Leech Heart (HE) Motor Neuron conductances contributions to NN activity (Lamb & Calabrese 2013)

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Accession:153355
"... To explore the relationship between conductances, and in particular how they influence the activity of motor neurons in the well characterized leech heartbeat system, we developed a new multi-compartmental Hodgkin-Huxley style leech heart motor neuron model. To do so, we evolved a population of model instances, which differed in the density of specific conductances, capable of achieving specific output activity targets given an associated input pattern. ... We found that the strengths of many conductances, including those with differing dynamics, had strong partial correlations and that these relationships appeared to be linked by their influence on heart motor neuron activity. Conductances that had positive correlations opposed one another and had the opposite effects on activity metrics when perturbed whereas conductances that had negative correlations could compensate for one another and had similar effects on activity metrics. "
Reference:
1 . Lamb DG, Calabrese RL (2013) Correlated conductance parameters in leech heart motor neurons contribute to motor pattern formation. PLoS One 8:e79267 [PubMed]
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Leech;
Cell Type(s): Leech heart motor neuron (HE);
Channel(s): I Na,p; I A; I K; I K,leak; I K,Ca; I Sodium; I Calcium; I Na, leak;
Gap Junctions: Gap junctions;
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: GENESIS;
Model Concept(s): Action Potential Initiation; Activity Patterns; Bursting; Temporal Pattern Generation; Detailed Neuronal Models; Parameter sensitivity; Conductance distributions;
Implementer(s): Lamb, Damon [Damon.Lamb at neurology.ufl.edu];
Search NeuronDB for information about:  I Na,p; I A; I K; I K,leak; I K,Ca; I Sodium; I Calcium; I Na, leak;
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LambCalabrese2013
lgenesis-noX
neurokit
prototypes
README
camit.p
compt_chop.g *
compt_chop.g.bu *
defaults.g *
defaults.g.bu *
hot *
Neurokit.g *
Neurokit.g.bu *
NEURON.g *
NEURON.g.bu *
newcamit.p
synactivator.g *
synactivator.g.bu *
userprefs.g *
userprefs.g.bu *
xall.g *
xall.g.bu *
xcell_funcs.g *
xcell_funcs.g.bu *
xchannel_funcs.g *
xchannel_funcs.g.bu *
xgeom.g *
xgeom.g.bu *
xgraph_funcs.g *
xgraph_funcs.g.bu *
xicons.g *
xicons.g.bu *
xout_funcs.g *
xout_funcs.g.bu *
xrun.g *
xrun.g.bu *
xselect.g *
xselect.g.bu *
xstartup.g *
xstartup.g.bu *
xtitle.g *
xtitle.g.bu *
                            
//genesis

int kincolor = 15

function do_xchannel_funcs
	create x1form /channel_params  \
	    [480,440,{user_screenwidth - 480},450]
	disable /channel_params
	pushe /channel_params
	create x1graph alpha [0,0,50%,42%] -range [-0.1,0,0.1,1]
	setfield alpha ymin 0 overlay 0 XUnits Volts YUnits "1/sec"
	create x1graph beta [50%,0,50%,42%] -range [-0.1,0,0.1,1]
	setfield beta ymin 0 overlay 0 XUnits Volts YUnits "1/sec"
	create x1graph taus [0,42%,50%,42%] -range [-0.1,0,0.1,1]
	setfield taus ymin 0 overlay 0 XUnits Volts YUnits "sec"
	create x1graph minf [50%,42%,50%,42%] -range [-0.1,0,0.1,1]
	setfield minf ymin 0 overlay 0 XUnits Volts YUnits "minf"
	create x1dialog gate [4,4:minf.bottom,19%,30] -value "X" -script  \
	    "do_plot_kinetics "<widget>
	create x1toggle overlay [20%,4:minf.bottom,19%,30]
	setfield ^ label0 "overlay off" label1 "overlay on"
	create x1label MODIFY [40%,4:minf.bottom,11%,30] -title "MODIFY:"
	create x1button alphabutton [52%,4:minf.bottom,11%,30] -title  \
	    alpha -script "scale_gate alpha"
	create x1button betabutton [64%,4:minf.bottom,11%,30] -title beta \
	     -script "scale_gate beta"
	create x1button taubutton [76%,4:minf.bottom,11%,30] -title tau  \
	    -script "scale_gate tau"
	create x1button minfbutton [88%,4:minf.bottom,11%,30] -title  \
	    m_inf -script "scale_gate minf"

	create x1button duplicate [0,4:overlay.bottom,14%,30] -title  \
	    "Dup Gate" -script dup_gate
	create x1button restore [14%,4:overlay.bottom,14%,30] -title  \
	    "Restore" -script "echo Not yet implemented"
	create x1dialog sx [28%,4:overlay.bottom,18%,30] -value 1.0
	create x1dialog sy [46%,4:overlay.bottom,18%,30] -value 1.0
	create x1dialog ox [64%,4:overlay.bottom,18%,30] -value 0.0
	create x1dialog oy [82%,4:overlay.bottom,18%,30] -value 0.0
	pope
end

function calc_cond(name)
	str name
	float len, dia, gmax
	float area = {getfield {comptpath} Cm}

	/*
	len = calc_len({comptpath})
	dia = calc_dia({comptpath})
	*/
	area = area/CM
	if (({strcmp {getfield {channelpath} object->name} hh_channel} == 0) \
 || ({strcmp {getfield {channelpath} object->name} tabchannel} == 0) \
 || ({strcmp {getfield {channelpath} object->name} tab2Dchannel} == 0))
		gmax = {getfield {name} Gbar}
	else
		if ( \
		    {strcmp {getfield {channelpath} object->name} vdep_channel} == 0 \
		    )
			gmax = {getfield {name} gbar}
		else
			gmax = {getfield {name} gmax}
		end
	end

	/*
	return({gmax/(len * dia * PI)})

	As a general rule, CM is less likely to be tweaked than RM and RA
	*/
	return ((gmax/area))
end

function calc_reversal(name)
	str name
	float rev
	if ( \
	    {strcmp {getfield {channelpath} object->name} hh_channel} == 0 \
	    )
		rev = {getfield {name} Ek}
	else
		rev = {getfield {name} Ek}
	end

	return ((rev))
end

function set_cond(widget)
	str widget

	/*
	float len,dia
	*/
	float gmax = {getfield {widget} value}
	float area
	str name, chan
	float temp

	chan = {getfield /compt_display/draw/{getfield /compt_display/draw pixchoose} text}


	if (({getfield /compt_select/scope state}) == 1)	// global

		if ( \
		    ({strcmp {getfield {channelpath} object->name} hh_channel} == 0) || ({strcmp {getfield {channelpath} object->name} tabchannel} == 0) \
		    )
			foreach name ( \
			    {el {cellpath}/#[][activation>0.99]})
				area = {getfield {name} Cm}
				area = area/CM
				temp = gmax*area
				setfield {name}/{chan} Gbar {temp}
			end
		else
			if ( \
			    {strcmp {getfield {channelpath} object->name} vdep_channel} == 0 \
			    )
				foreach name ( \
				    {el {cellpath}/#[][activation>0.99]} \
				    )
					area = {getfield {name} Cm}
					area = area/CM
					temp = gmax*area
					setfield {name}/{chan}  \
					    gbar {temp}
				end
			else
				foreach name ( \
				    {el {cellpath}/#[][activation>0.99]} \
				    )
					area = {getfield {name} Cm}
					area = area/CM
					temp = gmax*area
					setfield {name}/{chan}  \
					    gmax {temp}
				end
			end
		end
	else	// local

		area = {getfield {comptpath} Cm}
		area = area/CM

		gmax = gmax*area

		if ( \
		    ({strcmp {getfield {channelpath} object->name} hh_channel} == 0) || ({strcmp {getfield {channelpath} object->name} tabchannel} == 0) \
		    )
			setfield {channelpath} Gbar {gmax}
		else
			if ( \
			    {strcmp {getfield {channelpath} object->name} vdep_channel} == 0 \
			    )
				setfield {channelpath} gbar {gmax}
			else
				setfield {channelpath} gmax {gmax}
			end
		end
	end
end

function set_revpotl(widget)
	str widget

	float rev = {getfield {widget} value}
	float area
	str name, chan
	float temp

	chan = {getfield /compt_display/draw/{getfield /compt_display/draw pixchoose} text}
	if (({getfield /compt_select/scope state}) == 1)	// global

		foreach name ({el {cellpath}/#[][activation>0.99]})
			setfield {name}/{chan} Ek {rev}
		end
	else	// local

		setfield {channelpath} Ek {rev}
	end
end

function update_channel_params
	/*
	echo updating channel parameters
	*/
end

function hilight_channel
	float x, y
	str pix

	pushe /compt_display/draw
	pix = {getfield . pixchoose}
	setfield hilight tx {getfield {pix} tx} ty {getfield {pix} ty}
	xupdate .
	pope
end

function deleteelms(path)

	str	elm

	foreach elm ({el {path}})
	    delete {elm}
	end
end

function do_plot_kinetics(widget)
	str widget
	str gate = {getfield {widget} value}
	str channeltype
	str gatepath
	float x, y, a, b, tau
	float xmin = -0.1, xmax = 0.07, dx = 0.002
	float amax = -1.0, bmax = -1.0, mmax = -1.0, tmax = -1.0
	str kinname
	int i

	ce /channel_params
	dx = 0.005

	if (!({exists {channelpath}}))
		return
	end

	kinname = {getfield {channelpath} name} @ "->" @ (gate)

	channeltype = {getfield {channelpath} object->name}
	if (({getfield /channel_params/overlay state}) == 0)
		//DHB call alpha RESET
		//DHB call beta RESET
		//DHB call taus RESET
		//DHB call minf RESET
		deleteelms alpha/##[ISA=xplot]
		deleteelms beta/##[ISA=xplot]
		deleteelms taus/##[ISA=xplot]
		deleteelms minf/##[ISA=xplot]
		setfield alpha ymax 1e6
		setfield beta ymax 1e6
		setfield taus ymax 1e6
		setfield taus ymax 1e6
		kincolor = 15
	else
		kincolor = kincolor + 15
		if (kincolor > 63)
			kincolor = kincolor - 60
		end
		amax = {getfield alpha ymax}
		bmax = {getfield beta ymax}
		mmax = {getfield minf ymax}
		tmax = {getfield taus ymax}
	end

	if ({strcmp {channeltype} hh_channel} == 0)
		if ( \
		    !(({strcmp {gate} "X"} == 0) || ({strcmp {gate} "Y"} == 0)) \
		    )
			echo For hh channels, gate must be X or Y
			return
		end
	end

	if ({strcmp {channeltype} tabchannel} == 0)
		if ( \
		    !(({strcmp {gate} "X"} == 0) || ({strcmp {gate} "Y"} == 0) || ({strcmp {gate} "Z"} == 0)) \
		    )
			echo For vdep channels, gate must be X or Y or Z
			return
		end
		if ({getfield {channelpath} {gate}_alloced} == 1)
			xmin = {getfield {channelpath} {gate}_A->xmin}
			xmax = {getfield {channelpath} {gate}_A->xmax}
			dx = {getfield {channelpath} {gate}_A->dx}
			if (dx < ((xmax - xmin)/100.0))
				dx = (xmax - xmin)/100.0
			end
		else
			echo gate {gate} not allocated
			return
		end
	end

	if ( \
	    ({strcmp {channeltype} hh_channel} == 0) || ({strcmp {channeltype} tabchannel} == 0) \
	    )

		if (!{exists alpha/{kinname}})
		    create xplot alpha/{kinname}
		end

		if (!{exists beta/{kinname}})
		    create xplot beta/{kinname}
		end

		if (!{exists taus/{kinname}})
		    create xplot taus/{kinname}
		end

		for (x = xmin; x <= xmax; x = x + dx)

			a = {call {channelpath} CALC_ALPHA {gate} {x}}
			if (amax < a)
				amax = a
			end

			b = {call {channelpath} CALC_BETA {gate} {x}}
			if (bmax < b)
				bmax = b
			end
			tau = 1/(a + b)
			if (tau > tmax)
				tmax = tau
			end

			call alpha/{kinname} ADDPTS {x} {a}
			setfield alpha/{kinname} fg {kincolor}

			call beta/{kinname} ADDPTS {x} {b}
			setfield beta/{kinname} fg {kincolor}

			call taus/{kinname} ADDPTS {x} {tau}
			setfield taus/{kinname} fg {kincolor}
		end

		if (!{exists minf/{kinname}})
		    create xplot minf/{kinname}
		end

		for (x = xmin; x <= xmax; x = x + dx)
			y = {call {channelpath} CALC_MINF {gate} {x}}
			if (y > mmax)
				mmax = y
			end

			call minf/{kinname} ADDPTS {x} {y}
			setfield minf/{kinname} fg {kincolor}
		end

		setfield alpha ymax {amax} xmin {xmin} xmax {xmax}
		setfield beta ymax {bmax} xmin {xmin} xmax {xmax}
		setfield taus ymax {tmax} xmin {xmin} xmax {xmax}
		setfield minf ymax {mmax} xmin {xmin} xmax {xmax}
	end

	if ({strcmp {channeltype} vdep_channel} == 0)
		gatepath = (channelpath) @ "/" @ (gate)
		if (!({exists {gatepath}}))
			echo Gate {gatepath} does not exist.
			return
		end
		if ( \
		    {strcmp {getfield {gatepath} object->name} vdep_gate} != 0 \
		    )
			xmin = {getfield {gatepath} alpha->xmin}
			xmax = {getfield {gatepath} alpha->xmax}
			dx = {getfield {gatepath} alpha->dx}
			if (dx < ((xmax - xmin)/100.0))
				dx = (xmax - xmin)/100.0
			end
		end

		if (!{exists alpha/{kinname}})
		    create xplot alpha/{kinname}
		end

		if (!{exists beta/{kinname}})
		    create xplot beta/{kinname}
		end

		if (!{exists taus/{kinname}})
		    create xplot taus/{kinname}
		end

		for (x = xmin; x <= xmax; x = x + dx)

			a = {call {gatepath} CALC_ALPHA {x}}
			if (amax < a)
				amax = a
			end

			b = {call {gatepath} CALC_BETA {x}}
			if (bmax < b)
				bmax = b
			end
			tau = 1/(a + b)
			if (tau > tmax)
				tmax = tau
			end

			call alpha/{kinname} ADDPTS {x} {a}
			setfield alpha/{kinname} fg {kincolor}

			call beta/{kinname} ADDPTS {x} {b}
			setfield beta/{kinname} fg {kincolor}

			call taus/{kinname} ADDPTS {x} {tau}
			setfield taus/{kinname} fg {kincolor}
		end

		if (!{exists minf/{kinname}})
		    create xplot minf/{kinname}
		end
		for (x = xmin; x <= xmax; x = x + dx)
			y = {call {gatepath} CALC_MINF {x}}
			if (y > mmax)
				mmax = y
			end

			call minf/{kinname} ADDPTS {x} {y}
			setfield minf/{kinname} fg {kincolor}
		end

		setfield alpha ymax {amax} xmin {xmin} xmax {xmax}
		setfield beta ymax {bmax} xmin {xmin} xmax {xmax}
		setfield taus ymax {tmax} xmin {xmin} xmax {xmax}
		setfield minf ymax {mmax} xmin {xmin} xmax {xmax}
	end
	if ({strcmp {channeltype} channelC2} == 0)
	end
	if ({strcmp {channeltype} table} == 0)
	end

	ce /
end// do_plot_kinetics


function scale_gate(mode)
	str mode
	str gate
	float sx = {getfield /channel_params/sx value}
	float sy = {getfield /channel_params/sy value}
	float ox = {getfield /channel_params/ox value}
	float oy = {getfield /channel_params/oy value}
	str channeltype = {getfield {channelpath} object->name}

	if ({strcmp {channeltype} tabchannel} == 0)
		gate = {getfield /channel_params/gate value}
		scaletabchan {channelpath} {gate} {mode} {sx} {sy} {ox}  \
		    {oy}
		do_plot_kinetics /channel_params/gate
		return
	end
	if ({strcmp {channeltype} vdep_channel} == 0)
		gate = (channelpath) @ "/" @ ({getfield /channel_params/gate value})
		if (!{exists {gate}})
			echo gate '{gate}' does not exist
			return
		end
		if ({strcmp {getfield {gate} object->name} tabgate} != 0 \
		    )
			echo gate '{gate}' is not a tabgate
			return
		end
		// For tabgates, argv[1] is the tabgate path and argv[2] is ignored
		scaletabchan {gate} {gate} {mode} {sx} {sy} {ox} {oy}
		do_plot_kinetics /channel_params/gate
		return
	end
	echo channel type {channeltype} cannot be manipulated this way
end

function dup_gate
	str gate
	str channeltype = {getfield {channelpath} object->name}
	if ({strcmp {channeltype} tabchannel} == 0)
		gate = {getfield /channel_params/gate value}
		duplicatetable {channelpath} {gate}
		return
	end
	if ({strcmp {channeltype} vdep_channel} == 0)
		gate = (channelpath) @ "/" @ ({getfield /channel_params/gate value})
		if (!{exists {gate}})
			echo gate '{gate}' does not exist
			return
		end
		if ({strcmp {getfield {gate} object->name} tabgate} != 0 \
		    )
			echo gate '{gate}' is not a tabgate
			return
		end
		// For tabgates, argv[1] is the tabgate path and argv[2] is ignored
		duplicatetable {gate} {gate}
		return
	end
	echo channel type {channeltype} cannot be manipulated this way
end