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

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"... 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. "
1 . Lamb DG, Calabrese RL (2013) Correlated conductance parameters in leech heart motor neurons contribute to motor pattern formation. PLoS One 8:e79267 [PubMed]
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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;
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;
// This is the main genesis file for running the HE model simulations. 
//  It is called by the model specific file (e.g. 45_23_22_07_06_07_19_02_29_41_15_11_33.g).
//  Parameters for the simulation are set by the model itself (conductances), the input (duration, synaptic weights), and general simulation parameters ( in defaults.g and constants.g)
//  Additional simulation and output options may be adjusted below

int verbose = 1 // Where possible, additional information will be written to stdout

// May override HEganglia in .g files below if desired -- e.g. to simulation only one ganglion. 
// str HEganglia = "12"
float slowratio = 0.33 // Ratio between slow and fast portions of the HN to HE synapse. Default is 0.33.

str sgetaskid = {getenv SGE_TASK_ID}  
// set the environment variable SGE_TASK_ID to '' (blank string) if desired. Used for array-jobs of simulations on a cluster using Sun Grid Engine.

str inputsamplerate = 1000 //Hz. This is the sampling rate for the mod function, should be 1kHz unless mod functions are adjusted/recreated


// generic parameters and variables
str coordmodes = "peri sync" 
str HNganglia = "3 4 6 7" 
str currentHE, currentMode

if ({verbose} == 1)
	setprompt "       HE Model Version 9.2"
	echo      "  *    *   *  * ** *  *   *    *  "

//include files 
include defaults.g
include HEchan.g
include synEobj.g
include SynapticInput.g
include outputfile_multigang.g  

include compartments.g // Added for compatibility with readcell library
//include protocols.g // Note: the protocols contained in this file are not 100% functional

// simulation timestep //
float dt =  {5*10**-5}	// simulation timestep in s
// Note: Be careful adjusting this, although there should be no reason to do so!
// It is easy to get a superficially acceptable simulation with a insufficiently small time step.
setclock  0 {dt}       //set the simulation clock to dt
setclock  1 {5*10**-4}//  {2**-14}*2**3 = 2**-11 : 2048 samples/second saved

// build library of generic compartments and channels
pushe /library
	make_cylind_compartment		// makes "asymmetric cylindrical compartment" - the only type used in this simulation
	// These are some standard channels used in .p files 
	make_Na_ron			// makes "Na_ron" 
	make_K1_ron			// makes "K1_ron"
	make_K2_ron			// makes "K2_ron" 
	make_P_ron			// makes "P_ron" 
	make_CaS_ron        // makes "CaS_ron"
	make_Ca_conc        // makes "Ca_conc"  
	make_K_Ca  			// makes "K_Ca"	
	make_A_ron			// makes "A_ron"
	createHNsyn {HNganglia} // creates SynS objects from each HN/mode
pope // returning to the root element 

echo Making neuron(s)
foreach currentMode({arglist {coordmodes}})
	foreach currentHE({arglist {HEganglia}})
		echo "    " /HE{currentHE}_{currentMode}
		readcell {pfile} /HE{currentHE}_{currentMode} -hsolve // using hines solver

loadHNinput {coordmodes} {HNganglia} {inputdir} {inputduration} {inputsamplerate}
make_syn_connections {coordmodes} {HNganglia} {HEganglia} 0.020 {dt} 0.1

// Set synaptic weights for each HE ganglion
foreach currentHE({arglist {HEganglia}})
	set_gbar {syne_gbar} {currentHE}
set_slowsyn_wts {coordmodes} {HNganglia} {HEganglia} {slowratio}
// Note: We must setup output (save) messages before calling SETUP on hines-solved elements

save_soma_Vm {HEganglia}
// Uncomment the below for additional outputs if desired.

//save_all_Vm {coordmodes} {HEganglia} // saves all compartment membrane voltages
//save_syn_connections {coordmodes} {HNganglia} {HEganglia}                                                                                           
//  First argument for the below are verbosity level from 0 (none) to  2 (all).
//saveAllCurrents 2 {HEganglia} {coordmodes}  // saves all currents
//saveSynapseCurrents 2 {HEganglia} {coordmodes}
//saveMembraneCurrents 0 {HEganglia} {coordmodes}

// After all external messages have been setup (assuming chanmode 1):
// for each cell, setup hines solver options and method.
foreach currentMode({arglist {coordmodes}})
	foreach currentHE({arglist {HEganglia}})
		setfield /HE{currentHE}_{currentMode} \
		   path /HE{currentHE}_{currentMode}/##[][TYPE=compartment]  \
		   comptmode       1                       \
		   chanmode        1                       \
		   outclock        1                       \
		   storemode       1	// calcmode        0                       
		setmethod 11
		call /HE{currentHE}_{currentMode} SETUP


// test for output file existence before simulation if desired by uncommenting the below (helpful if hitting disk space or file count limits)
//foreach currentHE({arglist {HEganglia}})
//	sh "test -e HE"{currentHE}"soma_Vm.txt && echo HE"{currentHE}"soma_Vm.txt exists before simulation"

step {inputduration} -t

bye // Flushes and closes open file handles, then gracefully quits.