% This file contains all of the global variable definitions.
%
% Numerous global variables are used throughout the various functions
% rather than passing variables through function calls. To distinguish
% global variables from local variables, the last word in all global
% variable names is in capital letters. Also, unlike the preceeding
% words in a variable name, the last word is not separated from the
% others by an underline character. The words that make up local
% variables are always in lower case and are always separated by an
% underscore character.
%
% To maintain a consistent and coherent listing system, the global
% variables are are grouped according to the function in which they
% originate. The global variables are listed in the order that the
% function files are executed: neurosim.m, prm_init.m, menu.m, etc.
%
% by Diek W. Wheeler, Ph.D.
% 08/19/02 replaced all global variables with 'gvars.' structure
% 08/21/02 removed tspan, y0, options, iCLAMP, epscBUFFER, and synTEMPLATE from
% the gvars structure so they are now passed through the function
% calls
% added lenTEMPLATE to the gvars structure
% 11/22/02 added window of summation template mode, when it is
% active only two conductance pulse are generated, it
% works only in the steady rhythmic firing mode
% 04/09/03 renamed all of the global variables into 4 categories
% Global variables associated with the nicotinic synaptic conductance
%
% Synapse.eventTimeMsecArray
% 2-D array for the times of all of the primary and
% secondary nicotinic synaptic events for the total
% numerical integration time (ms)
% Synapse.firingModeArray
% flag to determine the firing mode of the nicotinic
% synapses: steady regular firing, no firing, stochastic
% Poisson-based firing
% Synapse.frequencyHz
% firing rate of the synapses, multiple values are looped
% through in turn by the simulation (Hz)
% Synapse.frequencyModulatorAmplitudeHz
% amplitude of the modulatory oscillations of the firing
% frequencies (Hz)
% Synapse.frequencyModulatorFunction
% determines the waveform function that is used to modulate
% the firing frequencies
% Synapse.frequencyModulatorPhaseRadianArray
% phase difference between the modulatory oscillations of
% the primary and secondary firing frequencies (radians)
% Synapse.frequencyModulatorRateHz
% rate at which the primary firing frequencies are modulated (Hz)
% Synapse.gsynBarNsiemenArray
% 1-D array for the maximum nicotinic synaptic conductances
% for both the primaries and secondaries (nS)
% Synapse.gsynFallTimeMsecArray
% 1-D array for the decay-time constants of the template
% waveform function describing the time evolution of the
% nicotinic synaptic conductance (ms)
% Synapse.gsynRiseTimeMsec
% rising time constant of the template waveform function
% describing the time evolution of the nicotinic synaptic
% conductance (ms)
% Synapse.gsynScaling
% scaling factor of the template function describing the time
% evolution of the nicotinic synaptic conductance height and
% is a function of Neuron.type
% Synapse.gsynThresholdNsiemen
% threshold value for the nicotinic synaptic conductance (nS)
% Synapse.nEventArray
% 1-D array for the counters that keep track of the number of
% primary and secondary synaptic events
% Synapse.nFrequency
% number of firing frequencies to be looped through
% Synapse.number
% number of nicotinic synapses to be modeled, must be at
% least 2: 1 primary and 1 secondary
% Synapse.fire.rate (change to Synapse.freq.primary)
%
% Synapse.freq.secondary.num number of secondary firing frequencies to loop
% through, calculated by multiplying the primary
% firing frequency times the number of secondary
% synapses
% Synapse.num.secondary number of secondary synapses
% Global variables associated with the postsynaptic neural activity
%
% Neuron.gcngBarNsiemen
% maximum conductance for the cyclic nucleotide-gated cation
% leak current (nS)
% Neuron.gmBarNsiemen
% maximum conductance for the M-type potassium current (nS)
% Neuron.initialValuesVmhnwArray
% 5-D array for the initial values of the simulation
% variables (V,m,h,n,w) to be used between multiple
% integration time segments
% Neuron.type
% selects the type of sympathetic neuron to be modeled
% Neuron.C Membrane capacitance (pF)
%
% Neuron.current.max maximum positive current during a total single
% integration cycle
% Neuron.E.CNG Nernst equilibrium potential for the cyclic
% nucleotide-gated cation leak current (mV)
% Neuron.E.K Nernst equilibrium potential for the
% delayed-rectifying potassium current (mV)
% Neuron.E.leak Nernst equilibrium potential for the
% voltage-independent leak current (mV)
% Neuron.E.Na Nernst equilibrium potential for the fast,
% inactivating, voltage-dependent sodium
% current (mV)
% Neuron.E.RCleak Nernst equilibrium potential for the RC-circuit
% voltage-independent leak current (mV)
% Neuron.E.syn Nernst equilibrium potential for the nicotinic
% synaptic current (mV)
% Neuron.g.CNG.end ending value when looping through multiple
% values of the max. conductance for the cyclic
% nucleotide-gated cation leak current (nS)
% Neuron.g.CNG.start starting value when looping through multiple
% values of the max. conductance for the cyclic
% nucleotide-gated cation leak current (nS)
% Neuron.g.CNG.step step value when looping through multiple values
% of the maximum conductance for the cyclic
% nucleotide-gated cation leak current (nS)
% Neuron.g.K.bar single value for the maximum conductance for the
% delayed-rectifying potassium conductance (nS)
% Neuron.g.leak.bar single value for the maximum conductance for the
% voltage-independent leak conductance (nS)
% Neuron.g.M.end ending value when looping through multiple
% values of the maximum conductance for the
% M-type potassium current (nS)
% Neuron.g.M.start starting value when looping through multiple
% values of the maximum conductance for the
% M-type potassium current (nS)
% Neuron.g.M.step step value when looping through multiple values
% of the maximum conductance for the M-type
% potassium current (nS)
% Neuron.g.Na.bar single value for the maximum conductance for the
% fast, inactivating, voltage-dependent sodium
% conductance (nS)
% Neuron.g.RCleak.bar single value for the maximum conductance for the
% RC-circuit voltage-independent leak
% conductance (nS)
% Neuron.Na.m.scale scaling factor for the Na activation parameter m
% which controls the rate of activation
% Global variables associate with the current clamp mode
%
% Iclamp.activationDurationMsec
% duration of activation of current clamp in either step or
% ramp mode (ms)
% Iclamp.mode
% flag to determine mode of operation of current clamp:
% inactive, step currents, ramp current, or ZAP
% Iclamp.postActivationLatencyMsec
% time for system to settle after conclusion of current clamp (ms)
% Iclamp.preActivationLatencyMsec
% delay until activation of current clamp in either step or
% ramp mode (ms)
% Iclamp.preRampActivationLatencyMsec
% time for current clamp to settle before starting the
% current ramp after the initial step is taken to the
% starting current value (ms)
% Iclamp.rampAmplitudeStartPamp
% starting current value for current ramp (pA)
% Iclamp.rampAmplitudeStopPamp
% ending current value for current ramp (pA)
% Iclamp.stepAmplitudePamp
% amplitude of the step currents during current-clamp
% simulations (pA)
% Iclamp.stepAmplitudeStartPamp
% starting current value when looping through multiple
% values of the step current during current-clamp
% simulations (pA)
% Iclamp.stepAmplitudeStopPamp
% stopping value when looping through multiple values of the
% step current during current-clamp simulations (pA)
% Iclamp.waveformAmplitudePamp
% amplitude to scale a single current waveform (pA)
% Iclamp.zapAmplitudePamp
% amplitude of sine wave used to compute the ZAP current function (pA)
% Iclamp.zapDurationMsec
% duration of the ZAP function (ms)
% Iclamp.zapFrequencyMaximumHz
% high end of the frequency spectrum used in generating the
% ZAP function (Hz)
% Iclamp.zapFrequencyMinimumHz
% low end of the frequency spectrum used in generating the
% ZAP function (Hz)
% Iclamp.zapMode
% determines whether the ZAP current function proceeds from
% low to high frequencies or high to low frequencies
% Iclamp.zapPhaseRadian
% phase lag of the ZAP current oscillations (rad)
% Iclamp.step.step step value when looping through multiple
% values of the step current during
% current-clamp simulations (pA)
%
%
% Global variables associated with the general maintenance of the program
%
% Misc.activationStartMsec
% the nicotinic synapses and the current clamp may not be
% activated before this time in order to allow the system
% to reach equilibrium (ms)
% Misc.avgInterEventIntervalMsec
% average time between synaptic events (ms)
% Misc.dataDirectoryName
% name of the subdirectory that holds the results of the
% simulation for the current parameter settings, a new
% subfolder is generated for each set of parameters
% Misc.dataSuffix
% suffix added to the names of datafiles and subdirectories
% that contains some of the parameter settings for a given
% parameter cycle
% Misc.executionMode
% determines how much of the total program will execute before
% the program terminates
% Misc.integrationSegmentStartMsec
% time at which the current integration time segment begins,
% updated for each integration time segment (ms)
% Misc.integrationSegmentStopMsec
% time at which the current integration time segment ends, the
% value is calculated by the program and changes depending on
% the number of integration segments the simulation must be
% broken up into in order to accomodate the limitations of the
% computer's memory (ms)
% Misc.isActionPotential
% indicates whether or not a new action potential has been
% found when scanning through the membrane voltage data
% Misc.isDebug
% flag for setting debugging mode, debug mode skips the menu
% program and has its own set of default parameter settings,
% all 3 execution modes are still available
% Misc.isMoreThanOneTimeSegment
% indicates if there is more than one integration time segment
% is to be cycled through
% Misc.lengthOfTemplate
% length of the nicotinic synaptic conductance template synTEMPLATE
% Misc.nActionPotential
% counter which tracks the number of action potentials found
% in the voltage data
% Misc.nEventStartArray
% 2-D array for the starting event count of the primary and
% secondary nicotinic synaptic events, the value of which is
% updated if the total numerical integration time has been
% broken into smaller segments
% Misc.nPoints
% number of data points to be saved during the current
% numerical integration segment
% Misc.randomNumberStateVector
% 35-element vector containing the current state of the random
% number generator
% Misc.randomSeedSourceName
% string that describe the source of seed for the random
% number generator: system clock, user input, read from file
% Misc.saveStepMsec
% how often the values of the variables of the
% simulation(t,V,m,h,n,w) are saved to file (ms)
% Misc.shouldComputeSynapticEvents
% determines the source of the nicotinic synaptic conductance
% template: menu options or file
% Misc.simulationDirectoryName
% name of the directory that holds the results of the
% simulation, a new directory is generated every time the
% simulation is run anew, each new directory is time stamped
% Misc.totalIntegrationTimeMsecArray
% 1-D array for the total integration times at each primary
% firing frequency to be looped through, the default value is
% a function of the frequency so that the simulation runs long
% enough to produce approximately 400 EPSPs (ms)
% Misc.twoEventTemplateMode
% determines the window of summation template mode, when it is
% active only two conductance pulse are generated, it works
% only in the steady rhythmic firing mode
% Misc.data.summary.file name of the file that holds the parameter
% settings of and the data produced by the
% simulation
% Misc.dynamics.flag flag to determine source of dynamics code:
% Yamada or Hermann & Boris
% Misc.dynamics.source 2-D text array for strings describing the source
% of dynamics code: Yamada or Hermann & Boris
% Misc.host.flag flag to determine on which host machine the
% simulation is currently running
% Misc.host.machine 3-D text array for strings describing the host
% machine on which the simulation is currently
% running: HornBlue1, HornDell5, HornDell6,
% HornDell7, HornDell9, Condor
% Misc.parameter.file Binary file source for the simulation parameters
%
% Misc.parameter.flag flag to determine source of simulation
% parameters: menu options or file
% Misc.parameter.source 2-D text array for strings describing the source
% of the simulation parameters: menu options or
% file
% Misc.rand.seed.source 3-D text array for strings describing the source
% of seed for random number generator: system
% clock, user input, read from file
% Misc.rand.state.file ????
%
% Misc.save.file Binary file source to which the simulation
% parameters are saved
% Misc.save.flag flag to determine source to which the simulation
% parameters are saved
% Misc.template.file Binary file source for the nicotinic synaptic
% conductance template
% Misc.template.file.mark marker to keep track of position in synaptic
% conductance template file when reading in
% multiple integration-time segments
% Misc.template.source 2-D text array for strings describing the source
% of the nicotinic synaptic conductance
% template: menu options or file
% Misc.time.downtime.LabVIEW the amount of downtime that the LabVIEW program
% will wait after it has run a synaptic template
% for the determination of gain (sec)
% Misc.time.segment integration-time segement size that long
% simulations will be broken down into to
% accomodate computer memory restrictions (ms)