Hippocampal CA3 network and circadian regulation (Stanley et al. 2013)

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Accession:142104
This model produces the hippocampal CA3 neural network model used in the paper below. It has two modes of operation, a default mode and a circadian mode. In the circadian mode, parameters are swept through a range of values. This model can be quite easily adapted to produce theta and gamma oscillations, as certain parameter sweeps will reveal (see Figures). BASH scripts interact with GENESIS 2.3 to implement parameter sweeps. The model contains four cell types derived from prior papers. CA3 pyramidal are derived from Traub et al (1991); Basket, stratum oriens (O-LM), and Medial Septal GABAergic (MSG) interneurons are taken from Hajos et al (2004).
Reference:
1 . Stanley DA, Talathi SS, Parekh MB, Cordiner DJ, Zhou J, Mareci TH, Ditto WL, Carney PR (2013) Phase shift in the 24-hour rhythm of hippocampal EEG spiking activity in a rat model of temporal lobe epilepsy. J Neurophysiol 110:1070-86 [PubMed]
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: Hippocampus; Medial Septum;
Cell Type(s): Hippocampus CA3 pyramidal GLU cell; Hippocampus CA3 interneuron basket GABA cell; Hippocampus CA3 stratum oriens lacunosum-moleculare interneuron; Hippocampus septum medial GABAergic neuron;
Channel(s): I Na,t; I A; I K; I h; I K,Ca; I Calcium;
Gap Junctions:
Receptor(s): GabaA; AMPA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: GENESIS; MATLAB;
Model Concept(s): Epilepsy; Brain Rhythms; Circadian Rhythms;
Implementer(s): Stanley, David A ;
Search NeuronDB for information about:  Hippocampus CA3 pyramidal GLU cell; Hippocampus CA3 interneuron basket GABA cell; GabaA; AMPA; I Na,t; I A; I K; I h; I K,Ca; I Calcium; Gaba; Glutamate; 

// ############# Like write_everything.g, except
// ############# display the total current from all
// ############# compartments, rather than just the
// ############# present compartment
// ## Dave Stanley Feb 10 2010


int scriptmode=7
int plot_HPo_channel=0
int show_calcium = 0

	//Called by plot_graphs
	//Writes Vm to graph and to file
function write_Vm (source, dest_plot, dest_save, graphics_on)
str diffampname = {{source} @ "/../soma/diffamp" @ {countelementlist {source}/../soma/#[TYPE=diffamp]}} // Create name & number for diffamp
str dest_info = {"." @ {dest_save} @ "_info"}

	openfile {dest_info} w

	create diffamp {diffampname}
	setfield {diffampname} plus 0 minus 0 gain 1000 saturation inf		// Convert V to mV

	if (scriptmode == 7)
//		addmsg {source}/../soma {diffampname} PLUS Vm
		addmsg {source} {diffampname} PLUS Vm
	else
		addmsg {source} {diffampname} PLUS Vm
	end
	if (graphics_on); addmsg {diffampname} {{dest_plot} @ "/Vm"} PLOT output *Vm  *blue; end
	addmsg {diffampname} {dest_save} SAVE output

end



function write_everything (source, dest_plot, dest_save, pfield, graphics_on, sum_currents)
	str curr_chan
	int col = 15
	str dest_info = {"." @ {dest_save} @ "_info"}
	
	
	
	openfile {dest_info} w
	
	xcolorscale hot
	
	
	
	// %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Enter calculator (sum) mode #########################################
	if (sum_currents == 1)
		str curr_chan_name
		str calc_path
		foreach curr_chan ({el {source}/../#/#[TYPE=GENvgpores]} {el {source}/../#/#[TYPE=GENVhalf]} {el {source}/../#/#[TYPE=GENtabchan]} \
						{el {source}/../#/#[TYPE=tabchannel]} {el {source}/../#/#[TYPE=vdep_channel]} {el {source}/../#/#[TYPE=GENsynpores]})
			
			curr_chan_name = {getfield {curr_chan} name}
			calc_path = {{curr_chan} @ "/../.."}
		//	echo {calc_path}
			
		
			if ({curr_chan_name} == "K_AHPs_m")
				curr_chan_name = "K_AHP_m"
			end
			if ({curr_chan_name} == "K_Cs_m")
				curr_chan_name = "K_C_m"
			end
			if ({curr_chan_name} == "K_AHPs")
				curr_chan_name = "K_AHP"
			end
			if ({curr_chan_name} == "K_Cs")
				curr_chan_name = "K_C"
			end
			if ({curr_chan_name} == "NaA")
				curr_chan_name = "Na"
			end
			if ({curr_chan_name} == "K_DRA")
				curr_chan_name = "K_DR"
			end
			
			if ( !({exists {calc_path}/sum_{curr_chan_name}}) )
				create calculator {calc_path}/sum_{curr_chan_name}
				setfield {calc_path}/sum_{curr_chan_name} resetclock 0
				addfield {calc_path}/sum_{curr_chan_name} channel_name
				setfield {calc_path}/sum_{curr_chan_name} channel_name {curr_chan_name}
			end
		
			addmsg {curr_chan} {calc_path}/sum_{curr_chan_name} SUM {pfield}k
			
		end
		
				// Adds messages from "pooled" channel and Ca_concen objects
		foreach curr_chan ({el {source}/../#/#[TYPE=calculator],{source}/../#/volweighted_Ca#[TYPE=diffamp]})
			curr_chan_name = {getfield {curr_chan} name}
			calc_path = {{curr_chan} @ "/../.."}
		//	echo {calc_path}
			
			if ( !({exists {calc_path}/sum_{curr_chan_name}}) )
				create calculator {calc_path}/sum_{curr_chan_name}
				setfield {calc_path}/sum_{curr_chan_name} resetclock 0
				addfield {calc_path}/sum_{curr_chan_name} channel_name
				setfield {calc_path}/sum_{curr_chan_name} channel_name {curr_chan_name}
			end
			addmsg {curr_chan} {calc_path}/sum_{curr_chan_name} SUM output
		end

		// Look after High Open Probability stuff for SK2 channels - get average
		if ( plot_HPo_channel )
			create neutral {source}/../HPo_stuff
			foreach curr_chan ({el {source}/../sum_HPo#[TYPE=calculator]})
				move {curr_chan} {source}/../HPo_stuff
			end		

			float total_Gk = 0
			foreach curr_chan ({el /pyr_array/pyr/#/allpools/#/HPo#})
				if ( {getfield {curr_chan} name} == "HPo_SK2" )
					total_Gk = {getfield {curr_chan} Gbar} + total_Gk
				elif ( {getfield {curr_chan} name} == "HPo_SK2_m" )
					total_Gk = {getfield {curr_chan} Nt}*{10.0*{onepS}} + total_Gk
				end
			end
			
			if ( !({exists {source}/../HPo_norm}) )
				create diffamp {source}/../HPo_norm
				setfield ^ gain {1.0/total_Gk} saturation 999
				addfield ^ channel_name
				setfield ^ channel_name {getfield {source}/../HPo_stuff/sum_HPo_allpools channel_name}
				addmsg {source}/../HPo_stuff/sum_HPo_allpools {source}/../HPo_norm PLUS output
			end
		end

		//	%%%%% Add calculator object messages 
		foreach curr_chan ({el {source}/../#[TYPE=calculator],{source}/../#[TYPE=diffamp]})
			//echo  calculator currentchannel {curr_chan}
			if (graphics_on); addmsg {curr_chan} {{dest_plot} @ "/Ik"} PLOT output *sum_{getfield {curr_chan} channel_name} *{col}; end
			addmsg {curr_chan} {dest_save} SAVE output
			writefile {dest_info} {curr_chan}
			col = col + 7
			if (col > 63)
			        col = col - 60
			end
		end
		
	// ############################# End calculator mode %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
	
	elif (sum_currents == 0)	
	/// %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Regular Mode %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
	
		foreach curr_chan ({el {source}/#[TYPE=GENvgpores]} {el {source}/#[TYPE=GENVhalf]} {el {source}/#[TYPE=GENsynpores]} {el {source}/#[TYPE=GENtabchan]})
			if ( {getfield {curr_chan} originalchannel} == "GABA_B" )
				if ( {getfield {curr_chan} mode} == "regular" )
					if (graphics_on) 
						addmsg {curr_chan}/G_protein {{dest_plot} @ "/Ik"} PLOT {pfield}k *{getfield {curr_chan} name}  *{col}
						addmsg {curr_chan}/K_pore {{dest_plot} @ "/Ik"} PLOT {pfield}k *{getfield {curr_chan} name}  *{col}
						//addmsg {curr_chan}/G_protein {{dest_plot} @ "/Ik"} PLOT Gconcs *{getfield {curr_chan} name}  *{col}
					end
		
		
					//addmsg {curr_chan}/G_protein {dest_save} SAVE {pfield}k
					addmsg {curr_chan}/K_pore {dest_save} SAVE {pfield}k
				else
					if (graphics_on); addmsg {curr_chan} {{dest_plot} @ "/Ik"} PLOT {pfield}k *{getfield {curr_chan} name}  *{col}; end
					addmsg {curr_chan} {dest_save} SAVE {pfield}k
				end
			else
				if (graphics_on); addmsg {curr_chan} {{dest_plot} @ "/Ik"} PLOT {pfield}k *{getfield {curr_chan} name}  *{col}; end
				addmsg {curr_chan} {dest_save} SAVE {pfield}k
			end
			writefile {dest_info} {curr_chan}
			col = col + 7
			if (col > 63)
			        col = col - 60
			end
		end
	
		
		
		foreach curr_chan ({el {source}/#[TYPE=tabchannel]} {el {source}/#[TYPE=vdep_channel]})
			if (graphics_on); addmsg {curr_chan} {{dest_plot} @ "/Ik"} PLOT {pfield}k *{getfield {curr_chan} name} *{col}; end
			addmsg {curr_chan} {dest_save} SAVE {pfield}k
			writefile {dest_info} {curr_chan}
			col = col + 7
			if (col > 63)
			        col = col - 60
			end
		end
		
		foreach curr_chan ({el {source}/#[TYPE=calculator],{source}/Ca#[TYPE=diffamp]})
			if (graphics_on); addmsg {curr_chan} {{dest_plot} @ "/Ik"} PLOT output *{getfield {curr_chan} name} *{col}; end
			addmsg {curr_chan} {dest_save} SAVE output
			writefile {dest_info} {curr_chan}
			col = col + 7
			if (col > 63)
			        col = col - 60
			end
		end
		
	// ############################# End regular mode %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
	elif (sum_currents == -1)
	// ############################# Single pool mode %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
	
		foreach curr_chan ({el {source}/#[TYPE=GENvgpores]} {el {source}/#[TYPE=GENVhalf]} {el {source}/#[TYPE=GENsynpores]} {el {source}/#[TYPE=GENtabchan]})
			if ( {getfield {curr_chan} originalchannel} == "GABA_B" )
				if ( {getfield {curr_chan} mode} == "regular" )
					if (graphics_on) 
						addmsg {curr_chan}/G_protein {{dest_plot} @ "/Ik"} PLOT {pfield}k *{getfield {curr_chan} name}  *{col}
						addmsg {curr_chan}/K_pore {{dest_plot} @ "/Ik"} PLOT {pfield}k *{getfield {curr_chan} name}  *{col}
						//addmsg {curr_chan}/G_protein {{dest_plot} @ "/Ik"} PLOT Gconcs *{getfield {curr_chan} name}  *{col}
					end
		
		
					//addmsg {curr_chan}/G_protein {dest_save} SAVE {pfield}k
					addmsg {curr_chan}/K_pore {dest_save} SAVE {pfield}k
				else
					if (graphics_on); addmsg {curr_chan} {{dest_plot} @ "/Ik"} PLOT {pfield}k *{getfield {curr_chan} name}  *{col}; end
					addmsg {curr_chan} {dest_save} SAVE {pfield}k
				end
			else
				if (graphics_on); addmsg {curr_chan} {{dest_plot} @ "/Ik"} PLOT {pfield}k *{getfield {curr_chan} name}  *{col}; end
				addmsg {curr_chan} {dest_save} SAVE {pfield}k
			end
			writefile {dest_info} {curr_chan}
			col = col + 7
			if (col > 63)
			        col = col - 60
			end
		end
	
		
		
		foreach curr_chan ({el {source}/#[TYPE=tabchannel]} {el {source}/#[TYPE=vdep_channel]})
			if (graphics_on); addmsg {curr_chan} {{dest_plot} @ "/Ik"} PLOT {pfield}k *{getfield {curr_chan} name} *{col}; end
			addmsg {curr_chan} {dest_save} SAVE {pfield}k
			writefile {dest_info} {curr_chan}
			col = col + 7
			if (col > 63)
			        col = col - 60
			end
		end
		
		
		// Add single pool currents
		foreach curr_chan ({el {source}/allpools/Capool_1/#[TYPE=GENvgpores]} {el {source}/allpools/Capool_1/#[TYPE=GENVhalf]} {el {source}/allpools/Capool_1/#[TYPE=GENsynpores]} {el {source}/allpools/Capool_1/#[TYPE=GENtabchan]})
			if ( {getfield {curr_chan} originalchannel} == "GABA_B" )
				if ( {getfield {curr_chan} mode} == "regular" )
					if (graphics_on) 
						addmsg {curr_chan}/G_protein {{dest_plot} @ "/Ik"} PLOT {pfield}k *{getfield {curr_chan} name}  *{col}
						addmsg {curr_chan}/K_pore {{dest_plot} @ "/Ik"} PLOT {pfield}k *{getfield {curr_chan} name}  *{col}
						//addmsg {curr_chan}/G_protein {{dest_plot} @ "/Ik"} PLOT Gconcs *{getfield {curr_chan} name}  *{col}
					end
		
		
					//addmsg {curr_chan}/G_protein {dest_save} SAVE {pfield}k
					addmsg {curr_chan}/K_pore {dest_save} SAVE {pfield}k
				else
					if (graphics_on); addmsg {curr_chan} {{dest_plot} @ "/Ik"} PLOT {pfield}k *{getfield {curr_chan} name}  *{col}; end
					addmsg {curr_chan} {dest_save} SAVE {pfield}k
				end
			else
				if (graphics_on); addmsg {curr_chan} {{dest_plot} @ "/Ik"} PLOT {pfield}k *{getfield {curr_chan} name}  *{col}; end
				addmsg {curr_chan} {dest_save} SAVE {pfield}k
			end
			writefile {dest_info} {curr_chan}
			col = col + 7
			if (col > 63)
			        col = col - 60
			end
		end
		
		foreach curr_chan ({el {source}/allpools/Capool_1/#[TYPE=tabchannel]} {el {source}/allpools/Capool_1/#[TYPE=vdep_channel]})
			if (graphics_on); addmsg {curr_chan} {{dest_plot} @ "/Ik"} PLOT {pfield}k *{getfield {curr_chan} name} *{col}; end
			addmsg {curr_chan} {dest_save} SAVE {pfield}k
			writefile {dest_info} {curr_chan}
			col = col + 7
			if (col > 63)
			        col = col - 60
			end
		end
		
		foreach curr_chan ({el {source}/allpools/Capool_1/#[TYPE=Ca_concen]})
			if (graphics_on); addmsg {curr_chan} {{dest_plot} @ "/Ik"} PLOT Ca *{getfield {curr_chan} name} *{col}; end
			addmsg {curr_chan} {dest_save} SAVE Ca
			writefile {dest_info} {curr_chan}
			col = col + 7
			if (col > 63)
			        col = col - 60
			end
		end
		
		foreach curr_chan ({el {source}/allpools/Capool_1/#[TYPE=difshell]})
			if (graphics_on); addmsg {curr_chan} {{dest_plot} @ "/Ik"} PLOT C *{getfield {curr_chan} name} *{col}; end
			addmsg {curr_chan} {dest_save} SAVE C
			writefile {dest_info} {curr_chan}
			col = col + 7
			if (col > 63)
			        col = col - 60
			end
		end
		
	// ############################# End single pool mode %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
	end
	
	
	
	create diffamp {source}/sum_synapses
	setfield ^ gain 1 saturation Inf minus 0
	int num_channels = 0
	foreach curr_chan ({el {source}/#[TYPE=GENsynpores]})
		num_channels = num_channels + 1
		addmsg {curr_chan} {source}/sum_synapses PLUS {pfield}k
	end
	if (num_channels > 0)
	//	if (graphics_on); addmsg {source}/sum_synapses {{dest_plot} @ "/Ik"} PLOT output *{"sum" @ {getfield {curr_chan} name}}  *{col}; end
		//addmsg {source}/sum_synapses {dest_save} SAVE output
		//writefile {dest_info} "tot_synaptic_activity"
		col = col + 7
		if (col > 63)
			col = col - 60
		end
	end
	
	
	
	foreach curr_chan ({el {source}/#[TYPE=GENgap]})
		echo addmsg {curr_chan} {{dest_plot} @ "/Ik"} PLOT {pfield}k *{getfield {curr_chan} name}  *{col}
		if (graphics_on); addmsg {curr_chan} {{dest_plot} @ "/Ik"} PLOT {pfield}k *{getfield {curr_chan} name}  *{col}; end
		addmsg {curr_chan} {dest_save} SAVE {pfield}k
		writefile {dest_info} {curr_chan}
	
		//create xform /form			//display voltage comparison
		//create xgraph /form/graph
		//xshow /form
		//addmsg {curr_chan} /form/graph PLOT Vk *Vk *blue
		//addmsg {curr_chan} /form/graph PLOT Vk2 *Vk2 *red
		col = col + 7
		if (col > 63)
		        col = col - 60
		end
	end
	
	
	
	
	
	foreach curr_chan ( {el {source}/#[TYPE=synchan2]} )
		if (graphics_on); addmsg {curr_chan} {{dest_plot} @ "/Ik"} PLOT {pfield}k *{getfield {curr_chan} name} *{col}; end
		addmsg {curr_chan} {dest_save} SAVE {pfield}k
		writefile {dest_info} {curr_chan}
		col = col + 7
		if (col > 63)
		        col = col - 60
		end
	end
	
	// For NaCa Pump
	foreach curr_chan ({el {source}/#[TYPE=tabcurrent]})
		if (graphics_on); addmsg {curr_chan} {{dest_plot} @ "/Ik"} PLOT {pfield}k *{getfield {curr_chan} name} *{col}; end
		addmsg {curr_chan} {dest_save} SAVE {pfield}k
		writefile {dest_info} {curr_chan}
		col = col + 7
		if (col > 63)
		        col = col - 60
		end
	end
	
	if (show_calcium)
		foreach curr_chan ({el {source}/#[TYPE=Ca_concen]})
			if (graphics_on); addmsg {curr_chan} {{dest_plot} @ "/Ik"} PLOT Ca *{getfield {curr_chan} name} *{col}; end
			addmsg {curr_chan} {dest_save} SAVE C
			writefile {dest_info} {curr_chan}
			col = col + 7
			if (col > 63)
			        col = col - 60
			end
		end
	end
	
	
	foreach curr_chan ({el {source}/#[TYPE=difshell]})
		if (graphics_on); addmsg {curr_chan} {{dest_plot} @ "/Ik"} PLOT C *{getfield {curr_chan} name} *{col}; end
		addmsg {curr_chan} {dest_save} SAVE C
		writefile {dest_info} {curr_chan}
		col = col + 7
		if (col > 63)
		        col = col - 60
		end
	end
	
	
	foreach curr_chan ({el {source}/../soma/#[TYPE=PID]})
		if (graphics_on); addmsg {curr_chan} {{dest_plot} @ "/Ik"} PLOT output *PID *{col}; end
		addmsg {curr_chan} {dest_save} SAVE output
		writefile {dest_info} {curr_chan}
		col = col + 7
		if (col > 63)
		        col = col - 60
		end
	end
	
	
	
	// Include soma current
	//addmsg {source}/../soma {{dest_plot} @ "/Ik"} PLOT Im *{getfield {source}/../soma name} *{col}
	//addmsg {source}/../soma {dest_save} SAVE Im
	//writefile {dest_info} "soma current"
	
	
	
	
	closefile {dest_info}

end


function plot_graphs (src_path, graph_name, file_name, graphics_on, sum_currents)

	if (graphics_on)
		create xform {graph_name} [10,10,900,350] -notitle
		create xlabel {graph_name}/label [10,0,98%,25] -label {src_path}
		create xgraph {graph_name}/Vm [10,10:label.bottom,50%,90%] -title \
		    "membrane potential"
		setfield {graph_name}/Vm XUnits "t (sec)" YUnits "voltage (V)"
		setfield {graph_name}/Vm xmax 0.03 ymin -150 ymax 40
		useclock {graph_name}/Vm 1
		create xgraph {graph_name}/Ik [10:Vm.right,10:label.bottom,49%,90%]  \
		    -title "channel current"
		setfield {graph_name}/Ik XUnits "t (sec)" YUnits "current (S)"
		setfield {graph_name}/Ik xmax 0.03 ymin -1e-7 ymax 9e-7
		useclock {graph_name}/Ik 1
		xshow {graph_name}
	end
	
		create asc_file {file_name}
		setfield ^  flush 0 leave_open 1 append 0 notime 0 float_format %0.12g
		useclock ^ 1


	write_Vm {src_path} {graph_name} {file_name} {graphics_on}
	write_everything {src_path} {graph_name} {file_name} I {graphics_on} {sum_currents}

end

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