b/neuron/BEH-N.md index d6a0227..c6dcd50 100644 --- a/neuron/BEH-N.md +++ b/neuron/BEH-N.md @@ -7,8 +7,8 @@ Questo container serve solo ad espandere AXO, SOMA e DB. ```Gen container: BEH-N - expansion: - - BEH-AXO ( active: 1x ) - - BEH-SOMA ( active: 1x ) - - BEH-DB ( active: 3x ) -``` \ No newline at end of file + expansion: + - BEH-AXO ( active: 1x ) + - BEH-SOMA ( active: 1x ) + - BEH-DB ( active: 3x ) +``` diff --git a/neuron/BEH-SOMA.md b/neuron/BEH-SOMA.md index b01657b..408bff6 100644 --- a/neuron/BEH-SOMA.md +++ b/neuron/BEH-SOMA.md @@ -4,11 +4,11 @@ container: BEH-SOMA expansion: - - BEH-SOMA-VCGG ( fullness: 50x, active: 20x, emptiness: 10x ) - # modulated_by: TUN-SOMA-VCGG # possible/actual + - BEH-SOMA-VCGG ( fullness: 50x, active: 20x, emptiness: 10x ) + # modulated_by: TUN-SOMA-VCGG # possible/actual - tub_intricated: - - SpikeTrainTraces ( contained_by: TUN-N ) + tub_intricated: + - SpikeTrainTraces ( contained_by: TUN-N ) ``` ## Context @@ -17,13 +17,13 @@ Qui mettiamo lo spike Dendritico. Sempre se vogliamo comprenderlo. ```Gen context: ???... - contained_by: BEH-SOMA + contained_by: BEH-SOMA - in_context: Fixed - rf: 60x + in_context: Fixed + rf: 60x - condition: - activate: xxx + condition: + activate: xxx ``` ## Episode @@ -36,8 +36,8 @@ episode: ?? rf: ( active: 1x ) hypothesis: - action: - trace: None + action: + trace: None ``` ## BEH-SOMA-VCGG: Container @@ -57,8 +57,8 @@ episode: ?? rf: ( active: 1x ) hypothesis: - action: - trace: None + action: + trace: None ``` -## \ No newline at end of file +## diff --git a/neuron/DEV-N.md b/neuron/DEV-N.md index 588fc73..bfefdff 100644 --- a/neuron/DEV-N.md +++ b/neuron/DEV-N.md @@ -4,15 +4,15 @@ Neuron Development - LTP-LTD Behavior: Il DEV-N lavora durante Night a tempi lunghi rispetto a BEH-N. In pratica cambia la forma delle possibilita’ di BEH-N. -Il DEV contiene quei behavior di modulazione che cambiano la somma (fullness + active). La modulazione DEV aumenta/diminuisce (fullness + active). Ovvero c’e’ creazione di nuova “forma” di possibilita’. +Il DEV contiene quei behavior di modulazione che cambiano la somma (fullness + active). La modulazione DEV aumenta/diminuisce (fullness + active). Ovvero c’e’ creazione di nuova “forma” di possibilita’. This is critical for long-term presynaptic changes. The postsynaptic cell, upon detecting specific activity patterns (like those for LTP/LTD), releases chemical signals that travel backwards to the presynaptic terminal, instructing it to change. -- For Presynaptic Strengthening (e.g., un LTP): +- For Presynaptic Strengthening (e.g., un LTP): - Nitric Oxide (NO): A gas that diffuses freely. During postsynaptic LTP induction (strong NMDAR activation), neuronal NO synthase (nNOS) is activated. NO diffuses into the presynaptic terminal and activates soluble guanylyl cyclase (sGC), raising cGMP levels. This enhances vesicle release via PKG, contributing to presynaptic LTP. - Endocannabinoid-Mediated LTP (eLTP): In some synapses, a postsynaptic depolarization triggers production of endocannabinoids (e.g., 2-AG). These bind to presynaptic CB1 receptors, but surprisingly, can initiate a signaling cascade (involving cAMP/PKA) that increases Pr for a long period. - Neurotrophins (BDNF): Released from the postsynapse in an activity-dependent manner. Presynaptic TrkB receptors activate pathways (PI3K, MAPK) that enhance vesicle docking and Pr. -- For Presynaptic Weakening (e.g., LTD): +- For Presynaptic Weakening (e.g., LTD): - Classical Endocannabinoid-Mediated LTD (eCB-LTD): More common. Moderate postsynaptic activity (mGluR activation or moderate Ca²⁺ rise) triggers 2-AG release. 2-AG binds presynaptic CB1 receptors, which inhibit VGCCs and directly inhibit the release machinery via Gi/o protein signaling, reducing Pr for a long time. - Other Lipid Mediators (like LPA) can also act as retrograde signals for depression. @@ -52,23 +52,23 @@ modulator: DEV-RF ```Gen 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! - - tub_dev: - - fulMod ( fullness: None, active: rf/fullness, emptiness: 0x ) - - actMod ( fullness: None, active: rf/active, emptiness: 0x ) + + tub_dev: + - fulMod ( fullness: None, active: rf/fullness, emptiness: 0x ) + - actMod ( fullness: None, active: rf/active, emptiness: 0x ) # qui stiamo modulando l'active di RF mantenendolo fra fullness e # emptiness dichiarato in VesciclesRecycling - - tub_local: + + tub_local: - tub_intricated: - - Nox ( contained_by: BEH-POST ) - - Ecb ( contained_by: BEH-POST ) + tub_intricated: + - Nox ( contained_by: BEH-POST ) + - Ecb ( contained_by: BEH-POST ) ``` #### Context @@ -79,15 +79,15 @@ modulator: DEV-PRE-VesciclesRecycling-RF ```Gen modulator: DEV-PRE-VesiclesFillingRP-RF - contained_by: DEV-RF + contained_by: DEV-RF - modulates: + modulates: - tub_local: + tub_local: - tub_intricated: - - Nox ( contained_by: BEH-POST ) - - Ecb ( contained_by: BEH-POST ) + tub_intricated: + - Nox ( contained_by: BEH-POST ) + - Ecb ( contained_by: BEH-POST ) ``` #### Context @@ -98,15 +98,15 @@ modulator: DEV-PRE-VesiclesFillingRP-RF ```Gen modulator: DEV-PRE-LactateAtp-RF - contained_by: DEV-RF + contained_by: DEV-RF - modulates: + modulates: - tub_local: + tub_local: - tub_intricated: - - Nox ( contained_by: BEH-POST ) - - Ecb ( contained_by: BEH-POST ) + tub_intricated: + - Nox ( contained_by: BEH-POST ) + - Ecb ( contained_by: BEH-POST ) ``` #### Context @@ -126,21 +126,21 @@ modulator: DEV-FULL ```Gen 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 - - tub_dev: - - fullMod ( fullness: 100x, active: Ca2+/fullness, emptiness: 50x ) # Ca2+Full "contains" a number of blocks equal to the current Full. + modulates: BEH-PRE/tub/Ca2+ # this is the tub whose "full" must be modulated + + tub_dev: + - 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 # active di fullMod. Cambiando active di fullMod, # si cambia la fullness di Ca2+ - tub_local: + tub_local: - tub_intricated: - - Nox ( contained_by: BEH-POST ) - - Ecb ( contained_by: BEH-POST ) + tub_intricated: + - Nox ( contained_by: BEH-POST ) + - Ecb ( contained_by: BEH-POST ) ``` #### Context @@ -155,13 +155,13 @@ context: CheckPreTubCa2+ rf: 60x condition: ( empty ) - out_context: DecreaseFull + out_context: DecreaseFull condition: NOT ( empty ) AND NOT ( Ca2+ full ) - out_context: Nothing + out_context: Nothing condition: ( full) - out_context: IncreaseFull + out_context: IncreaseFull ``` #### Episode @@ -174,31 +174,31 @@ episode: VgccOpen rf: 1x hypothesis: NOT ( full ) AND NOT ( empty ) - action: [ increase, decrease] - trace: None + action: [ increase, decrease] + trace: None ``` -### DEV-PRE-RRP-FULL: Modulator +### DEV-PRE-RRP-FULL: Modulator ```Gen 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 - - tub_dev: - - fullMod ( fullness: 100x, active: Rrp/fullness, emptiness: 50x ) # RrpFull "contains" a number of blocks equal to the current Full. + modulates: BEH-PRE/tub/Rrp # this is the tub whose "full" must be modulated + + tub_dev: + - 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 # active di fullMod. Cambiando active di fullMod, # si cambia la fullness di Rrp - tub_local: + tub_local: - tub_intricated: - - Nox ( contained_by: BEH-POST ) - - Ecb ( contained_by: BEH-POST ) + tub_intricated: + - Nox ( contained_by: BEH-POST ) + - Ecb ( contained_by: BEH-POST ) ``` #### Context -#### Episode \ No newline at end of file +#### Episode diff --git a/neuron/README.md b/neuron/README.md index 63b65e9..e96bbba 100644 --- a/neuron/README.md +++ b/neuron/README.md @@ -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. --- \ No newline at end of file diff --git a/neuron/TUN-N.md b/neuron/TUN-N.md index 7b549b2..aef32a2 100644 --- a/neuron/TUN-N.md +++ b/neuron/TUN-N.md @@ -8,11 +8,11 @@ Il TUN contiene quei behavior di modulazione che non cambiano la somma (fullness ```Gen modulator: TUN-N - contained_by: N + contained_by: N - tub_local: - - SpikeTrainTraces (fullness: 50x, active: 0x, emptiness: 0x) - # intricated with BEH-SOMA + tub_local: + - SpikeTrainTraces (fullness: 50x, active: 0x, emptiness: 0x) + # intricated with BEH-SOMA ``` ## IntegrateTunPossibility: Context @@ -22,60 +22,60 @@ Qui controlliamo di essere lontani da uno spike train. Siamo in Day con BEH. ```Gen context: IntegrateTunPossibility - contained_by: TUN-N - in_context: Fixed - rf: 60x + contained_by: TUN-N + in_context: Fixed + rf: 60x - condition: ( SpikeTrainTraces Empty ) # Day - out_context: TunPossible + condition: ( SpikeTrainTraces Empty ) # Day + out_context: TunPossible ``` ## TUN-SYN: Modulator Qui la PRE e la POST si predispongono per dare le condizioni a SYN di stabilire o eliminare una sinapsi. Per ora questo comportamento lo mettiamo in TUN perche’ non si tratta di creare o distruggere PRE o POST, ma di rendere disponibile a SYN la possibilita’ di creare o distruggere una SYN. Durante il Day c’e’ il TUN che mette a disposizione, durante il Night SYN crea o distrugge gli accoppiamenti PRE POST. -ATTENZIONE: Questo e POST e’ da cambiare, perche’ c’e’ il passaggio da TubPoss a TubPossSyn a TubAct. E’ la SYN che passa in TubAct. +ATTENZIONE: Questo e POST e’ da cambiare, perche’ c’e’ il passaggio da TubPoss a TubPossSyn a TubAct. E’ la SYN che passa in TubAct. > Minutes/hours Time Scale ```Gen modulator: TUN-SYN - contained_by: TUN-N + contained_by: TUN-N ``` ### TUN-SYN-AXO-PRE: Modulator ```Gen modulator: TUN-SYN-AXO-PRE - contained_by: TUN-SYN - - modulates: BEH-AXO/expansion/BEH-PRE + contained_by: TUN-SYN + + modulates: BEH-AXO/expansion/BEH-PRE # 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 - - 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 + tub_modulation: # in TUN agiamo su fullness <-> active + - 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 - context_intricated: - - TunPossible ( contained_by: TUN-N ) + context_intricated: + - TunPossible ( contained_by: TUN-N ) - tub_local: + tub_local: - tub_intricated: + tub_intricated: ``` #### Context ```Gen context: CheckTunSynAxoPrePossibility - contained_by: TUN-SYN-AXO-PRE + contained_by: TUN-SYN-AXO-PRE - in_context: TunPossible - rf: ( active: 60x ) + in_context: TunPossible + rf: ( active: 60x ) - condition: - out_context: + condition: + out_context: ``` #### Episode @@ -88,8 +88,8 @@ episode: TunSynAxoPre rf: 1x hypothesis: NOT () AND NOT () - action: [ increase, decrease] - trace: None + action: [ increase, decrease] + trace: None ``` ### TUN-SYN-BD-POST: Modulator @@ -97,7 +97,7 @@ episode: TunSynAxoPre ```Gen 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 modulator: TUN-CHAN - contained_by: TUN-N + contained_by: TUN-N ``` ### TUN-PRE-VGCC: Modulator @@ -122,24 +122,24 @@ modulator: TUN-CHAN ```Gen modulator: TUN-PRE-VGCC - contained_by: TUN-CHAN + contained_by: TUN-CHAN - modulates: BEH-PRE/expansion/BEH-PRE-VCGG - - 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 - - actMod ( fullness: None, active: BEH-PRE-VCGG/active, empty: BEH-PRE-VCGG/emptiness) # riferimento a active di BEH-PRE-VCGG + modulates: BEH-PRE/expansion/BEH-PRE-VCGG + + 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 + - 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 # a posMod e actMod. Non serve associare una fullness perche' # la modulazione e' una pompa fra posMod e actMod e controlliamo # solo empty - context_intricated: - - TunPossible ( contained_by: TUN-N ) + context_intricated: + - TunPossible ( contained_by: TUN-N ) - tub_local: + tub_local: - tub_intricated: + tub_intricated: ``` #### Context @@ -152,7 +152,7 @@ context: Check rf: ( active: 60x ) condition: - out_context: TunPreVcgg + out_context: TunPreVcgg ``` #### Episode @@ -165,8 +165,8 @@ episode: Tun rf: ( active: x ) hypothesis: - action: - trace: + action: + trace: ``` ### TUN-POST-AMPA: Modulator @@ -174,20 +174,20 @@ episode: Tun ```Gen 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 - - 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 + tub_modulation: # in TUN agiamo su POS/ACT + - 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 - context_intricated: - - TunPossible ( contained_by: TUN-N ) + context_intricated: + - TunPossible ( contained_by: TUN-N ) - tub_local: + tub_local: - tub_intricated: + tub_intricated: ``` #### Context @@ -200,7 +200,7 @@ context: Check rf: ( active: 60x ) condition: - out_context: TunPostIc + out_context: TunPostIc ``` #### Episode @@ -213,8 +213,8 @@ episode: ? rf: ( active: x ) hypothesis: - action: - trace: + action: + trace: ``` ### TUN-SOMA-VCGG: Modulator @@ -222,21 +222,21 @@ episode: ? ```Gen 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 - tub_modulation: # in TUN agiamo su POS/ACT - - 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 + expansion: BEH-SOMA-VCGG + tub_modulation: # in TUN agiamo su POS/ACT + - 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 - context_intricated: - - TunPossible ( contained_by: TUN-N ) + context_intricated: + - TunPossible ( contained_by: TUN-N ) - tub_local: + tub_local: - tub_intricated: + tub_intricated: ``` #### Context @@ -249,7 +249,7 @@ context: Check rf: ( active: 60x ) condition: - out_context: TunSomaVcgg + out_context: TunSomaVcgg ``` #### Episode @@ -262,6 +262,6 @@ episode: ? rf: ( active: x ) hypothesis: - action: - trace: -``` \ No newline at end of file + action: + trace: +``` diff --git a/winnertakeall/BEH-WTA.md b/winnertakeall/BEH-WTA.md index a405cb1..3cb616e 100644 --- a/winnertakeall/BEH-WTA.md +++ b/winnertakeall/BEH-WTA.md @@ -1,26 +1,32 @@ +# beh-WTA.md + Qui comprendiamo: + - BEH-WTA -# BEH-WTA: Container -**Winner Take All**: +## BEH-WTA: Container + +**Winner Take All**: ```Gen container: BEH-WTA expansion: - INTERNAL-001: - - NEU-001.AXO -[AST-001]-> NEU-003.BD-001, NEU-004.BD-001 - - NEU-002.AXO -[AST-001]-> NEU-003.BD-001 - OUTGOING-001: - - NEU-003.AXO -[@]-> @.BD-001 - - NEU-004.AXO -[@]-> @.BD-001 - INCOMING-001: - - @.AXO -[@]-> NEU-001.BD-001, NEU-002.BD-001 - - @.AXO -[@]-> NEU-004.BD-001, NEU-003.BD-001 + INTERNAL-001: + - NEU-001.AXO -[AST-001]-> NEU-003.BD-001, NEU-004.BD-001 + - NEU-002.AXO -[AST-001]-> NEU-003.BD-001 + OUTGOING-001: + - NEU-003.AXO -[@]-> @.BD-001 + - NEU-004.AXO -[@]-> @.BD-001 + INCOMING-001: + - @.AXO -[@]-> NEU-001.BD-001, NEU-002.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. -L'espansione: +L'espansione: + - dichiara N1 e N2 - dichiara AST1 - 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. Problemi da risolver: + - 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: + - NEU-001.axon.terminal-1 -[excites: ast=AST-001]-> AREA.Input-001 E questo potrebbe rendere generale l'approccio. diff --git a/winnertakeall/WTA.md b/winnertakeall/WTA.md index 7c0c5b1..bb47d0e 100644 --- a/winnertakeall/WTA.md +++ b/winnertakeall/WTA.md @@ -1,12 +1,13 @@ # WTA: Comprehension + Qui comprendiamo un primo circuito Winner Take All, sia BEH, che TUN e DEV ```Gen comprehension: WTA - include: - - BEH-WTA.md - - TUN-WTA.md - - DEV-WTA.md + include: + - BEH-WTA.md + - TUN-WTA.md + - DEV-WTA.md -``` \ No newline at end of file +```