diff --git a/chans/ak_plot/README.md b/chans/ak_plot/README.md deleted file mode 100644 index 41e9e7e1d..000000000 --- a/chans/ak_plot/README.md +++ /dev/null @@ -1,64 +0,0 @@ -# A-type Potassium Channel - -This voltage-gated K channel, found especially on dendrites of pyramidal neurons for example, has a narrow window of activation between the M and H gates, around -37 mV. The M activating gate has a fast time constant on the scale of a msec, while the H inactivating gate has a linearly increasing time constant as a function of V. - -It is particularly important for counteracting the excitatory effects of voltage gated calcium channels which can otherwise drive runaway excitatory currents. - -```Go - K = -1.8 - 1/(1+exp((vbio+40)/5)) -``` - -```Go - Alpha(V,K) = exp(0.03707 * K * (V - 1)) -``` - -```Go - Beta(V,K) = exp(0.01446 * K * (V - 1)) -``` - -```Go - H(V) = 1 / (1 + epx(0.1133 * (V + 56))) -``` - -```Go - Htau(V) = 0.26 * (V + 50) > 2 -``` - -```Go - M(Alpha) = 1 / (1 + Alpha) -``` - -```Go - Mtau(Alpha, Beta) = 1 + Beta / (0.5 * (1 + Alpha)) -``` - -NOTE: to work properly with 1 msec Dt updating, the MTau adds a 1 -- otherwise MTau goes to high. - -![G from V](fig_ak_chan_g_from_v.png?raw=true "G = M * H as a function of V (biological units)") - -![M and H gating from V](fig_ak_chan_m_h_from_v.png?raw=true "M and H gating factors as a function of V (biological units)") - -![Mtau from V](fig_ak_chan_mtau_from_v.png?raw=true "Mtau rate of change of M as a function of V (biological units)") - -![Htau from V](fig_ak_chan_htau_from_v.png?raw=true "Htau rate of change of H as a function of V (biological units)") - -![Gak and M over time](fig_ak_chan_time_plot.png?raw=true "Gak developing over time in response to simulated spiking potentials, with a baseline Vm of -50 -- H quickly inactivates.") - -The `Time Run` plot (above) shows how the Gak current develops over time in response to spiking, which it tracks directly due to very fast M dynamics. The H current inactivates significantly when the consistent Vm level (TimeVstart) is elevated -- e.g., -50 as shown in the figure. - -# Simplified AKs channel - -The `AKsParams` provides a much simpler, stateless version of the AK channel that is useful to just get a high-level cutoff to membrane potentials in the dendrites, e.g., as might otherwise emerge from the VGCC channel. - -![Gaks from V](fig_aks_vs_ak.png?raw=true "Gak for simplified AK channel vs. Gak from full version") - -This function is: -```Go - if vbio > -37 { // flat response above cutoff -- real function goes back down.. - vbio = -37 - } - return 0.076 / (1.0 + math32.FastExp(-0.075*(vbio+2))) -``` - - - diff --git a/chans/ak_plot/typegen.go b/chans/ak_plot/typegen.go deleted file mode 100644 index 15cf429ba..000000000 --- a/chans/ak_plot/typegen.go +++ /dev/null @@ -1,9 +0,0 @@ -// Code generated by "core generate -add-types"; DO NOT EDIT. - -package ak_plot - -import ( - "cogentcore.org/core/types" -) - -var _ = types.AddType(&types.Type{Name: "github.com/emer/axon/v2/chans/ak_plot.Plot", IDName: "plot", Doc: "Plot holds the params, table, etc", Methods: []types.Method{{Name: "GVRun", Doc: "GVRun plots the conductance G (and other variables) as a function of V.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}, {Name: "TimeRun", Doc: "TimeRun runs the equation over time.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}}, Fields: []types.Field{{Name: "Dir", Doc: "Dir is the directory for our plot data."}, {Name: "AK", Doc: "AK function"}, {Name: "AKs", Doc: "AKs simplified function"}, {Name: "Vstart", Doc: "starting voltage"}, {Name: "Vend", Doc: "ending voltage"}, {Name: "Vstep", Doc: "voltage increment"}, {Name: "TimeSteps", Doc: "number of time steps"}, {Name: "TimeSpike", Doc: "do spiking instead of voltage ramp"}, {Name: "SpikeFreq", Doc: "spiking frequency"}, {Name: "TimeVstart", Doc: "time-run starting membrane potential"}, {Name: "TimeVend", Doc: "time-run ending membrane potential"}}}) diff --git a/chans/chanplots/README.md b/chans/chanplots/README.md new file mode 100644 index 000000000..b9c360812 --- /dev/null +++ b/chans/chanplots/README.md @@ -0,0 +1,219 @@ +# Channel Plots + +## A-type Potassium Channel + +This voltage-gated K channel, found especially on dendrites of pyramidal neurons for example, has a narrow window of activation between the M and H gates, around -37 mV. The M activating gate has a fast time constant on the scale of a msec, while the H inactivating gate has a linearly increasing time constant as a function of V. + +It is particularly important for counteracting the excitatory effects of voltage gated calcium channels which can otherwise drive runaway excitatory currents. + +```Go + K = -1.8 - 1/(1+exp((vbio+40)/5)) +``` + +```Go + Alpha(V,K) = exp(0.03707 * K * (V - 1)) +``` + +```Go + Beta(V,K) = exp(0.01446 * K * (V - 1)) +``` + +```Go + H(V) = 1 / (1 + epx(0.1133 * (V + 56))) +``` + +```Go + Htau(V) = 0.26 * (V + 50) > 2 +``` + +```Go + M(Alpha) = 1 / (1 + Alpha) +``` + +```Go + Mtau(Alpha, Beta) = 1 + Beta / (0.5 * (1 + Alpha)) +``` + +NOTE: to work properly with 1 msec Dt updating, the MTau adds a 1 -- otherwise MTau goes to high. + +![G from V](fig_ak_chan_g_from_v.png?raw=true "G = M * H as a function of V (biological units)") + +![M and H gating from V](fig_ak_chan_m_h_from_v.png?raw=true "M and H gating factors as a function of V (biological units)") + +![Mtau from V](fig_ak_chan_mtau_from_v.png?raw=true "Mtau rate of change of M as a function of V (biological units)") + +![Htau from V](fig_ak_chan_htau_from_v.png?raw=true "Htau rate of change of H as a function of V (biological units)") + +![Gak and M over time](fig_ak_chan_time_plot.png?raw=true "Gak developing over time in response to simulated spiking potentials, with a baseline Vm of -50 -- H quickly inactivates.") + +The `Time Run` plot (above) shows how the Gak current develops over time in response to spiking, which it tracks directly due to very fast M dynamics. The H current inactivates significantly when the consistent Vm level (TimeVstart) is elevated -- e.g., -50 as shown in the figure. + +### Simplified AKs channel + +The `AKsParams` provides a much simpler, stateless version of the AK channel that is useful to just get a high-level cutoff to membrane potentials in the dendrites, e.g., as might otherwise emerge from the VGCC channel. + +![Gaks from V](fig_aks_vs_ak.png?raw=true "Gak for simplified AK channel vs. Gak from full version") + +This function is: +```Go + if vbio > -37 { // flat response above cutoff -- real function goes back down.. + vbio = -37 + } + return 0.076 / (1.0 + math32.FastExp(-0.075*(vbio+2))) +``` + +## GABA-B + +Explores the GABA-B dynamics from Sanders et al (2013) and Thomson & Destexhe, 1999. + +GABA-B is an inhibitory channel activated by the usual GABA inhibitory neurotransmitter, which is coupled to the GIRK *G-protein coupled inwardly rectifying potassium (K) channel*. It is ubiquitous in the brain, and is likely essential for basic neural function (especially in spiking networks from a computational perspective). The inward rectification is caused by a Mg+ ion block *from the inside* of the neuron, which means that these channels are most open when the neuron is hyperpolarized (inactive), and thus it serves to *keep inactive neurons inactive*. + +Based on Fig 15 of TD99, using a double-exponential function with 60 msec time to peak, and roughly 200 msec time to return to baseline, along with sigmoidal function of spiking for peak conductance, and the Mg inverse rectification curve. + +Double exponential can't quite fit the right time-course, but 45 rise and 50 decay gives pretty reasonable looking overall distribution with peak at 47, and about .2 left after 200 msec. 35 / 40 has peak around 37 and .1 left after 100. + +## kIR potassium inward rectifying channel + + +## M-type voltage gated potassium channel: mAHP + +This voltage-gated K channel, which is also inactivated by ACh muscarinic receptor activation, plays a role in medium time-scale afterhyperpolarization (mAHP). + +Original formulation due to Mainen & Sejnowski (1996) is widely used, and used here. + +```Go + vo = (V - Voff) + a = 0.001 * vo / (1 - exp(-vo/Vslope)) + b = -0.001 * vo / (1 - exp(vo/Vslope)) + + tau = 1 / (a + b) + ninf = a / (a + b) +``` + +![Ninf from V](fig_mahp_ninf.png?raw=true "Ninf as a function of V (biological units)") + +![Tau from V](fig_mahp_tau.png?raw=true "Tau as a function of V (biological units)") + +![mAHP vs. fKNA](fig_mahp_vs_fkna.png?raw=true "mAHP vs. fast KNa (tau = 50, rise = 0.05)") + +The `Time Run` plot (above) shows how the mAHP current develops over time in response to spiking, in comparison to the KNa function, with the default "fast" parameters of 50msec and rise = 0.05. The mAHP is much more "anticipatory" due to the direct V sensitivity, whereas KNa is much more "reactive", responding only the the Na after spiking. + +## NMDA + +This plots the NMDA current function from Sanders et al, 2013 and Brunel & Wang (2001) (BW01), which is the most widely used active maintenance model. + +See also: https://brian2.readthedocs.io/en/stable/examples/frompapers.Brunel_Wang_2001.html + +Also used in: WeiWangWang12, FurmanWang08, NassarHelmersFrank18 + +Voltage dependence function based on Mg ion blocking is: + +```Go +1 / (1 + (C/3.57)*exp(-0.062 * vm)) +``` + +Jahr & Stevens (1990) originally derived this equation, using a Mg+ concentration C of 1 mM, so that factor = 0.28, used in BW01. Urakubo et al. (2008) used a concentration of 1.5 mM, citing Froemke & Dan (2002). Various other sources (Vink & Nechifor) indicate physiological ranges being around 1.2 - 1.4. + +![g_NMDA from V](fig_sandersetal_2013.png?raw=true "NMDA voltage gating conductance according to parameters from Sanders et al, 2013") + +In addition to this v-dependent Mg factor, conductance depends on presynaptic glutamate release, which in the basic BW01 model just increments with spikes and decays with a time constant of about 100 msec. + +The Urakubo et al (2008) model introduces allosteric dynamics, based on data from Froemke & Dan (2002), which we can capture simply using an inhibitory factor that increments with each spike and decays with a 100 msec time constant. However, their model has an effective Glu-binding decay time of only 30 msec. + +## slow AHP (sAHP): Calcium + +This channel is driven by a M-type mechanism operating on calcium sensor pathways that have longer time constants, updated at the theta cycle level so that guarantees a long baseline already. The logistic gating function operates with a high cutoff on the underlying Ca signal + +The logistic operates on integrated Ca: + +```Go + co = (ca - Off) + a = co / TauMax * (1 - exp(-co/Slope)) + b = -co / TauMax * (1 - exp(co/Slope)) + + tau = 1 / (a + b) + ninf = a / (a + b) +``` + +![Ninf from Ca](fig_sahp_ninf.png?raw=true "Ninf as a function of V (biological units)") + +![Tau from Ca](fig_sahp_tau.png?raw=true "Tau as a function of V (biological units)") + +![mAHP vs. fKNA](fig_mahp_vs_fkna.png?raw=true "mAHP vs. fast KNa (tau = 50, rise = 0.05)") + +The `Time Run` plot (above) shows how the mAHP current develops over time in response to spiking, in comparison to the KNa function, with the default "fast" parameters of 50msec and rise = 0.05. The mAHP is much more "anticipatory" due to the direct V sensitivity, whereas KNa is much more "reactive", responding only the the Na after spiking. + +## sKCa: Voltage-gated Calcium Channels + +This plots the sKCa current function, which describes the small-conductance calcium-activated potassium channel, using the equations described in Fujita et al (2012) based on Gunay et al (2008), (also Muddapu & Chakravarthy, 2021). There is a gating factor M that depends on the Ca concentration, modeled using an X / (X + C50) form Hill equation: + +```Go +M_hill(ca) = ca^h / (ca^h + c50^h) +``` + +This function is .5 when `ca == c50`, and the `h` default power (`Hill` param) of 4 makes it a sharply nonlinear function. + +SKCa can be activated by intracellular stores in a way that drives pauses in firing, and can require inactivity to recharge the Ca available for release. These intracellular stores can release quickly, have a slow decay once released, and the stores can take a while to rebuild, leading to rapidly triggered, long-lasting pauses that don't recur until stores have rebuilt, which is the observed pattern of firing of STNp pausing neurons, that open up a window for BG gating. + +`CaIn` = intracellular stores available for release; `CaR` = released amount from stores; `CaM` = K channel conductance gating factor driven by CaR binding. + +```Go + CaR -= CaR * CaRDecayDt + if spike { + CaR += CaIn * KCaR + } + if CaD < CaInThr { + CaIn += CaInDt * (1 - CaIn) + } +``` + + + +**Figure 1:** M gating as a function of Ca, using Hill function with exponent 4, C50 = .5. + + + +**Figure 2:** Time plot showing pausing and lack of recovery. The spiking input to the neuron is toggled every 200 msec (theta cycle), with 3 cycles shown. The CaIn level does not recover during the off phase -- 2 or more such phases are required. + +## VGCC: Voltage-gated Calcium Channels + +This plots the VGCC current function, which is an L-type Ca channel that opens as a function of membrane potential. It tends to broaden the effect of action potential spikes in the dendrites. + +```Go +G(vm) = -vm / (1 - exp(0.0756 * vm)) +``` + +```Go +M(vm) = 1 / (1 + exp(-(vm + 37))) // Tau = 3.6 msec +``` + +```Go +H(vm) = 1 / (1 + exp((vm + 41) * 2)) // Tau = 29 msec +``` + +```Go +VGCC(vm) = M^3 H * G(vm) +``` + +![M and H gating from V](fig_vgcc_m_h_from_v.png?raw=true "M and H gating factors as a function of V (biological units)") + +The intersection of M and H produces a very narrow membrane potential window centered around -40 mV where the gates are both activated, with the fast updating (3.6 msec tau) and cubic dependence on M essentially shutting off the current very quickly when the action potential goes away. The longer H time constant provides a slow adaptation-like dynamic that is sensitive to frequency (more adaptation at higher frequencies). + +![M and H over time](fig_vgcc_time_plot.png?raw=true "M and H gating factors developing over time in response to simulated spiking potentials") + +The `Time Run` plot (above) shows these dynamics playing out with a sequence of spiking. + +Functionally, the narrow voltage window restricts the significance of this channel to the peri-spiking time window, where the Ca++ influx provides a bit of extra sustain on the trailing edge of the spike. More importantly, the Ca++ provides a postsynaptic-only spiking signal for learning. + +# References + +* Jahr, C. E., & Stevens, C. F. (1990). A quantitative description of NMDA receptor-channel kinetic behavior. Journal of Neuroscience, 10(6), 1830–1837. https://doi.org/10.1523/JNEUROSCI.10-06-01830.1990 + +* Sanders, H., Berends, M., Major, G., Goldman, M. S., & Lisman, J. E. (2013). NMDA and GABAB (KIR) Conductances: The "Perfect Couple" for Bistability. Journal of Neuroscience, 33(2), 424–429. https://doi.org/10.1523/JNEUROSCI.1854-12.2013 + +* Thomson AM, Destexhe A (1999) Dual intracellular recordings and computational models of slow inhibitory postsynaptic potentials in rat neocortical and hippocampal slices. Neuroscience 92:1193–1215. + +* Vink, R., & Nechifor, M. (Eds.). (2011). Magnesium in the Central Nervous System. University of Adelaide Press. https://doi.org/10.1017/UPO9780987073051 + +* Urakubo, H., Honda, M., Froemke, R. C., & Kuroda, S. (2008). Requirement of an allosteric kinetics of NMDA receptors for spike timing-dependent plasticity. *The Journal of Neuroscience, 28(13),* 3310–3323. http://www.ncbi.nlm.nih.gov/pubmed/18367598 + diff --git a/chans/ak_plot/ak_plot.go b/chans/chanplots/ak_plot.go similarity index 94% rename from chans/ak_plot/ak_plot.go rename to chans/chanplots/ak_plot.go index e31ed4f15..b313ae6c9 100644 --- a/chans/ak_plot/ak_plot.go +++ b/chans/chanplots/ak_plot.go @@ -2,8 +2,7 @@ // Use of this source code is governed by a BSD-style // license that can be found in the LICENSE file. -// ak_plot plots A-type Potassium (K) channel equations. -package ak_plot +package chanplots //go:generate core generate -add-types @@ -18,7 +17,7 @@ import ( "github.com/emer/axon/v2/chans" ) -type Plot struct { +type AKPlot struct { // AK function AK chans.AKParams @@ -55,7 +54,7 @@ type Plot struct { } // Config configures the plot -func (pl *Plot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { +func (pl *AKPlot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { pl.Dir = parent.Dir("AK") pl.Tabs = tabs @@ -74,12 +73,12 @@ func (pl *Plot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { pl.Update() } -func (pl *Plot) Update() { +func (pl *AKPlot) Update() { pl.AK.Update() } // GVRun plots the conductance G (and other variables) as a function of V. -func (pl *Plot) GVRun() { //types:add +func (pl *AKPlot) GVRun() { //types:add pl.Update() dir := pl.Dir.Dir("G_V") @@ -130,7 +129,7 @@ func (pl *Plot) GVRun() { //types:add } // TimeRun runs the equations over time. -func (pl *Plot) TimeRun() { //types:add +func (pl *AKPlot) TimeRun() { //types:add pl.Update() dir := pl.Dir.Dir("G_Time") nv := pl.TimeSteps @@ -201,7 +200,7 @@ func (pl *Plot) TimeRun() { //types:add } } -func (pl *Plot) MakeToolbar(p *tree.Plan) { +func (pl *AKPlot) MakeToolbar(p *tree.Plan) { tree.Add(p, func(w *core.FuncButton) { w.SetFunc(pl.GVRun).SetIcon(icons.PlayArrow) }) diff --git 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--git a/chans/gabab_plot/fig_thomson_destexhe99_g_time.svg b/chans/chanplots/fig_thomson_destexhe99_g_time.svg similarity index 100% rename from chans/gabab_plot/fig_thomson_destexhe99_g_time.svg rename to chans/chanplots/fig_thomson_destexhe99_g_time.svg diff --git a/chans/gabab_plot/fig_thomson_destexhe99_s_g_sigmoid.png b/chans/chanplots/fig_thomson_destexhe99_s_g_sigmoid.png similarity index 100% rename from chans/gabab_plot/fig_thomson_destexhe99_s_g_sigmoid.png rename to chans/chanplots/fig_thomson_destexhe99_s_g_sigmoid.png diff --git a/chans/gabab_plot/fig_thomson_destexhe99_s_g_sigmoid.svg b/chans/chanplots/fig_thomson_destexhe99_s_g_sigmoid.svg similarity index 100% rename from chans/gabab_plot/fig_thomson_destexhe99_s_g_sigmoid.svg rename to chans/chanplots/fig_thomson_destexhe99_s_g_sigmoid.svg diff --git a/chans/vgcc_plot/fig_vgcc_m_h_from_v.png b/chans/chanplots/fig_vgcc_m_h_from_v.png similarity index 100% rename from chans/vgcc_plot/fig_vgcc_m_h_from_v.png rename to chans/chanplots/fig_vgcc_m_h_from_v.png diff --git a/chans/vgcc_plot/fig_vgcc_time_plot.png b/chans/chanplots/fig_vgcc_time_plot.png similarity index 100% rename from chans/vgcc_plot/fig_vgcc_time_plot.png rename to chans/chanplots/fig_vgcc_time_plot.png diff --git a/chans/gabab_plot/gabab_plot.go b/chans/chanplots/gabab_plot.go similarity index 93% rename from chans/gabab_plot/gabab_plot.go rename to chans/chanplots/gabab_plot.go index 9534b9121..d11761f60 100644 --- a/chans/gabab_plot/gabab_plot.go +++ b/chans/chanplots/gabab_plot.go @@ -2,10 +2,7 @@ // Use of this source code is governed by a BSD-style // license that can be found in the LICENSE file. -// gabab_plot plots GABA-B long-duration inhibitory channel equations. -package gabab_plot - -//go:generate core generate -add-types +package chanplots import ( "math" @@ -20,7 +17,7 @@ import ( "github.com/emer/axon/v2/chans" ) -type Plot struct { +type GababPlot struct { // standard chans version of GABAB GABAstd chans.GABABParams @@ -71,7 +68,7 @@ type Plot struct { } // Config configures all the elements using the standard functions -func (pl *Plot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { +func (pl *GababPlot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { pl.Dir = parent.Dir("GabaB") pl.Tabs = tabs @@ -93,13 +90,13 @@ func (pl *Plot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { } // Update updates computed values -func (pl *Plot) Update() { +func (pl *GababPlot) Update() { pl.TauFact = math.Pow(pl.DecayTau/pl.RiseTau, pl.RiseTau/(pl.DecayTau-pl.RiseTau)) pl.MaxTime = ((pl.RiseTau * pl.DecayTau) / (pl.DecayTau - pl.RiseTau)) * math.Log(pl.DecayTau/pl.RiseTau) } // GVRun plots the conductance G (and other variables) as a function of V. -func (pl *Plot) GVRun() { //types:add +func (pl *GababPlot) GVRun() { //types:add pl.Update() dir := pl.Dir.Dir("G_V") @@ -132,7 +129,7 @@ func (pl *Plot) GVRun() { //types:add } // GSRun plots conductance over spiking. -func (pl *Plot) GSRun() { //types:add +func (pl *GababPlot) GSRun() { //types:add pl.Update() dir := pl.Dir.Dir("G_Spike") @@ -165,7 +162,7 @@ func (pl *Plot) GSRun() { //types:add } // TimeRun runs the equations over time. -func (pl *Plot) TimeRun() { //types:add +func (pl *GababPlot) TimeRun() { //types:add pl.Update() dir := pl.Dir.Dir("G_Time") nv := pl.TimeSteps @@ -216,7 +213,7 @@ func (pl *Plot) TimeRun() { //types:add } } -func (pl *Plot) MakeToolbar(p *tree.Plan) { +func (pl *GababPlot) MakeToolbar(p *tree.Plan) { tree.Add(p, func(w *core.FuncButton) { w.SetFunc(pl.GVRun).SetIcon(icons.PlayArrow) }) diff --git a/chans/kir_plot/kir_plot.go b/chans/chanplots/kir_plot.go similarity index 91% rename from chans/kir_plot/kir_plot.go rename to chans/chanplots/kir_plot.go index 31fce649e..a7f797e86 100644 --- a/chans/kir_plot/kir_plot.go +++ b/chans/chanplots/kir_plot.go @@ -2,10 +2,7 @@ // Use of this source code is governed by a BSD-style // license that can be found in the LICENSE file. -// kir_plot plots the kIR inward rectifying potassium (K) channel equations. -package kir_plot - -//go:generate core generate -add-types +package chanplots import ( "cogentcore.org/core/core" @@ -17,7 +14,7 @@ import ( "github.com/emer/axon/v2/chans" ) -type Plot struct { +type KirPlot struct { // kIR function Kir chans.KirParams @@ -51,7 +48,7 @@ type Plot struct { } // Config configures all the elements using the standard functions -func (pl *Plot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { +func (pl *KirPlot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { pl.Dir = parent.Dir("kIR") pl.Tabs = tabs @@ -69,11 +66,11 @@ func (pl *Plot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { } // Update updates computed values -func (pl *Plot) Update() { +func (pl *KirPlot) Update() { } // VmRun plots the equation as a function of V -func (pl *Plot) GVRun() { //types:add +func (pl *KirPlot) GVRun() { //types:add pl.Update() dir := pl.Dir.Dir("G_V") @@ -111,7 +108,7 @@ func (pl *Plot) GVRun() { //types:add } // TimeRun runs the equation over time. -func (pl *Plot) TimeRun() { //types:add +func (pl *KirPlot) TimeRun() { //types:add pl.Update() dir := pl.Dir.Dir("G_Time") nv := pl.TimeSteps @@ -171,7 +168,7 @@ func (pl *Plot) TimeRun() { //types:add } } -func (pl *Plot) MakeToolbar(p *tree.Plan) { +func (pl *KirPlot) MakeToolbar(p *tree.Plan) { tree.Add(p, func(w *core.FuncButton) { w.SetFunc(pl.GVRun).SetIcon(icons.PlayArrow) }) diff --git a/chans/mahp_plot/mahp_plot.go b/chans/chanplots/mahp_plot.go similarity index 89% rename from chans/mahp_plot/mahp_plot.go rename to chans/chanplots/mahp_plot.go index 0c76205a6..ea1fed822 100644 --- a/chans/mahp_plot/mahp_plot.go +++ b/chans/chanplots/mahp_plot.go @@ -2,11 +2,7 @@ // Use of this source code is governed by a BSD-style // license that can be found in the LICENSE file. -// mahp_plot plots the M-type voltage gated potassium channel, -// important for after-hyperpolarization (AHP). -package mahp_plot - -//go:generate core generate -add-types +package chanplots import ( "cogentcore.org/core/core" @@ -18,8 +14,7 @@ import ( "github.com/emer/axon/v2/chans" ) -// Plot holds the params, table, etc -type Plot struct { +type MahpPlot struct { // mAHP function Mahp chans.MahpParams `display:"inline"` @@ -53,7 +48,7 @@ type Plot struct { } // Config configures all the elements using the standard functions -func (pl *Plot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { +func (pl *MahpPlot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { pl.Dir = parent.Dir("Mahp") pl.Tabs = tabs @@ -71,11 +66,11 @@ func (pl *Plot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { } // Update updates computed values -func (pl *Plot) Update() { +func (pl *MahpPlot) Update() { } // GVRun plots the conductance G (and other variables) as a function of V. -func (pl *Plot) GVRun() { //types:add +func (pl *MahpPlot) GVRun() { //types:add pl.Update() dir := pl.Dir.Dir("G_V") @@ -106,7 +101,7 @@ func (pl *Plot) GVRun() { //types:add } // TimeRun runs the equation over time. -func (pl *Plot) TimeRun() { //types:add +func (pl *MahpPlot) TimeRun() { //types:add pl.Update() dir := pl.Dir.Dir("G_Time") nv := pl.TimeSteps @@ -168,7 +163,7 @@ func (pl *Plot) TimeRun() { //types:add } } -func (pl *Plot) MakeToolbar(p *tree.Plan) { +func (pl *MahpPlot) MakeToolbar(p *tree.Plan) { tree.Add(p, func(w *core.FuncButton) { w.SetFunc(pl.GVRun).SetIcon(icons.PlayArrow) }) diff --git a/chans/nmda_plot/nmda_plot.go b/chans/chanplots/nmda_plot.go similarity index 92% rename from chans/nmda_plot/nmda_plot.go rename to chans/chanplots/nmda_plot.go index 36f462793..818ef04ea 100644 --- a/chans/nmda_plot/nmda_plot.go +++ b/chans/chanplots/nmda_plot.go @@ -2,10 +2,7 @@ // Use of this source code is governed by a BSD-style // license that can be found in the LICENSE file. -// nmda_plot plots NMDA Ca++ channel equations. -package nmda_plot - -//go:generate core generate -add-types +package chanplots import ( "math" @@ -20,7 +17,7 @@ import ( "github.com/emer/axon/v2/chans" ) -type Plot struct { +type NMDAPlot struct { // standard NMDA implementation in chans NMDAStd chans.NMDAParams @@ -66,7 +63,7 @@ type Plot struct { } // Config configures all the elements using the standard functions -func (pl *Plot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { +func (pl *NMDAPlot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { pl.Dir = parent.Dir("NMDA") pl.Tabs = tabs @@ -88,14 +85,14 @@ func (pl *Plot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { } // Update updates computed values -func (pl *Plot) Update() { +func (pl *NMDAPlot) Update() { } // Equation here: // https://brian2.readthedocs.io/en/stable/examples/frompapers.Brunel_Wang_2001.html // GVRun plots the conductance G (and other variables) as a function of V. -func (pl *Plot) GVRun() { //types:add +func (pl *NMDAPlot) GVRun() { //types:add pl.Update() dir := pl.Dir.Dir("G_V") @@ -136,7 +133,7 @@ func (pl *Plot) GVRun() { //types:add } // TimeRun runs the equation over time. -func (pl *Plot) TimeRun() { //types:add +func (pl *NMDAPlot) TimeRun() { //types:add pl.Update() dir := pl.Dir.Dir("G_Time") nv := pl.TimeSteps @@ -172,7 +169,7 @@ func (pl *Plot) TimeRun() { //types:add } } -func (pl *Plot) MakeToolbar(p *tree.Plan) { +func (pl *NMDAPlot) MakeToolbar(p *tree.Plan) { tree.Add(p, func(w *core.FuncButton) { w.SetFunc(pl.GVRun).SetIcon(icons.PlayArrow) }) diff --git a/chans/sahp_plot/sahp_plot.go b/chans/chanplots/sahp_plot.go similarity index 89% rename from chans/sahp_plot/sahp_plot.go rename to chans/chanplots/sahp_plot.go index 4cb309a0b..b71a66e55 100644 --- a/chans/sahp_plot/sahp_plot.go +++ b/chans/chanplots/sahp_plot.go @@ -2,10 +2,7 @@ // Use of this source code is governed by a BSD-style // license that can be found in the LICENSE file. -// sahp_plot plots the slow afterhyperpolarizing (sAHP) channel, -package sahp_plot - -//go:generate core generate -add-types +package chanplots import ( "cogentcore.org/core/core" @@ -17,8 +14,7 @@ import ( "github.com/emer/axon/v2/chans" ) -// Plot holds the params, table, etc -type Plot struct { +type SahpPlot struct { // sAHP function Sahp chans.SahpParams `display:"inline"` @@ -46,7 +42,7 @@ type Plot struct { } // Config configures all the elements using the standard functions -func (pl *Plot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { +func (pl *SahpPlot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { pl.Dir = parent.Dir("sAHP") pl.Tabs = tabs @@ -62,11 +58,11 @@ func (pl *Plot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { } // Update updates computed values -func (pl *Plot) Update() { +func (pl *SahpPlot) Update() { } // GCaRun plots the conductance G (and other variables) as a function of Ca. -func (pl *Plot) GCaRun() { //types:add +func (pl *SahpPlot) GCaRun() { //types:add pl.Update() dir := pl.Dir.Dir("G_Ca") @@ -97,7 +93,7 @@ func (pl *Plot) GCaRun() { //types:add } // TimeRun runs the equation over time. -func (pl *Plot) TimeRun() { //types:add +func (pl *SahpPlot) TimeRun() { //types:add pl.Update() dir := pl.Dir.Dir("G_Time") nv := pl.TimeSteps @@ -140,7 +136,7 @@ func (pl *Plot) TimeRun() { //types:add } } -func (pl *Plot) MakeToolbar(p *tree.Plan) { +func (pl *SahpPlot) MakeToolbar(p *tree.Plan) { tree.Add(p, func(w *core.FuncButton) { w.SetFunc(pl.GCaRun).SetIcon(icons.PlayArrow) }) diff --git a/chans/skca_plot/skca_plot.go b/chans/chanplots/skca_plot.go similarity index 90% rename from chans/skca_plot/skca_plot.go rename to chans/chanplots/skca_plot.go index 728eaeab1..559722d62 100644 --- a/chans/skca_plot/skca_plot.go +++ b/chans/chanplots/skca_plot.go @@ -2,10 +2,7 @@ // Use of this source code is governed by a BSD-style // license that can be found in the LICENSE file. -// skca_plot plots the small-conductance calcium-activated potassium channel. -package skca_plot - -//go:generate core generate -add-types +package chanplots import ( "cogentcore.org/core/core" @@ -18,8 +15,7 @@ import ( "github.com/emer/axon/v2/kinase" ) -// Plot holds the params, table, etc -type Plot struct { +type SKCaPlot struct { // SKCa params SKCa chans.SKCaParams @@ -47,7 +43,7 @@ type Plot struct { } // Config configures all the elements using the standard functions -func (pl *Plot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { +func (pl *SKCaPlot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { pl.Dir = parent.Dir("SKCa") pl.Tabs = tabs @@ -63,11 +59,11 @@ func (pl *Plot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { } // Update updates computed values -func (pl *Plot) Update() { +func (pl *SKCaPlot) Update() { } // GCaRun plots the conductance G (and other variables) as a function of Ca. -func (pl *Plot) GCaRun() { //types:add +func (pl *SKCaPlot) GCaRun() { //types:add pl.Update() dir := pl.Dir.Dir("G_V") @@ -97,7 +93,7 @@ func (pl *Plot) GCaRun() { //types:add } // TimeRun runs the equation over time. -func (pl *Plot) TimeRun() { //types:add +func (pl *SKCaPlot) TimeRun() { //types:add pl.Update() dir := pl.Dir.Dir("G_Time") nv := pl.TimeSteps @@ -152,7 +148,7 @@ func (pl *Plot) TimeRun() { //types:add } } -func (pl *Plot) MakeToolbar(p *tree.Plan) { +func (pl *SKCaPlot) MakeToolbar(p *tree.Plan) { tree.Add(p, func(w *core.FuncButton) { w.SetFunc(pl.GCaRun).SetIcon(icons.PlayArrow) }) diff --git a/chans/chanplots/typegen.go b/chans/chanplots/typegen.go new file mode 100644 index 000000000..bb6f97abc --- /dev/null +++ b/chans/chanplots/typegen.go @@ -0,0 +1,23 @@ +// Code generated by "core generate -add-types"; DO NOT EDIT. + +package chanplots + +import ( + "cogentcore.org/core/types" +) + +var _ = types.AddType(&types.Type{Name: "github.com/emer/axon/v2/chans/chanplots.AKPlot", IDName: "ak-plot", Methods: []types.Method{{Name: "GVRun", Doc: "GVRun plots the conductance G (and other variables) as a function of V.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}, {Name: "TimeRun", Doc: "TimeRun runs the equations over time.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}}, Fields: []types.Field{{Name: "AK", Doc: "AK function"}, {Name: "AKs", Doc: "AKs simplified function"}, {Name: "Vstart", Doc: "starting voltage"}, {Name: "Vend", Doc: "ending voltage"}, {Name: "Vstep", Doc: "voltage increment"}, {Name: "TimeSteps", Doc: "number of time steps"}, {Name: "TimeSpike", Doc: "do spiking instead of voltage ramp"}, {Name: "SpikeFreq", Doc: "spiking frequency"}, {Name: "TimeVstart", Doc: "time-run starting membrane potential"}, {Name: "TimeVend", Doc: "time-run ending membrane potential"}, {Name: "Dir"}, {Name: "Tabs"}}}) + +var _ = types.AddType(&types.Type{Name: "github.com/emer/axon/v2/chans/chanplots.GababPlot", IDName: "gabab-plot", Methods: []types.Method{{Name: "GVRun", Doc: "GVRun plots the conductance G (and other variables) as a function of V.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}, {Name: "GSRun", Doc: "GSRun plots conductance over spiking.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}, {Name: "TimeRun", Doc: "TimeRun runs the equations over time.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}}, Fields: []types.Field{{Name: "GABAstd", Doc: "standard chans version of GABAB"}, {Name: "GABAbv", Doc: "multiplier on GABAb as function of voltage"}, {Name: "GABAbo", Doc: "offset of GABAb function"}, {Name: "GABAberev", Doc: "GABAb reversal / driving potential"}, {Name: "Vstart", Doc: "starting voltage"}, {Name: "Vend", Doc: "ending voltage"}, {Name: "Vstep", Doc: "voltage increment"}, {Name: "Smax", Doc: "max number of spikes"}, {Name: "RiseTau", Doc: "rise time constant"}, {Name: "DecayTau", Doc: "decay time constant -- must NOT be same as RiseTau"}, {Name: "GsXInit", Doc: "initial value of GsX driving variable at point of synaptic input onset -- decays expoentially from this start"}, {Name: "MaxTime", Doc: "time when peak conductance occurs, in TimeInc units"}, {Name: "TauFact", Doc: "time constant factor used in integration: (Decay / Rise) ^ (Rise / (Decay - Rise))"}, {Name: "TimeSteps", Doc: "total number of time steps to take"}, {Name: "TimeInc", Doc: "time increment per step"}, {Name: "Dir"}, {Name: "Tabs"}}}) + +var _ = types.AddType(&types.Type{Name: "github.com/emer/axon/v2/chans/chanplots.KirPlot", IDName: "kir-plot", Methods: []types.Method{{Name: "GVRun", Doc: "VmRun plots the equation as a function of V", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}, {Name: "TimeRun", Doc: "TimeRun runs the equation over time.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}}, Fields: []types.Field{{Name: "Kir", Doc: "kIR function"}, {Name: "Vstart", Doc: "starting voltage"}, {Name: "Vend", Doc: "ending voltage"}, {Name: "Vstep", Doc: "voltage increment"}, {Name: "TimeSteps", Doc: "number of time steps"}, {Name: "TimeSpike", Doc: "do spiking instead of voltage ramp"}, {Name: "SpikeFreq", Doc: "spiking frequency"}, {Name: "TimeVstart", Doc: "time-run starting membrane potential"}, {Name: "TimeVend", Doc: "time-run ending membrane potential"}, {Name: "Dir"}, {Name: "Tabs"}}}) + +var _ = types.AddType(&types.Type{Name: "github.com/emer/axon/v2/chans/chanplots.MahpPlot", IDName: "mahp-plot", Methods: []types.Method{{Name: "GVRun", Doc: "GVRun plots the conductance G (and other variables) as a function of V.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}, {Name: "TimeRun", Doc: "TimeRun runs the equation over time.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}}, Fields: []types.Field{{Name: "Mahp", Doc: "mAHP function"}, {Name: "Vstart", Doc: "starting voltage"}, {Name: "Vend", Doc: "ending voltage"}, {Name: "Vstep", Doc: "voltage increment"}, {Name: "TimeSteps", Doc: "number of time steps"}, {Name: "TimeSpike", Doc: "do spiking instead of voltage ramp"}, {Name: "SpikeFreq", Doc: "spiking frequency"}, {Name: "TimeVstart", Doc: "time-run starting membrane potential"}, {Name: "TimeVend", Doc: "time-run ending membrane potential"}, {Name: "Dir"}, {Name: "Tabs"}}}) + +var _ = types.AddType(&types.Type{Name: "github.com/emer/axon/v2/chans/chanplots.NMDAPlot", IDName: "nmda-plot", Methods: []types.Method{{Name: "GVRun", Doc: "GVRun plots the conductance G (and other variables) as a function of V.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}, {Name: "TimeRun", Doc: "TimeRun runs the equation over time.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}}, Fields: []types.Field{{Name: "NMDAStd", Doc: "standard NMDA implementation in chans"}, {Name: "NMDAv", Doc: "multiplier on NMDA as function of voltage"}, {Name: "MgC", Doc: "magnesium ion concentration -- somewhere between 1 and 1.5"}, {Name: "NMDAd", Doc: "denominator of NMDA function"}, {Name: "NMDAerev", Doc: "NMDA reversal / driving potential"}, {Name: "BugVoff", Doc: "for old buggy NMDA: voff value to use"}, {Name: "Vstart", Doc: "starting voltage"}, {Name: "Vend", Doc: "ending voltage"}, {Name: "Vstep", Doc: "voltage increment"}, {Name: "Tau", Doc: "decay time constant for NMDA current -- rise time is 2 msec and not worth extra effort for biexponential"}, {Name: "TimeSteps", Doc: "number of time steps"}, {Name: "TimeV", Doc: "voltage for TimeRun"}, {Name: "TimeGin", Doc: "NMDA Gsyn current input at every time step"}, {Name: "Dir"}, {Name: "Tabs"}}}) + +var _ = types.AddType(&types.Type{Name: "github.com/emer/axon/v2/chans/chanplots.SahpPlot", IDName: "sahp-plot", Methods: []types.Method{{Name: "GCaRun", Doc: "GCaRun plots the conductance G (and other variables) as a function of Ca.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}, {Name: "TimeRun", Doc: "TimeRun runs the equation over time.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}}, Fields: []types.Field{{Name: "Sahp", Doc: "sAHP function"}, {Name: "CaStart", Doc: "starting calcium"}, {Name: "CaEnd", Doc: "ending calcium"}, {Name: "CaStep", Doc: "calcium increment"}, {Name: "TimeSteps", Doc: "number of time steps"}, {Name: "TimeCaStart", Doc: "time-run starting calcium"}, {Name: "TimeCaD", Doc: "time-run CaD value at end of each theta cycle"}, {Name: "Dir"}, {Name: "Tabs"}}}) + +var _ = types.AddType(&types.Type{Name: "github.com/emer/axon/v2/chans/chanplots.SKCaPlot", IDName: "sk-ca-plot", Methods: []types.Method{{Name: "GCaRun", Doc: "GCaRun plots the conductance G (and other variables) as a function of Ca.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}, {Name: "TimeRun", Doc: "TimeRun runs the equation over time.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}}, Fields: []types.Field{{Name: "SKCa", Doc: "SKCa params"}, {Name: "CaParams", Doc: "time constants for integrating Ca from spiking across M, P and D cascading levels"}, {Name: "NoSpikeThr", Doc: "threshold of SK M gating factor above which the neuron cannot spike"}, {Name: "CaStep", Doc: "Ca conc increment for M gating func plot"}, {Name: "TimeSteps", Doc: "number of time steps"}, {Name: "TimeSpike", Doc: "do spiking instead of Ca conc ramp"}, {Name: "SpikeFreq", Doc: "spiking frequency"}, {Name: "Dir"}, {Name: "Tabs"}}}) + +var _ = types.AddType(&types.Type{Name: "github.com/emer/axon/v2/chans/chanplots.VGCCPlot", IDName: "vgcc-plot", Methods: []types.Method{{Name: "GVRun", Doc: "GVRun plots the conductance G (and other variables) as a function of V.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}, {Name: "TimeRun", Doc: "TimeRun runs the equation over time.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}}, Fields: []types.Field{{Name: "VGCC", Doc: "VGCC function"}, {Name: "Vstart", Doc: "starting voltage"}, {Name: "Vend", Doc: "ending voltage"}, {Name: "Vstep", Doc: "voltage increment"}, {Name: "TimeSteps", Doc: "number of time steps"}, {Name: "TimeSpike", Doc: "do spiking instead of voltage ramp"}, {Name: "SpikeFreq", Doc: "spiking frequency"}, {Name: "TimeVstart", Doc: "time-run starting membrane potential"}, {Name: "TimeVend", Doc: "time-run ending membrane potential"}, {Name: "Dir"}, {Name: "Tabs"}}}) diff --git a/chans/vgcc_plot/vgcc_plot.go b/chans/chanplots/vgcc_plot.go similarity index 91% rename from chans/vgcc_plot/vgcc_plot.go rename to chans/chanplots/vgcc_plot.go index 5c18e5fcb..b1a24a0fe 100644 --- a/chans/vgcc_plot/vgcc_plot.go +++ b/chans/chanplots/vgcc_plot.go @@ -2,10 +2,7 @@ // Use of this source code is governed by a BSD-style // license that can be found in the LICENSE file. -// vgcc_plot plots the voltage gated calcium channel equations. -package vgcc_plot - -//go:generate core generate -add-types +package chanplots import ( "cogentcore.org/core/core" @@ -17,7 +14,7 @@ import ( "github.com/emer/axon/v2/chans" ) -type Plot struct { +type VGCCPlot struct { // VGCC function VGCC chans.VGCCParams @@ -51,7 +48,7 @@ type Plot struct { } // Config configures all the elements using the standard functions -func (pl *Plot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { +func (pl *VGCCPlot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { pl.Dir = parent.Dir("VGCC") pl.Tabs = tabs @@ -69,11 +66,11 @@ func (pl *Plot) Config(parent *tensorfs.Node, tabs databrowser.Tabber) { } // Update updates computed values -func (pl *Plot) Update() { +func (pl *VGCCPlot) Update() { } // GVRun plots the conductance G (and other variables) as a function of V. -func (pl *Plot) GVRun() { //types:add +func (pl *VGCCPlot) GVRun() { //types:add pl.Update() dir := pl.Dir.Dir("G_V") @@ -110,7 +107,7 @@ func (pl *Plot) GVRun() { //types:add } // TimeRun runs the equation over time. -func (pl *Plot) TimeRun() { //types:add +func (pl *VGCCPlot) TimeRun() { //types:add pl.Update() dir := pl.Dir.Dir("G_Time") nv := pl.TimeSteps @@ -169,7 +166,7 @@ func (pl *Plot) TimeRun() { //types:add } } -func (pl *Plot) MakeToolbar(p *tree.Plan) { +func (pl *VGCCPlot) MakeToolbar(p *tree.Plan) { tree.Add(p, func(w *core.FuncButton) { w.SetFunc(pl.GVRun).SetIcon(icons.PlayArrow) }) diff --git a/chans/gabab_plot/README.md b/chans/gabab_plot/README.md deleted file mode 100644 index 1be3bc668..000000000 --- a/chans/gabab_plot/README.md +++ /dev/null @@ -1,14 +0,0 @@ -# gabab - -Explores the GABA-B dynamics from Sanders et al (2013) and Thomson & Destexhe, 1999. - -GABA-B is an inhibitory channel activated by the usual GABA inhibitory neurotransmitter, which is coupled to the GIRK *G-protein coupled inwardly rectifying potassium (K) channel*. It is ubiquitous in the brain, and is likely essential for basic neural function (especially in spiking networks from a computational perspective). The inward rectification is caused by a Mg+ ion block *from the inside* of the neuron, which means that these channels are most open when the neuron is hyperpolarized (inactive), and thus it serves to *keep inactive neurons inactive*. - -Based on Fig 15 of TD99, using a double-exponential function with 60 msec time to peak, and roughly 200 msec time to return to baseline, along with sigmoidal function of spiking for peak conductance, and the Mg inverse rectification curve. - -Double exponential can't quite fit the right time-course, but 45 rise and 50 decay gives pretty reasonable looking overall distribution with peak at 47, and about .2 left after 200 msec. 35 / 40 has peak around 37 and .1 left after 100. - -* Sanders, H., Berends, M., Major, G., Goldman, M. S., & Lisman, J. E. (2013). NMDA and GABAB (KIR) Conductances: The “Perfect Couple” for Bistability. Journal of Neuroscience, 33(2), 424–429. https://doi.org/10.1523/JNEUROSCI.1854-12.2013 - -* Thomson AM, Destexhe A (1999) Dual intracellular recordings and computational models of slow inhibitory postsynaptic potentials in rat neocortical and hippocampal slices. Neuroscience 92:1193–1215. - diff --git a/chans/gabab_plot/typegen.go b/chans/gabab_plot/typegen.go deleted file mode 100644 index b0944a22d..000000000 --- a/chans/gabab_plot/typegen.go +++ /dev/null @@ -1,9 +0,0 @@ -// Code generated by "core generate -add-types"; DO NOT EDIT. - -package gabab_plot - -import ( - "cogentcore.org/core/types" -) - -var _ = types.AddType(&types.Type{Name: "github.com/emer/axon/v2/chans/gabab_plot.Plot", IDName: "plot", Methods: []types.Method{{Name: "GVRun", Doc: "GVRun plots the conductance G (and other variables) as a function of V.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}, {Name: "GSRun", Doc: "GSRun plots conductance over spiking.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}, {Name: "TimeRun", Doc: "TimeRun runs the equations over time.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}}, Fields: []types.Field{{Name: "Dir"}, {Name: "Tabs"}, {Name: "GABAstd", Doc: "standard chans version of GABAB"}, {Name: "GABAbv", Doc: "multiplier on GABAb as function of voltage"}, {Name: "GABAbo", Doc: "offset of GABAb function"}, {Name: "GABAberev", Doc: "GABAb reversal / driving potential"}, {Name: "Vstart", Doc: "starting voltage"}, {Name: "Vend", Doc: "ending voltage"}, {Name: "Vstep", Doc: "voltage increment"}, {Name: "Smax", Doc: "max number of spikes"}, {Name: "RiseTau", Doc: "rise time constant"}, {Name: "DecayTau", Doc: "decay time constant -- must NOT be same as RiseTau"}, {Name: "GsXInit", Doc: "initial value of GsX driving variable at point of synaptic input onset -- decays expoentially from this start"}, {Name: "MaxTime", Doc: "time when peak conductance occurs, in TimeInc units"}, {Name: "TauFact", Doc: "time constant factor used in integration: (Decay / Rise) ^ (Rise / (Decay - Rise))"}, {Name: "TimeSteps", Doc: "total number of time steps to take"}, {Name: "TimeInc", Doc: "time increment per step"}}}) diff --git a/chans/kir_plot/README.md b/chans/kir_plot/README.md deleted file mode 100644 index 026061723..000000000 --- a/chans/kir_plot/README.md +++ /dev/null @@ -1,24 +0,0 @@ -# slow AHP (sAHP): Calcium - -This channel is driven by a M-type mechanism operating on calcium sensor pathways that have longer time constants, updated at the theta cycle level so that guarantees a long baseline already. The logistic gating function operates with a high cutoff on the underlying Ca signal - -The logistic operates on integrated Ca: - -```Go - co = (ca - Off) - a = co / TauMax * (1 - exp(-co/Slope)) - b = -co / TauMax * (1 - exp(co/Slope)) - - tau = 1 / (a + b) - ninf = a / (a + b) -``` - -![Ninf from Ca](fig_sahp_ninf.png?raw=true "Ninf as a function of V (biological units)") - -![Tau from Ca](fig_sahp_tau.png?raw=true "Tau as a function of V (biological units)") - -![mAHP vs. fKNA](fig_mahp_vs_fkna.png?raw=true "mAHP vs. fast KNa (tau = 50, rise = 0.05)") - -The `Time Run` plot (above) shows how the mAHP current develops over time in response to spiking, in comparison to the KNa function, with the default "fast" parameters of 50msec and rise = 0.05. The mAHP is much more "anticipatory" due to the direct V sensitivity, whereas KNa is much more "reactive", responding only the the Na after spiking. - - diff --git a/chans/kir_plot/typegen.go b/chans/kir_plot/typegen.go deleted file mode 100644 index b3fd6ccd4..000000000 --- a/chans/kir_plot/typegen.go +++ /dev/null @@ -1,9 +0,0 @@ -// Code generated by "core generate -add-types"; DO NOT EDIT. - -package kir_plot - -import ( - "cogentcore.org/core/types" -) - -var _ = types.AddType(&types.Type{Name: "github.com/emer/axon/v2/chans/kir_plot.Plot", IDName: "plot", Methods: []types.Method{{Name: "GVRun", Doc: "VmRun plots the equation as a function of V", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}, {Name: "TimeRun", Doc: "TimeRun runs the equation over time.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}}, Fields: []types.Field{{Name: "Kir", Doc: "kIR function"}, {Name: "Vstart", Doc: "starting voltage"}, {Name: "Vend", Doc: "ending voltage"}, {Name: "Vstep", Doc: "voltage increment"}, {Name: "TimeSteps", Doc: "number of time steps"}, {Name: "TimeSpike", Doc: "do spiking instead of voltage ramp"}, {Name: "SpikeFreq", Doc: "spiking frequency"}, {Name: "TimeVstart", Doc: "time-run starting membrane potential"}, {Name: "TimeVend", Doc: "time-run ending membrane potential"}, {Name: "Dir"}, {Name: "Tabs"}}}) diff --git a/chans/mahp_plot/README.md b/chans/mahp_plot/README.md deleted file mode 100644 index 38f57829d..000000000 --- a/chans/mahp_plot/README.md +++ /dev/null @@ -1,24 +0,0 @@ -# M-type voltage gated potassium channel: mAHP - -This voltage-gated K channel, which is also inactivated by ACh muscarinic receptor activation, plays a role in medium time-scale afterhyperpolarization (mAHP). - -Original formulation due to Mainen & Sejnowski (1996) is widely used, and used here. - -```Go - vo = (V - Voff) - a = 0.001 * vo / (1 - exp(-vo/Vslope)) - b = -0.001 * vo / (1 - exp(vo/Vslope)) - - tau = 1 / (a + b) - ninf = a / (a + b) -``` - -![Ninf from V](fig_mahp_ninf.png?raw=true "Ninf as a function of V (biological units)") - -![Tau from V](fig_mahp_tau.png?raw=true "Tau as a function of V (biological units)") - -![mAHP vs. fKNA](fig_mahp_vs_fkna.png?raw=true "mAHP vs. fast KNa (tau = 50, rise = 0.05)") - -The `Time Run` plot (above) shows how the mAHP current develops over time in response to spiking, in comparison to the KNa function, with the default "fast" parameters of 50msec and rise = 0.05. The mAHP is much more "anticipatory" due to the direct V sensitivity, whereas KNa is much more "reactive", responding only the the Na after spiking. - - diff --git a/chans/mahp_plot/typegen.go b/chans/mahp_plot/typegen.go deleted file mode 100644 index bc80f0817..000000000 --- a/chans/mahp_plot/typegen.go +++ /dev/null @@ -1,9 +0,0 @@ -// Code generated by "core generate -add-types"; DO NOT EDIT. - -package mahp_plot - -import ( - "cogentcore.org/core/types" -) - -var _ = types.AddType(&types.Type{Name: "github.com/emer/axon/v2/chans/mahp_plot.Plot", IDName: "plot", Doc: "Plot holds the params, table, etc", Methods: []types.Method{{Name: "GVRun", Doc: "GVRun plots the conductance G (and other variables) as a function of V.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}, {Name: "TimeRun", Doc: "TimeRun runs the equation over time.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}}, Fields: []types.Field{{Name: "Mahp", Doc: "mAHP function"}, {Name: "Vstart", Doc: "starting voltage"}, {Name: "Vend", Doc: "ending voltage"}, {Name: "Vstep", Doc: "voltage increment"}, {Name: "TimeSteps", Doc: "number of time steps"}, {Name: "TimeSpike", Doc: "do spiking instead of voltage ramp"}, {Name: "SpikeFreq", Doc: "spiking frequency"}, {Name: "TimeVstart", Doc: "time-run starting membrane potential"}, {Name: "TimeVend", Doc: "time-run ending membrane potential"}, {Name: "Dir"}, {Name: "Tabs"}}}) diff --git a/chans/nmda_plot/README.md b/chans/nmda_plot/README.md deleted file mode 100644 index d2cf3edde..000000000 --- a/chans/nmda_plot/README.md +++ /dev/null @@ -1,33 +0,0 @@ -# nmda - -This plots the NMDA current function from Sanders et al, 2013 and Brunel & Wang (2001) (BW01), which is the most widely used active maintenance model. - -See also: https://brian2.readthedocs.io/en/stable/examples/frompapers.Brunel_Wang_2001.html - -Also used in: WeiWangWang12, FurmanWang08, NassarHelmersFrank18 - -Voltage dependence function based on Mg ion blocking is: - -```Go -1 / (1 + (C/3.57)*exp(-0.062 * vm)) -``` - -Jahr & Stevens (1990) originally derived this equation, using a Mg+ concentration C of 1 mM, so that factor = 0.28, used in BW01. Urakubo et al. (2008) used a concentration of 1.5 mM, citing Froemke & Dan (2002). Various other sources (Vink & Nechifor) indicate physiological ranges being around 1.2 - 1.4. - -![g_NMDA from V](fig_sandersetal_2013.png?raw=true "NMDA voltage gating conductance according to parameters from Sanders et al, 2013") - -In addition to this v-dependent Mg factor, conductance depends on presynaptic glutamate release, which in the basic BW01 model just increments with spikes and decays with a time constant of about 100 msec. - -The Urakubo et al (2008) model introduces allosteric dynamics, based on data from Froemke & Dan (2002), which we can capture simply using an inhibitory factor that increments with each spike and decays with a 100 msec time constant. However, their model has an effective Glu-binding decay time of only 30 msec. - - -# References - -* Jahr, C. E., & Stevens, C. F. (1990). A quantitative description of NMDA receptor-channel kinetic behavior. Journal of Neuroscience, 10(6), 1830–1837. https://doi.org/10.1523/JNEUROSCI.10-06-01830.1990 - -* Sanders, H., Berends, M., Major, G., Goldman, M. S., & Lisman, J. E. (2013). NMDA and GABAB (KIR) Conductances: The "Perfect Couple" for Bistability. Journal of Neuroscience, 33(2), 424–429. https://doi.org/10.1523/JNEUROSCI.1854-12.2013 - -* Vink, R., & Nechifor, M. (Eds.). (2011). Magnesium in the Central Nervous System. University of Adelaide Press. https://doi.org/10.1017/UPO9780987073051 - -* Urakubo, H., Honda, M., Froemke, R. C., & Kuroda, S. (2008). Requirement of an allosteric kinetics of NMDA receptors for spike timing-dependent plasticity. *The Journal of Neuroscience, 28(13),* 3310–3323. http://www.ncbi.nlm.nih.gov/pubmed/18367598 - diff --git a/chans/nmda_plot/typegen.go b/chans/nmda_plot/typegen.go deleted file mode 100644 index 2dc9a7066..000000000 --- a/chans/nmda_plot/typegen.go +++ /dev/null @@ -1,9 +0,0 @@ -// Code generated by "core generate -add-types"; DO NOT EDIT. - -package nmda_plot - -import ( - "cogentcore.org/core/types" -) - -var _ = types.AddType(&types.Type{Name: "github.com/emer/axon/v2/chans/nmda_plot.Plot", IDName: "plot", Methods: []types.Method{{Name: "GVRun", Doc: "GVRun plots the conductance G (and other variables) as a function of V.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}, {Name: "TimeRun", Doc: "TimeRun runs the equation over time.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}}, Fields: []types.Field{{Name: "NMDAStd", Doc: "standard NMDA implementation in chans"}, {Name: "NMDAv", Doc: "multiplier on NMDA as function of voltage"}, {Name: "MgC", Doc: "magnesium ion concentration -- somewhere between 1 and 1.5"}, {Name: "NMDAd", Doc: "denominator of NMDA function"}, {Name: "NMDAerev", Doc: "NMDA reversal / driving potential"}, {Name: "BugVoff", Doc: "for old buggy NMDA: voff value to use"}, {Name: "Vstart", Doc: "starting voltage"}, {Name: "Vend", Doc: "ending voltage"}, {Name: "Vstep", Doc: "voltage increment"}, {Name: "Tau", Doc: "decay time constant for NMDA current -- rise time is 2 msec and not worth extra effort for biexponential"}, {Name: "TimeSteps", Doc: "number of time steps"}, {Name: "TimeV", Doc: "voltage for TimeRun"}, {Name: "TimeGin", Doc: "NMDA Gsyn current input at every time step"}, {Name: "Dir"}, {Name: "Tabs"}}}) diff --git a/chans/sahp_plot/README.md b/chans/sahp_plot/README.md deleted file mode 100644 index 026061723..000000000 --- a/chans/sahp_plot/README.md +++ /dev/null @@ -1,24 +0,0 @@ -# slow AHP (sAHP): Calcium - -This channel is driven by a M-type mechanism operating on calcium sensor pathways that have longer time constants, updated at the theta cycle level so that guarantees a long baseline already. The logistic gating function operates with a high cutoff on the underlying Ca signal - -The logistic operates on integrated Ca: - -```Go - co = (ca - Off) - a = co / TauMax * (1 - exp(-co/Slope)) - b = -co / TauMax * (1 - exp(co/Slope)) - - tau = 1 / (a + b) - ninf = a / (a + b) -``` - -![Ninf from Ca](fig_sahp_ninf.png?raw=true "Ninf as a function of V (biological units)") - -![Tau from Ca](fig_sahp_tau.png?raw=true "Tau as a function of V (biological units)") - -![mAHP vs. fKNA](fig_mahp_vs_fkna.png?raw=true "mAHP vs. fast KNa (tau = 50, rise = 0.05)") - -The `Time Run` plot (above) shows how the mAHP current develops over time in response to spiking, in comparison to the KNa function, with the default "fast" parameters of 50msec and rise = 0.05. The mAHP is much more "anticipatory" due to the direct V sensitivity, whereas KNa is much more "reactive", responding only the the Na after spiking. - - diff --git a/chans/sahp_plot/typegen.go b/chans/sahp_plot/typegen.go deleted file mode 100644 index 97984b776..000000000 --- a/chans/sahp_plot/typegen.go +++ /dev/null @@ -1,9 +0,0 @@ -// Code generated by "core generate -add-types"; DO NOT EDIT. - -package sahp_plot - -import ( - "cogentcore.org/core/types" -) - -var _ = types.AddType(&types.Type{Name: "github.com/emer/axon/v2/chans/sahp_plot.Plot", IDName: "plot", Doc: "Plot holds the params, table, etc", Methods: []types.Method{{Name: "GVRun", Doc: "GCaRun plots the conductance G (and other variables) as a function of Ca.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}, {Name: "TimeRun", Doc: "TimeRun runs the equation over time.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}}, Fields: []types.Field{{Name: "Sahp", Doc: "sAHP function"}, {Name: "CaStart", Doc: "starting calcium"}, {Name: "CaEnd", Doc: "ending calcium"}, {Name: "CaStep", Doc: "calcium increment"}, {Name: "TimeSteps", Doc: "number of time steps"}, {Name: "TimeCaStart", Doc: "time-run starting calcium"}, {Name: "TimeCaD", Doc: "time-run CaD value at end of each theta cycle"}, {Name: "Dir"}, {Name: "Tabs"}}}) diff --git a/chans/skca_plot/README.md b/chans/skca_plot/README.md deleted file mode 100644 index 196fb094c..000000000 --- a/chans/skca_plot/README.md +++ /dev/null @@ -1,34 +0,0 @@ -# sKCa: Voltage-gated Calcium Channels - -This plots the sKCa current function, which describes the small-conductance calcium-activated potassium channel, using the equations described in Fujita et al (2012) based on Gunay et al (2008), (also Muddapu & Chakravarthy, 2021). There is a gating factor M that depends on the Ca concentration, modeled using an X / (X + C50) form Hill equation: - -```Go -M_hill(ca) = ca^h / (ca^h + c50^h) -``` - -This function is .5 when `ca == c50`, and the `h` default power (`Hill` param) of 4 makes it a sharply nonlinear function. - -SKCa can be activated by intracellular stores in a way that drives pauses in firing, and can require inactivity to recharge the Ca available for release. These intracellular stores can release quickly, have a slow decay once released, and the stores can take a while to rebuild, leading to rapidly triggered, long-lasting pauses that don't recur until stores have rebuilt, which is the observed pattern of firing of STNp pausing neurons, that open up a window for BG gating. - -`CaIn` = intracellular stores available for release; `CaR` = released amount from stores; `CaM` = K channel conductance gating factor driven by CaR binding. - -```Go - CaR -= CaR * CaRDecayDt - if spike { - CaR += CaIn * KCaR - } - if CaD < CaInThr { - CaIn += CaInDt * (1 - CaIn) - } -``` - - - -**Figure 1:** M gating as a function of Ca, using Hill function with exponent 4, C50 = .5. - - - -**Figure 2:** Time plot showing pausing and lack of recovery. The spiking input to the neuron is toggled every 200 msec (theta cycle), with 3 cycles shown. The CaIn level does not recover during the off phase -- 2 or more such phases are required. - - - diff --git a/chans/skca_plot/typegen.go b/chans/skca_plot/typegen.go deleted file mode 100644 index 0fc4f0288..000000000 --- a/chans/skca_plot/typegen.go +++ /dev/null @@ -1,9 +0,0 @@ -// Code generated by "core generate -add-types"; DO NOT EDIT. - -package skca_plot - -import ( - "cogentcore.org/core/types" -) - -var _ = types.AddType(&types.Type{Name: "github.com/emer/axon/v2/chans/skca_plot.Plot", IDName: "plot", Doc: "Plot holds the params, table, etc", Methods: []types.Method{{Name: "GCaRun", Doc: "GCaRun plots the conductance G (and other variables) as a function of Ca.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}, {Name: "TimeRun", Doc: "TimeRun runs the equation over time.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}}, Fields: []types.Field{{Name: "SKCa", Doc: "SKCa params"}, {Name: "CaParams", Doc: "time constants for integrating Ca from spiking across M, P and D cascading levels"}, {Name: "NoSpikeThr", Doc: "threshold of SK M gating factor above which the neuron cannot spike"}, {Name: "CaStep", Doc: "Ca conc increment for M gating func plot"}, {Name: "TimeSteps", Doc: "number of time steps"}, {Name: "TimeSpike", Doc: "do spiking instead of Ca conc ramp"}, {Name: "SpikeFreq", Doc: "spiking frequency"}, {Name: "Dir"}, {Name: "Tabs"}}}) diff --git a/chans/vgcc_plot/README.md b/chans/vgcc_plot/README.md deleted file mode 100644 index 1c9afdd68..000000000 --- a/chans/vgcc_plot/README.md +++ /dev/null @@ -1,30 +0,0 @@ -# VGCC: Voltage-gated Calcium Channels - -This plots the VGCC current function, which is an L-type Ca channel that opens as a function of membrane potential. It tends to broaden the effect of action potential spikes in the dendrites. - -```Go -G(vm) = -vm / (1 - exp(0.0756 * vm)) -``` - -```Go -M(vm) = 1 / (1 + exp(-(vm + 37))) // Tau = 3.6 msec -``` - -```Go -H(vm) = 1 / (1 + exp((vm + 41) * 2)) // Tau = 29 msec -``` - -```Go -VGCC(vm) = M^3 H * G(vm) -``` - -![M and H gating from V](fig_vgcc_m_h_from_v.png?raw=true "M and H gating factors as a function of V (biological units)") - -The intersection of M and H produces a very narrow membrane potential window centered around -40 mV where the gates are both activated, with the fast updating (3.6 msec tau) and cubic dependence on M essentially shutting off the current very quickly when the action potential goes away. The longer H time constant provides a slow adaptation-like dynamic that is sensitive to frequency (more adaptation at higher frequencies). - -![M and H over time](fig_vgcc_time_plot.png?raw=true "M and H gating factors developing over time in response to simulated spiking potentials") - -The `Time Run` plot (above) shows these dynamics playing out with a sequence of spiking. - -Functionally, the narrow voltage window restricts the significance of this channel to the peri-spiking time window, where the Ca++ influx provides a bit of extra sustain on the trailing edge of the spike. More importantly, the Ca++ provides a postsynaptic-only spiking signal for learning. - diff --git a/chans/vgcc_plot/typegen.go b/chans/vgcc_plot/typegen.go deleted file mode 100644 index 9646ab88c..000000000 --- a/chans/vgcc_plot/typegen.go +++ /dev/null @@ -1,9 +0,0 @@ -// Code generated by "core generate -add-types"; DO NOT EDIT. - -package vgcc_plot - -import ( - "cogentcore.org/core/types" -) - -var _ = types.AddType(&types.Type{Name: "github.com/emer/axon/v2/chans/vgcc_plot.Plot", IDName: "plot", Methods: []types.Method{{Name: "GVRun", Doc: "GVRun plots the conductance G (and other variables) as a function of V.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}, {Name: "TimeRun", Doc: "TimeRun runs the equation over time.", Directives: []types.Directive{{Tool: "types", Directive: "add"}}}}, Fields: []types.Field{{Name: "VGCC", Doc: "VGCC function"}, {Name: "Vstart", Doc: "starting voltage"}, {Name: "Vend", Doc: "ending voltage"}, {Name: "Vstep", Doc: "voltage increment"}, {Name: "TimeSteps", Doc: "number of time steps"}, {Name: "TimeSpike", Doc: "do spiking instead of voltage ramp"}, {Name: "SpikeFreq", Doc: "spiking frequency"}, {Name: "TimeVstart", Doc: "time-run starting membrane potential"}, {Name: "TimeVend", Doc: "time-run ending membrane potential"}, {Name: "Dir"}, {Name: "Tabs"}}}) diff --git a/examples/_attn/README.md b/sims/_attn/README.md similarity index 100% rename from examples/_attn/README.md rename to sims/_attn/README.md diff --git a/examples/_attn/attn.go b/sims/_attn/attn.go similarity index 100% rename from examples/_attn/attn.go rename to sims/_attn/attn.go diff --git a/examples/_attn/attn_env.go b/sims/_attn/attn_env.go similarity index 100% rename from examples/_attn/attn_env.go rename to sims/_attn/attn_env.go diff --git a/examples/_attn/fig_attn_trn_reynolds_heeger_09_small_big_attn.png b/sims/_attn/fig_attn_trn_reynolds_heeger_09_small_big_attn.png similarity index 100% rename from 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sims/deep_music/typegen.go diff --git a/examples/equations/README.md b/sims/equations/README.md similarity index 100% rename from examples/equations/README.md rename to sims/equations/README.md diff --git a/examples/equations/equations.go b/sims/equations/equations.go similarity index 85% rename from examples/equations/equations.go rename to sims/equations/equations.go index d0af626da..283b3e582 100644 --- a/examples/equations/equations.go +++ b/sims/equations/equations.go @@ -10,14 +10,7 @@ package main import ( "cogentcore.org/core/tensor/tensorfs" - "github.com/emer/axon/v2/chans/ak_plot" - "github.com/emer/axon/v2/chans/gabab_plot" - "github.com/emer/axon/v2/chans/kir_plot" - "github.com/emer/axon/v2/chans/mahp_plot" - "github.com/emer/axon/v2/chans/nmda_plot" - "github.com/emer/axon/v2/chans/sahp_plot" - "github.com/emer/axon/v2/chans/skca_plot" - "github.com/emer/axon/v2/chans/vgcc_plot" + "github.com/emer/axon/v2/chans/chanplots" "github.com/emer/emergent/v2/egui" ) @@ -46,7 +39,7 @@ type Plots struct { // voltage gated calcium channels which can otherwise drive runaway excitatory currents. // See AKsParams for a much simpler version that works fine when full AP-like spikes are // not simulated, as in our standard axon models. - AK ak_plot.Plot `new-window:"+" display:"no-inline"` + AK chanplots.AKPlot `new-window:"+" display:"no-inline"` // GABA-B is an inhibitory channel activated by the usual GABA inhibitory neurotransmitter, // which is coupled to the GIRK G-protein coupled inwardly rectifying potassium (K) channel. @@ -54,12 +47,12 @@ type Plots struct { // The inward rectification is caused by a Mg+ ion block *from the inside* of the neuron, // which means that these channels are most open when the neuron is hyperpolarized (inactive), // and thus it serves to keep inactive neurons inactive. Based on Thomson & Destexhe (1999). - GABAB gabab_plot.Plot `new-window:"+" display:"no-inline"` + GABAB chanplots.GababPlot `new-window:"+" display:"no-inline"` // Kir is the kIR potassium inwardly rectifying current, // based on the equations from Lindroos et al (2018). // The conductance is highest at low membrane potentials. - Kir kir_plot.Plot `new-window:"+" display:"no-inline"` + Kir chanplots.KirPlot `new-window:"+" display:"no-inline"` // Mahp implements an M-type medium afterhyperpolarizing (mAHP) channel, // where m also stands for muscarinic due to the ACh inactivation of this channel. @@ -68,14 +61,14 @@ type Plots struct { // There is one gating variable n updated over time with a tau that is also voltage dependent. // The infinite-time value of n is voltage dependent according to a logistic function // of the membrane potential, centered at Voff with slope Vslope. - Mahp mahp_plot.Plot `new-window:"+" display:"no-inline"` + Mahp chanplots.MahpPlot `new-window:"+" display:"no-inline"` // NMDA implements NMDA dynamics, based on Jahr & Stevens (1990) equations // which are widely used in models, from Brunel & Wang (2001) to Sanders et al. (2013). // The overall conductance is a function of a voltage-dependent postsynaptic factor based // on Mg ion blockage, and presynaptic Glu-based opening, which in a simple model just // increments - NMDA nmda_plot.Plot `new-window:"+" display:"no-inline"` + NMDA chanplots.NMDAPlot `new-window:"+" display:"no-inline"` // Sahp implements a slow afterhyperpolarizing (sAHP) channel, // It has a slowly accumulating calcium value, aggregated at the @@ -85,7 +78,7 @@ type Plots struct { // For the theta-cycle updating, the normal m-type tau is all within // the scope of a single theta cycle, so we just omit the time integration // of the n gating value, but tau is computed in any case. - Sahp sahp_plot.Plot `new-window:"+" display:"no-inline"` + Sahp chanplots.SahpPlot `new-window:"+" display:"no-inline"` // SKCa describes the small-conductance calcium-activated potassium channel, // activated by intracellular stores in a way that drives pauses in firing, @@ -98,11 +91,11 @@ type Plots struct { // CaM = K channel conductance gating factor driven by CaR binding, // computed using the Hill equations described in Fujita et al (2012), Gunay et al (2008) // (also Muddapu & Chakravarthy, 2021): X^h / (X^h + C50^h) where h ~= 4 (hard coded) - SKCa skca_plot.Plot `new-window:"+" display:"no-inline"` + SKCa chanplots.SKCaPlot `new-window:"+" display:"no-inline"` // VGCC control the standard L-type Ca channel. // All functions based on Urakubo et al (2008). - VGCC vgcc_plot.Plot `new-window:"+" display:"no-inline"` + VGCC chanplots.VGCCPlot `new-window:"+" display:"no-inline"` } func (pl *Plots) Config(root *tensorfs.Node) { diff --git a/examples/equations/typegen.go b/sims/equations/typegen.go similarity index 100% rename from examples/equations/typegen.go rename to sims/equations/typegen.go diff --git a/examples/hip/README.md b/sims/hip/README.md similarity index 100% rename from examples/hip/README.md rename to sims/hip/README.md diff --git a/examples/hip/config.go 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examples/ra25x/grunter_ror.py rename to sims/ra25x/grunter_ror.py diff --git a/examples/ra25x/params.go b/sims/ra25x/params.go similarity index 100% rename from examples/ra25x/params.go rename to sims/ra25x/params.go diff --git a/examples/ra25x/params_good/config.toml b/sims/ra25x/params_good/config.toml similarity index 100% rename from examples/ra25x/params_good/config.toml rename to sims/ra25x/params_good/config.toml diff --git a/examples/ra25x/params_good/params.toml b/sims/ra25x/params_good/params.toml similarity index 100% rename from examples/ra25x/params_good/params.toml rename to sims/ra25x/params_good/params.toml diff --git a/examples/ra25x/params_good/params_all.txt b/sims/ra25x/params_good/params_all.txt similarity index 100% rename from examples/ra25x/params_good/params_all.txt rename to sims/ra25x/params_good/params_all.txt diff --git a/examples/ra25x/params_good/params_layers.txt b/sims/ra25x/params_good/params_layers.txt similarity index 100% rename from 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