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Index

Symbols!(logical NOT operator) – see hoc syntax:

expressions: operators!= (inequality operator) – see hoc syntax:

expressions: operators$ – see funcs and procs: arguments:

positional syntax$1 – see funcs and procs: arguments:

positional syntax$i – see funcs and procs: arguments:

symbolic positional syntax$o – see funcs and procs: arguments:

positional syntax$s – see funcs and procs: arguments:

positional syntax% (remainder operator) – see hoc syntax:

expressions: operators& (pointer operator) – see hoc syntax: pointer

operator&& (logical AND operator) – see hoc syntax:

expressions: operators'(apostrophe) – see DERIVATIVE block:

'(apostrophe)()(paired left and right parentheses) – see

hoc syntax: expressions: operators (1) – see units: dimensionless* (multiplication operator) – see hoc syntax:

expressions: operators*/ – see hoc syntax: comments� (addition operator) – see hoc syntax:

expressions: operators� (subtraction operator) – see hoc syntax:

expressions: operators� (unaryminus operator) – see hoc syntax:

expressions: operators–> (sink reaction indicator) – see KINETIC

block: –> (sink reaction indicator)

/ (division operator) – see hoc syntax:expressions: operators

/* – see hoc syntax: comments// – see hoc syntax: comments: (colon) – see NMODL: comments, range

variable: linear taper< (less than operator) – see hoc syntax:

expressions: operators<–> (reaction indicator) – see KINETIC

block: <–> (reaction indicator)<< (explicit flux) – see KINETIC block:

<< (explicit flux)<= (less than or equal to operator) – see hoc

syntax: expressions: operators= (assignment operator) – see hoc syntax:

expressions: operators== (equality operator) – see hoc syntax:

expressions: operators> (greater than operator) – see hoc syntax:

expressions: operators>= (greater than or equal to operator) –

see hoc syntax: expressions: operators

[] (index operator) – see hoc syntax:variables: double, Vector class,object: array, section: array, NMODL:arrays, STATE variable: array inNMODL

\(backslash) – see hoc syntax: continuationcharacter

ˆ(exponentiation operator) – see hoc syntax:expressions: operators

ˆC (Control C) – see hoc: interruptingexecution

ˆD (Control D) – see hoc: starting and exiting

_(underscore) – see hoc syntax: names

413

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_ion – see ion mechanism: _ion suffixx_ion – see ion mechanism:

automatically createdxi0_x_ion – see ion mechanism: default

concentration: specification in hocxo0_x_ion – see ion mechanism: default

concentration: specification in hoc{} – see hoc syntax: statements: compound

statement|| (logical OR operator) – see hoc syntax:

expressions: operators~ (tilde) – see KINETIC block: ~ (tilde)

33 – see nseg: why triple nseg?3-D model – see model: 3-D, 3-D

specification of geometry3-D specification of geometry 103, 105, 144

3-D information 105, 109arc3d() 109calculation of L, diam, area(), and ri()

105, 108coordinates

absolute vs. relative 146–147data – see 3-D specification of geometry:

3-D informationalso see quantitative morphometric data

diam3d() 105checking 108

diameter 105problems 108also see 3-D specification of geometry:

calculation of L, diam, area(),and ri()

n3d() 105, 109number of 3-D points

effect on computational efficiency 106vs. nseg 106also see n3d()

origin of cell – see section: root section: is3-D origin of cell

points – see 3-D specification of geometry:3-D information

pt3dadd() 105also see stylized specification of geometry

Aabrupt change – see variable: abrupt change

of, NET_RECEIVE block: handlingabrupt changes and discontinuities

absolute error 63, 71–72local 75

tolerance 75, 79, 251also see STATE block: specifying local

absolute error tolerancealso see relative error, numerical error

absolute tolerance—see absolute error: local:tolerance

abstraction 33–34AC length constant – see length constant: ACaccess 100, 143

also see section: currently accessed: defaultsection

accumulation – see ion accumulationaccuracy 33, 64, 91

effect of boundary conditions 54of ionic currents – see membrane current:

ionic: accuracy, standard run system:fcurrent()

order – see numeric integration: order ofaccuracy

physiological 79, 85quantitative 67spatial – see spatial accuracyvs. speed 73, 117temporal – see temporal accuracyalso see judgment, discretization, numerical

error, parameters: sensitivity toacell_home_ – see NetWork Builder:

exporting reusable code: acell_home_active current – see channel: voltage-gatedactive transport 41, 199

electrically silent 256initialization 203–205

pump transient 204kinetic scheme 200

also see Example 9.9: a calcium pumppump current 255–258

countering with a NONSPECIFIC_CURRENT 256

initialization 258also see buffer, diffusion, ion accumulation

adaptive integration – see numeric integration:adaptive

adaptive time step – see numeric integration:adaptive

adding items to NEURON Main Menu – seeNEURONMainMenu class:miscellaneous_add()

adding new functions to NEURON – seeNMODL

adding new mechanisms – see mechanisms:user-defined, nrniv: adding newmechanisms, NMODL

414 Index






addition operator – see hoc syntax:expressions: operators

addplot() – see standard run system:addplot()

advance microstep – see numeric integration:adaptive: advance microstep

also see standard run system: fadvance():local time step integration

advance() – see standard run system:advance()

afferent event – see event: externalaggregation of events to time step boundaries

– see numeric integration: fixed timestep: event aggregation

algebralinear – see linear algebra

algebraic equation – see equation: algebraicalgebraic difference equation – see equation:

differenceAlphaSynapse 19

graphical interface – seePointProcessManager GUI

parameters 20preserving spatial accuracy – see point

process: preserving spatial accuracyalso see Example 10.4: alpha function

synapsealpha function synapse – see AlphaSynapse,

Example 10.4: alpha function synapseAlt key – see Graph class: menu_tool()amount of material – see material: amountampa.mod – see Example 10.6: saturating

synapsesAMPAergic synapse – see Example 10.3:

synapse with exponential decay, Example10.6: saturating synapses

amplification factor – see amplifier: gainamplifier 45

feedback – see feedback: amplifiergain 45, 49headstage 49also see circuit: element: amplifier

analysis 24initialization – see initialization: analysis

analytic solutionand discrete event simulation – see discrete

event simulation: conditions forcable equation – see equation: cable:

analytic solutionanatomical data – see quantitative

morphometric dataanatomical distance – see distance

anatomical propertiesseparating biology from numerical issues 92

also see section, range, range variablespecifying – see 3-D specification of

geometry, stylized specification ofgeometry, topology: specifying

also see geometry, topologyAND operator – see hoc syntax: expressions:

operatorsapostrophe – see DERIVATIVE block:

'(apostrophe)approximate Jacobian – see Jacobian:

approximateapproximation 25, 34, 52–53

of a continuous system by a discrete system60, 90

piecewise linear – see continuous variable:piecewise linear approximation

also see Jacobian: approximatearc length – see rangearc3d() – see 3-D specification of

geometry: arc3d()architecture – see topologyarea

membrane – see surface area, membrane areasurface – see surface area, membrane areazero area nodes – see section: nodes: zero area

areaas an ASSIGNED variable – see ASSIGNED

variable: v, celsius, t, dt, diam,and area

also see area()area() 104

calculation of – see stylized specification ofgeometry: calculation of area() andri(), 3-D specification of geometry:calculation of L, diam, area(), andri()

effect of creating a Shape – see Shapeobject: creating: effect on diam,area(), and ri()

effect of define_shape() – seedefine_shape(): effect on diam,area(), and ri()

stylized vs. 3-D surface integral 110arguments – see funcs and procs: arguments

section as – see SectionRef classtrapping – see good programming style:

bulletproofing against nonsensearguments

also see FUNCTION block, PROCEDUREblock, NET_RECEIVE block

Index 415






arithmetic operators – see hoc syntax:expressions: operators

arraysin NMODL – see NMODL: arrays, STATE

variable: array in NMODLof numbers – see hoc syntax: variables:

double, Vector classof objects – see object: arrayof sections – see section: array

ArtCellGUIbringing up an ArtCellGUI 311cell names – see NetWork Builder: cells:

nameschanging – see ArtCellGUI: specifying

cell typeschanging cell parameters – see NetWork

Builder: caveatsalso see PointProcessGroupManager

specifying cell types 311Artificial Cell – see ArtCellGUIartificial cell – see artificial spiking cellartificial neuron – see artificial spiking cellartificial spiking cell 82–83, 289

advantages and uses 265computational efficiency 290, 292

differences from other point processes290–291

implemented as point processes 290IntFire1 – see IntFire1 class,

Example 10.7: IntFire1, a basicintegrate and fire model

IntFire2 – see IntFire2 class,Example 10.8: IntFire2, firing rateproportional to input

IntFire4 – see IntFire4 class,Example 10.9: IntFire4, differentsynaptic time constants

under CVODE 88also see biophysical neuron model,

integrate and fire, IntFire1 class,IntFire2 class, IntFire4 class,NEURON block: ARTIFICIAL_CELL

ARTIFICIAL_CELL – see NEURON block:ARTIFICIAL_CELL, artificial spikingcell

ASCII file – see plain text fileASSIGNED block 212, 222, 231, 250

also see PARAMETER block, STATE blockASSIGNED variable 184, 195, 212

abrupt change of – see variable: abruptchange of, NetCon class: event(),NET_RECEIVE block: handlingabrupt changes and discontinuities

accuracy 169, 172GLOBAL

spatial variation 232vs. RANGE 215, 230also see NEURON block: GLOBAL

initialization 187also see initialization

is a range variable by default 213also see NEURON block: RANGE, range

variablev, celsius, t, dt, diam, and area

213visibility at the hoc level 213, 218when to use for an equilbrium potential 223also see PARAMETER variable, STATE

variable, state variable: as anASSIGNED variable, ion_style()

assignment operator – see hoc syntax:expressions: operators

assumptions 1, 41–42, 46, 51, 53at_time() – see CVODE: and model

descriptions: at_time(), variable:abrupt change of, NET_RECEIVE block:handling abrupt changes anddiscontinuities

atol 79also see absolute error: local: tolerance

attaching a section – see connectattenuation

at high frequencies 122also see membrane time constant: and

attenuation of fast signals, spatialdecay of fast signals

Avogadro’s number – see units: moleaxial current 51–54, 56

positive current convention 51axial resistance 52–53

infinite 107, 115also see diameter: zero or narrow diameter

also see ri(), Ra, cytoplasmic resistivity

Bb_flux – see KINETIC block: b_fluxbackward Euler method 61, 66–68, 165

and LONGITUDINAL_DIFFUSION 253iteration coefficient 62local error 67, 83stability 67summary 86also see modified Euler method, numeric

integration: fixed time stepbackward flux – see flux: backward,

KINETIC block: b_flux

416 Index






backslash (\) – see hoc syntax: continuationcharacter

balancecharge – see charge: conservationmass – see material: conservation

ball and stick 34bandpass 122barbed wire shape – see stylized specification

of geometry: strange shapesbase class – see class: base class, object-

oriented programming: polymorphism,object-oriented programming: inheritance

biological properties vs. purely computationalissues 92

biophysical mechanism – see distributedmechanism, point process

biophysical neuron model 82, 265also see artificial spiking cell

biophysical propertiesseparating biology from numerical issues 92

also see section, range, range variablespecifying 111, 133also see distributed mechanism, point

processblocks – see NMODL: named blocksboundary conditions 51

effect on accuracy – see accuracy: effect ofboundary conditions

sealed end 54, 56branch

cell 92also see neurite, section

circuit – see circuit: edgebranched architecture 51, 53, 91, 98

also see topologybranched cable – see cable: branchedbreak – see hoc syntax: flow control:

breakBREAKPOINT block 213, 223

abrupt change of a variable – see variable:abrupt change of, NetCon class:event(), NET_RECEIVE block:handling abrupt changes anddiscontinuities

and computations that must be performedonly once per time step 224

and counts, flags, and random numbers 223and PROCEDUREs 224and rate functions 224and variables that depend on the number of

executions 223at_time() – see CVODE: and model

descriptions: at_time(), variable:

abrupt change of, NET_RECEIVEblock: handling abrupt changes anddiscontinuities

currents assigned at end of 223METHOD – see BREAKPOINT block:

SOLVESOLVE 168–170, 223, 225cnexp 225derivimplicit 226is not a function call 224sparse 87, 243also see STATE variable

state_discontinuity() – seeCVODE: and model descriptions:state_discontinuity(),variable: abrupt change of,NET_RECEIVE block: handlingabrupt changes and discontinuities

time-dependent PARAMETER – seePARAMETER variable: time-dependent, Vector class: play()

translation of 168, 170browser – see directory browser, variable

browser, Plot what? GUIbuffer 37

also see ion accumulation, diffusion,Example 9.8: calcium diffusion withbuffering

built-in constants – see hoc syntax: variables:built-in constants

built-in editor – see em, emacsbulletproofing against nonsense arguments –

see good programming style:bulletproofing against nonsensearguments

CC code

embedding – see NMODL: VERBATIM . . .ENDVERBATIM

ca_ion – see ion mechanism: automaticallycreated

cable 50branched 53equation – see equation: cablepassive cylindrical 56–58, 60unbranched 50, 53–54, 92

CABLE 164cadif.mod – see Example 9.8: calcium

diffusion with bufferingcagk.mod – see Example 9.5: a calcium-

activated, voltage-gated currentcai – see calcium, ion mechanism

Index 417






cai0_ca_ion – see calcium, ionmechanism: default concentration:specification in hoc

calciumamount of 41buffering – see Example 9.8: calcium

diffusion with bufferingconcentration 42

free 80current 199

effect on concentration 200diffusion – see Example 9.8: calcium

diffusion with bufferingpump 41, 79, 199

also see Example 9.9: a calcium pump,active transport

also see ion mechanismcalcium-activated current – see Example 9.5: a

calcium-activated, voltage-gated currentcall by reference vs. call by value – see funcs

and procs: arguments: call by referencevs. call by value, NET_RECEIVE block:arguments are call by reference,FUNCTION block: arguments are call byvalue, PROCEDURE block: arguments arecall by value

also see funcs and procs: arguments:pointer, hoc syntax: pointer operator

cao – see calcium, ion mechanismcao0_ca_ion – see calcium, ion

mechanism: default concentration:specification in hoc

capacitanceelectrode – see electrode: capacitancecompensation – see electrode: capacitance:

compensationmembrane – see cm, membrane capacitance,

specific membrane capacitancecapacitive current – see membrane current:

capacitivecapacitor

feedback – see feedback: capacitoralso see circuit: element: capacitor

Cell Map – see NetWork Builder: cells: Cell Mapcell time queue – see standard run system:

event delivery system: cell time queueCellBuilder 5

bringing up 6hoc output

exported cell 135root section 8, 21

also see section: default section

spatial grid – see CellBuilder GUI:Geometry page: d_lambda

CellBuilder GUIBiophysics page 13

assigning values 16specifying strategy 15

Continuous Create 17, 152–153Geometry page 12

assigning values 14d_lambda 14

also see spatial accuracy, spatial grid,d_lambda rule

specifying strategy 13Management page 16

Export 16, 135Subsets page 8, 10

all subset 11making a new subset 12

Topology page 8base name 10Basename 10changing the name of a section 11making a new section 9

celsius 212–213, 231as an ASSIGNED variable – see

ASSIGNED variable: v, celsius, t,dt, diam, and area

central difference method – see Crank–Nicholson method

changing a variable in mid-run – seePARAMETER variable: time-dependent,variable: abrupt change of

changing point process location with hoccode – see point process: loc()

changing standard functions and procedures –see standard GUI library: redefiningfunctions and procedures, standard runlibrary: redefining functions andprocedures

channel 53analytic integration of states – see numeric

integration: analytic integration ofchannel states

calcium-activated – see Example 9.5: acalcium-activated, voltage-gatedcurrent

conductance 53current

accuracy – see membrane current: ionic:accuracy, standard run system:fcurrent()

density 84, 92

418 Index






gating model 87HH type 70, 225

also see channel: linearnonlinear 226under CVODE 88

initialization – see initialization: channelmodel

ligand-gated 36also see Example 10.1: graded synaptic

transmission, Example 10.5: use-dependent synaptic plasticity,Example 10.6: saturating synapses

linear 87also see channel: gating model: HH-type

model 36nonlinear 87

under CVODE 88ohmic – see channel: linearvoltage-gated 36

also see Example 9.4: a voltage-gatedcurrent, Example 9.5: a calcium-activated, voltage-gated current,Example 9.7: kinetic scheme for avoltage-gated current

chaos and numerical error – see numericalerror: chaotic system

chaotic system – see initialization: categories:to a desired state

charge 50conservation 51–52

also see Kirchhoff’s current law, gapjunction: conservation of charge

electronic – see e: electronic charge vs.units conversion factor

chemicalnotation – see kinetic schemereaction – see kinetic schemesignal – see signal: chemical

child section – see section: childchord conductance – see conductance: chordcircuit 44

analysis 44branch 44edge 44element 45

amplifier 45capacitor 45current source 45ground 45resistor 45voltage source 45wire 45

equivalent 48, 53also see section: equivalent circuit

linear – see linear circuitnode 44parallel RC 45positive current convention 45

clamp – see current clamp, voltage clampclass 363

base class 376also see object-oriented programming:

polymorphism, object-orientedprogramming: inheritance

defining a new class – see template: writinga template

subclass 376also see object-oriented programming:

polymorphism, object-orientedprogramming: inheritance

vs. object 363also see object, object-oriented

programming, templateclass definition – see template, classClose button – see GUI: tools: Close buttonclosed end – see boundary conditions: sealed endclosed system 36, 38, 40cm 13, 15–16, 94

default value 103also see specific membrane capacitance,

membrane capacitanceCm – see cmcnexp – see DERIVATIVE block,

BREAKPOINT block: SOLVE: cnexpcollection

of numbers – see hoc syntax: variables:double, Vector class

of objects – see object: array, List classof sections – see SectionList class,

CellBuilder GUI: Subsets pagecommand history – see hoc: history functionCOMMENT . . . ENDCOMMENT – see

NMODL: commentscomments – see hoc syntax: comments,

NMODL: commentscomparison of real values – see hoc syntax:

float_epsilonCOMPARTMENT – see KINETIC block:

COMPARTMENTcompartment 37, 52, 60

adjacent 53, 56size 37, 41–42, 52, 92vs. biologically relevant structures 92, 96vs. conceptual clarity 96also see segment

Index 419






compartmental model – see model:compartmental

compartmentalization 8, 14also see discretization

complexity 32–34, 91compound statement – see hoc syntax:

statements: compound statementcomputational efficiency 68–74, 82, 87–88,

91, 98, 126, 163, 181, 207, 210, 225, 239,243, 253, 261

and STATEs 83rate tables – see numeric integration:

analytic integration of channel statesstaggered time steps – see Crank–Nicholson

method: staggered time stepstree topology 165, 167, 169why is NEURON fast? 344also see d_lambda rule, function table,

IntFire2 class: firing time: efficientcomputation, IntFire4 class: firingtime: efficient computation, synaptictransmission: spike-triggered:computational efficiency in NEURON,discrete event simulation:computational efficiency

computational modelimplementing with hoc 130also see model: computational

computational solution – see numeric solutioncomputer display – see GUI: screencomputing

purpose – see insightconcentration 36, 41, 42

and accuracy 87default – see ion mechanism: default

concentrationspecification in hoc – see ion


gradient 50initialization – see ion mechanism: default

concentration, initialization: ionspecification – see ion mechanism: default

concentration, initialization: ionalso see ion accumulation, ion mechanism,

initialization: ionconceptual clarity 129, 144, 207–208, 239, 261conceptual model – see model: conceptualconductance

absolute 112density 111

also see channel: density

ion channel – see channel: conductancemembrane – see specific membrane

conductance, membrane resistanceslope 70

conflicts between hoc and GUI tools – seehoc: conflicts with GUI

connect 101, 130preserving spatial accuracy 102preventing confusion – see section: child:

connect 0 end to parentalso see section

connectivity – see NetCon class, List object:managing network connections with

conservation law 50also see charge: conservation, material:

conservation, kinetic scheme:conservation rules

CONSERVE – see KINETIC block: CONSERVEconsistency of units – see units: consistencyCONSTANT

vs. PARAMETER or LOCAL variable 257CONSTANT block 257constant

built-in constant – see hoc syntax:variables: built-in constants

length – see length constantmembrane time – see membrane time

constantrate – see rate constanttime – see time constant

constant current mechanism 196also see initialization: strategies: injecting a

constant currentcontinuation character (\) 348continue – see hoc syntax: flow control:

continuecontinuerun() – see standard run system:

continuerun()continuous function – see function: continuouscontinuous system – see system: continuouscontinuous variable 90–91

piecewise linear approximation 96–97also see range variable: estimating by linear

interpolation between nodesControl C – see hoc: interrupting executionControl D – see hoc: starting and exitingControl key – see Graph class:

menu_tool()control – see simulation controlconvergence 275–276

also see synaptic transmission: spike-triggered

420 Index






conversion factor – see scale factor, NMODL:units conversion factor, UNITS block:units scaling

correspondence between conceptual andcomputational model – see model:correspondence between conceptual andcomputational

Crank–Nicholson method 61, 68–72, 165hybrid of backward and forward Euler 68iteration coefficient 62local error 68, 84, 166

kinetic scheme 87second order correct plots 180stability 70staggered time steps 70–72, 165, 169summary 86unstaggered time steps 70–71also see secondorder

create 101, 130also see section

creating an object – see object: creatingcreating an object reference – see object

reference: declaringcriterion for proper initialization – see

initialization: criterion for properinitialization

Ctrl key – see Graph class: menu_tool()current 44

absolute 112also see current: density

axial – see axial currentbalance – see equation: current balance,

Kirchhoff’s current lawcalcium-activated – see Example 9.5: a

calcium-activated, voltage-gatedcurrent

capacitive 122also see membrane current: capacitive

density 51, 54, 111also see current: absolute

electrode 49, 51also see ELECTRODE_CURRENT

ionic – see membrane current: ionicmembrane – see membrane currentsign convention – see membrane current:

positive current convention, axialcurrent: positive current convention,circuit: positive current convention

source 51, 53also see circuit: element: current source

transmembrane – see membrane currentvoltage-gated – see channel: voltage-gated

current clamp 48preserving spatial accuracy – see point

process: preserving spatial accuracyalso see IClamp class, Example 9.3: an

intracellular stimulating electrodecurrently accessed section – see section:

currently accessedcursor – see focus: cursorcustom GUI – see user interface: custom GUIcustom initialization – see initialization:

categories, initialization: strategiesCVODE 73–82, 171

abrupt changes and discontinuities – seeCVODE: and model descriptions,variable: abrupt change of,NET_RECEIVE block: handlingabrupt changes and discontinuities

and LONGITUDINAL_DIFFUSION 253and model descriptions 88at_time() 171, 218, 260–262state_discontinuity()

260–262also see NET_RECEIVE block:

state_discontinuity()as generic term for adaptive integration

172default error criteria 80interpolation formulas – see numeric

integration: adaptive: interpolationformulas

local error 75, 79step() under – see standard run system:

step(): under CVODEsummary 88also see numeric integration: adaptive,

standard run system: CVODECVode class 172re_init() 161, 187–188, 196, 263

also see initialization: strategies:changing a state variable

record() 83, 166, 179, 187CVODES 172

also see CVODE, numeric integration:adaptive

cytoplasmic resistivity 15, 54, 56, 94also see Ra

Dd_lambda rule 8, 122–126

also see discretization, spatial gridd_X rule 123

also see discretization, spatial grid

Index 421






DASPK 73–74, 172summary 88also see numeric integration: adaptive,

standard run system: DASPK, IDAdaughter section – see section: childDC length constant – see length constant: DCdeclaring an object reference – see object

reference: declaringdeclaring variables – see NMODL: declaring

variablesdefault section – see access, section:

currently accessed: default sectiondeferred computation – see standard run

system: event delivery system:implementing deferred computation

DEFINE – see NMODL: DEFINEdefine_shape()

effect on diam, area(), and ri() 108defining a new class – see template: writing a

templatedefining a new template – see template:

writing a templatedelayed action – see standard run system:

event delivery system: implementingdeferred computation

delta function – see function: deltademonstration program – see neurondemodensity 36, 42

also see channel: density, conductance:density, current: density, material:density, state: as density

density mechanism – see distributed mechanismDERIVATIVE block 225, 232, 237'(apostrophe) 225and CVODE 88dependent variable

is a STATE variable 184also see initialization: channel model:

Hodgkin–Huxley stylederivimplicit – see DERIVATIVE

block, BREAKPOINT block: SOLVE:derivimplicit

detaching a section – see disconnect()detail 33–34

how much 1, 27also see judgment

developing new GUI tools – see GUI tooldevelopment

diam 13, 94, 132as an ASSIGNED variable – see

ASSIGNED variable: v, celsius, t,dt, diam, and area

calculation from 3-D data – see 3-Dspecification of geometry: calculationof L, diam, area(), and ri()

checking 108also see 3-D specification of geometry:

diam3d(): checkingdefault value 103effect of creating a Shape – see Shape

object: creating: effect on diam,area(), and ri()


specifying3-D specification – see 3-D specification

of geometry: calculation of L,diam, area(), and ri()

stylized specification 104tapering 115updating from 3-D data 109

diam3d() – see 3-D specification ofgeometry: diam3d()

diameter 3, 94abrupt change 110change flag 168checking – see diam: checking, 3-D

specification of geometry:diam3d(): checking

problems – see 3-D specification ofgeometry: diameter: problems

zero or narrow diameter 107also see axial resistance: infinite, diam:

checking, 3-D specification ofgeometry: diam3d(): checking

also see diam, stylized specification ofgeometry, 3-D specification ofgeometry: diam3d()

difference equation – see equation: differencedifferential algebraic solver – see DASPKdifferential equation – see equation:

differentialdiffusion 41, 199

kinetic scheme 200, 238longitudinal 253

model geometry – see ion accumulation:initialization: of model geometry

radial 246, 254restricted – see Example 9.6: extracellular

potassium accumulationunder CVODE 88with buffering – see Example 9.8: calcium

diffusion with buffering

422 Index






also see active transport, buffer, ionaccumulation, Example 9.8: calciumdiffusion with buffering

dimensionless variable – see units: dimensionlessdimensions – see unitsdirectory browser 17–18disconnect() 101discontinuity – see variable: abrupt change of,

diameter: abrupt changealso see function: discrete

discrepancybetween conceptual model and

computational model 34also see model: correspondence between

conceptual and computationalbetween physical system and conceptual

model 28between prediction and simulation 27, 29

discrete event simulation 83, 88computational efficiency 290conditions for 83, 88, 290also see standard run system:

fadvance(): global time stepintegration, standard run system:fadvance(): local time stepintegration

discrete event system – see standard runsystem: event delivery system

discrete events and adaptive integration – seestandard run system: event deliverysystem: adaptive integration and, standardrun system: fadvance(): global timestep integration, standard run system:fadvance(): local time step integration

discrete input event – see event: externaldiscrete simulation – see discrete event

simulationdiscretization 14, 25, 51, 56

guidelines 121intent and judgment 91, 118parameter – see nsegrule – see d_lambda rule, d_X rule,

discretization: guidelinesspatial 51, 53–54, 91–92

also see �, length constant, d_lambdarule, spatial grid, spatial accuracy

temporal 51, 91, 118also see dt, t

testing – see spatial accuracy, temporalaccuracy

discretization interval – see x, spatial griddisplay – see GUI: screen

distancenormalized distance along a section – see

rangephysical distance along a section 114

distributed mechanism 13, 18, 111, 113, 133,208, 220

adding new – see mechanisms: user-defined, NMODL

insert – see insertvs. point process 113also see NEURON block: SUFFIX

Distributed Mechanism GUIManager

Inserter 214Distributed Mechanism Manager – see

Distributed Mechanism GUI: Managerdistributed physical system – see system:

continuousdivergence 275


divide and conquer – see good programmingstyle: divide and conquer

division operator – see hoc syntax:expressions: operators

doEvents() – see standard run system:doEvents()

dot notationaccessing object members – see object:

public members: dot notationspecifying section properties – see section:

currently accessed: dot notationdouble – see hoc syntax: variables: doubledt 24

as an ASSIGNED variable – seeASSIGNED variable: v, celsius, t,dt, diam, and area

also see dt: use in NMODLfixed – see numeric integration: fixed time

stepuse in NMODL 210, 213variable – see numeric integration: adaptivealso see standard run system: setdt(),

standard run system: fadvance(),RunControl GUI: dt, RunControl GUI:Points plotted/ms

t 61–72, 91fixed – see numeric integration: fixed time

stepalso see discretization

x 59–61also see spatial grid, discretization

Index 423






Ee

electronic charge vs. units conversion factor231

also see NMODL: units conversion factoralso see units: e

e_pas – see pas mechanismedge – see circuit: edgeefficiency – see computational efficiencyeigenfunction 65–66eigenvalue 48, 65elapsed simulation time 24

also see telectrical synapse – see gap junction, synapse:

ephapticelectrode

capacitance 48compensation 48

current – see current: electrode,ELECTRODE_CURRENT

intracellular stimulating – see Example 9.3:an intracellular stimulating electrode

resistance 48shunting effect of sharp microelectrode –

see Example 9.2: a localized shuntELECTRODE_CURRENT 186electronic charge – see e: electronic charge vs.

units conversion factorelectronic instrumentation – see linear circuitelectrotonic architecture

spurious effect of changing nseg 102else – see hoc syntax: flow control: elseem 362

also see emacsemacs

blocks of textcopying to the kill buffer 408cutting to the kill buffer 408marking 408pasting from the kill buffer 408

buffers 406, 409cursor movement 407entering 407exiting 407files 409modes 406, 408repeating commands

kill current command 407macros 411repeating commands 411

search and replace 409send command to OS 409

textdeleting 408formatting 409inserting 408

windows 410embedding C code – see NMODL:

VERBATIM . . . ENDVERBATIMempty temporal resolution – see temporal

accuracy: emptyencapsulating code – see object-oriented

programming: encapsulating codeENDCOMMENT – see NMODL: commentsENDVERBATIM – see NMODL:

VERBATIM . . . ENDVERBATIMenhancing NEURON – see NMODLEOT (ˆD) – see hoc: starting and exitingephapse – see synapse: ephapticephaptic synapse – see synapse: ephapticequality operator – see hoc syntax:

expressions: operatorsequation

algebraic 36, 74, 86–87, 114cable 50, 53

analytic solution 56characteristic 45conservation 211current balance 44, 46, 167–169, 211

also see Kirchhoff’s current lawdifference 51differential 36–39, 42, 46, 48, 50, 63, 65, 114

coupled vs. independent 66, 71ordinary 46, 53partial 51stiff – see system: stiff

iteration – see iteration: equationnode – see equation: current balance,

Kirchhoff’s current lawsacred runes 85system – see system equations

equilibrium potentialASSIGNED vs. PARAMETER – see

ASSIGNED variable: when to use foran equilibrium potential

computation 186, 195also see ion_style(), NEURON block:

NONSPECIFIC_CURRENT:equilibrium potential

initialization – see initialization: ionalso see ion_style()

equivalent circuit – see circuit: equivalent,section: equivalent circuit

Erase – see Graph GUI: primary menu: Erase

424 Index






erasing traces – see Graph GUI: primarymenu: Erase

error – see numerical error, hoc: errorhandling, error message

error messagediam = 0 107no accessed section 143no message for pt3dadd with zero

diameter 108also see hoc: error handling

Euler method – see backward Euler method,forward Euler method

event 81, 87afferent – see event: externalaggregation – see numeric integration: fixed

time step: event aggregationdelivery 80–81delivery system – see standard run system:

event delivery systemdiscrete – see discrete event simulationexternal 288

distinguishing from a self-event 288flag 288

also see event: external: distinguishingfrom a self-event

handler – see NetCon class: event()input 80–81

also see event: externallogical 80mouse – see mouse: eventsnet_send 186queue – see standard run system: event

delivery system: cell time queue,standard run system: event deliverysystem: event time queue

self-event 261, 288distinguishing from an external event –

see event: external: distinguishingfrom a self-event

implementing absolute refractory period– see IntFire1 class: refractoryperiod

implementing deferred computation – seestandard run system: event deliverysystem: implementing deferredcomputation

implementing transmitter release duration– see Example 10.6: saturatingsynapses

also see event: external, NET_RECEIVEblock: net_move(),NET_RECEIVE block:

net_send(), IntFire2 class:firing time: role of self-events,IntFire4 class: firing time: roleof self-events

spike – see event: externaltimes

notification – see CVODE: and modeldescriptions: at_time(), NetConclass: event()

with adaptive integration 218, 263also see NetCon class: event()

with fixed time step integration – seenumeric integration: fixed time step:event aggregation

also see standard run system: eventdelivery system: event time queue

event aggregation to time step boundaries –see numeric integration: fixed time step:event aggregation

event handler – see NetCon class: event()event queue – see standard run system: event

delivery system: event time queueevent times – see event: timesevent-driven simulation – see discrete event

simulationevent() – see NetCon class: event()Example 9.1: a passive “leak” current 208Example 9.2: a localized shunt 214Example 9.3: an intracellular stimulating

electrode 217Example 9.4: a voltage-gated current 220Example 9.5: a calcium-activated, voltage-

gated current 228Example 9.6: extracellular potassium

accumulation 233Example 9.7: kinetic scheme for a voltage-

gated current 240Example 9.8: calcium diffusion with

buffering 245Example 9.9: a calcium pump 255Example 10.1: graded synaptic transmission

266Example 10.2: a gap junction 271Example 10.3: synapse with exponential

decay 277Example 10.4: alpha function synapse 280Example 10.5: use-dependent synaptic

plasticity 281Example 10.6: saturating synapses 284Example 10.7: IntFire1, a basic integrate

and fire model 290

Index 425






Example 10.8: IntFire2, firing rateproportional to input 297

Example 10.9: IntFire4, different synaptictime constants 301

execute() 385exiting hoc – see hoc: starting and exitingexiting NEURON – see NEURON: starting

and exitingExp2Syn

computational efficiency 280also see Example 10.4: alpha function

synapseexplicit Euler method – see forward Euler

methodexplicit flux – see KINETIC block:

<<(explicit flux)exploiting reusable code – see good

programming style: exploiting reusablecode

exploratory simulations – see GUI: vs. hoc

exponentiation operator – see hoc syntax:expressions: operators

ExpSyn – see Example 10.3: synapse withexponential decay

expsyn1.mod – see Example 10.3: synapsewith exponential decay

extensive variable – see variable: extensiveexternal event – see event: externalextracellular field – see extracellular

mechanism, system equations: matrixform: extracellular field

extracellular mechanism 56, 74, 87computational efficiency 167effect of ELECTRODE_CURRENT – see

NEURON block:ELECTRODE_CURRENT: effect onextracellular mechanism

initialization – see initialization:extracellular mechanism

vext 186also see NEURON block:

ELECTRODE_CURRENT: effect onextracellular mechanism

extracellular potassium accumulation – seeExample 9.6: extracellular potassiumaccumulation

Ff_flux – see KINETIC block: f_fluxF-H space – see Example 9.6: extracellular

potassium accumulation

factoramplification – see amplifier: gainconversion or scale – see scale factor,

NMODL: units conversion factor,UNITS block: units scaling

fadvance.c 164, 185also see initialization: finitialize()

fadvance() – see standard run system:fadvance()

FALSE – see hoc syntax: expressions: logicalexpressions

fan-in – see convergencealso see synaptic transmission: spike-triggered

fan-out – see divergencealso see synaptic transmission: spike-triggered

faraday – see units: faradayfast signals

spatial decay – see spatial decay of fast signalsfast_flushPlot() – see standard run

system: fast_flushPlot()fast_flush_list – see standard run

system: plotting system:fast_flush_list

fcurrent() – see standard run system:fcurrent()

feedbackamplifier 49capacitor 49positive 49

field – see extracellular mechanismfilehoc file – see hocmod file – see mod file, NMODLreading and writing – see hoc syntax: basic

input and outputses file – see session filesession file – see session file

finitialize() – see initialization:finitialize()

fixeddt – see numeric integration: fixed time step t – see numeric integration: fixed time steptime step – see numeric integration: fixed

time stepfloat_epsilon – see hoc syntax:

float_epsilonflow control – see hoc syntax: flow controlflushPlot() – see standard run system:

flushPlot()flush_list – see standard run system:

plotting system: flush_listflux 37–39, 42

426 Index






backward 39also see KINETIC block: b_flux

forward 39also see KINETIC block: f_flux

also see KINETIC block: << (explicit flux)FOCAL 164focus

cursor 10for – see hoc syntax: flow control: forfor (x) 114forall 100forsec 100forward Euler method 61

iteration coefficient 61local error 64, 83stability 62, 64, 243also see numerical integration: fixed time

stepforward flux – see flux: forward, KINETIC

block: f_fluxFourier theory 56fprint() – see hoc syntax: basic input and

output: fprint()FROM . . . TO . . . – see NMODL:

FROM . . . TO . . . (loop statement)Frankenhaeuser-Hodgkin space – see Example

9.6: extracellular potassium accumulationfrecord_init() – see initialization:

frecord_init()frequency 66

spatial 57, 59–61, 122also see spatial accuracy, spatial grid,

numerical error: spatialtemporal 122

fscan() – see hoc syntax: basic input andoutput: fscan()

funcs and procs$ – see funcs and procs: arguments:

positional syntax$i – see funcs and procs: arguments:

symbolic positional syntax$o – see funcs and procs: arguments:

objects and objrefs$s – see funcs and procs: arguments:

strdef& – see hoc syntax: pointer operatorarguments

call by reference vs. call by value 359, 366numarg() 358objects and objrefs 358–359, 366pointer 358

also see hoc syntax: pointer operator

positional syntax 358strdef 358–359symbolic positional syntax 358

defining 357local variable 360

also see hoc syntax: namesrecursion 360return 357

also see hoc syntax: flow control: returnreturned value – see funcs and procs:

returnFUNCTION

calling from hoc – see hoc: calling anNMODL FUNCTION or PROCEDURE

functioncontinuous

of space 51also see range variable

of time 51delta 51discrete 77piecewise linear 78, 80

also see continuous variable: piecewiselinear approximation

rate – see BREAKPOINT block: and ratefunctions, KINETIC block: reactionrates: voltage sensitive

table – see function tablealso see funcs and procs, FUNCTION

FUNCTION block 226, 232arguments are call by value 283

function call operator – see hoc syntax:expressions: operators

function table 114, 170also see NMODL: FUNCTION_TABLE

FUNCTION_TABLE – see NMODL:FUNCTION_TABLE

Gg_pas – see pas mechanismgain – see amplifier: gaingap junction 265–266, 271

computational efficiency 167conservation of charge 271

also see charge: conservation, equation:current balance, Kirchhoff’s currentlaw

spurious oscillations 271under CVODE 88also see Example 10.2: a gap junction,

synapse: ephaptic, LinearCircuitBuilder:for gap junctions

Index 427






gap.mod – see Example 10.2: a gap junctiongating model – see channel: gating modelgating state

initialization – see initialization: channelmodel

custom initialization – see initialization:strategies: changing a state variable

gating variable – see gating stateGaussian elimination 74, 167–169generic starting point for GUI tool

development – see GUI tooldevelopment: generic starting point

GENESIS 207, 210geometry 98

artifactsstylized specification reinterpreted as 3-D

specification 108zero diameter 107

specifying – see 3-D specification ofgeometry, stylized specification ofgeometry

also see CellBuilder GUI: Geometry pagealso see topology, anatomical properties

getstr() – see hoc syntax: basic input andoutput: getstr()

GLOBAL – see NEURON block: GLOBAL,ASSIGNED variable: GLOBAL,PARAMETER variable: is GLOBAL bydefault

also see LOCAL variable: declared outside an equation block: scope andpersistence

global – see GLOBAL, global variableglobal error – see numerical error: globalglobal time step – see numeric integration:

adaptive: global time stepglobal variable – see variable: local vs.

nonlocal, hoc syntax: names, template:writing a template: external

GMODL 210good programming style

bulletproofing against nonsense arguments330

divide and conquer 5exploiting reusable code 307, 324, 328iterative development 155, 329, 378, 381modular programming 5, 142, 328

control – see simulation controlinstrumentation – see instrumentationmodel specification – see model

specificationprogram organization 98, 154

separating model specification from userinterface 155, 328

also see hoc: idiomgraded synapse – see synaptic transmission:

gradedgradient – see concentration: gradient, voltage:

gradientgradsyn.mod – see Example 10.1: graded

synaptic transmissionGraph

automatically updating plots and x axis –see standard run system: addplot()

creatingShape plot 22Space Plot 22Voltage axis 21

incorporating into plotting system – seestandard run system: plotting system:incorporating Graphs and objects,standard run system: addplot()

Graph classaddexpr() 180addvar() 180begin() 180–181

also see initialization: initPlot(),standard run system: Plot()

beginline() 390erase_all() 337, 389exec_menu() 392flush() 180–181, 393mark() 393menu_tool() 380plot() 180–181

also see standard run system: Plot()save_name() 385size() 181, 337, 391view_count() 180–181view_info() 394view() 335also see standard run system: addplot()

Graph GUIprimary menu

Erase 29Keep Lines 28Plot what? – see Plot what? GUI

graphraster – see spike trains: recording and

plotting, NetWork Builder: buttons:SpikePlot

also see Graphgraph lists – see standard run system: plotting

system: graphLists

428 Index






graph theory 44, 317graphical interface – see user interface:

custom GUI, NEURON Main Menugraphical tools – see NEURON Main Menu,

CellBuilder, Graph, PFWM,PointProcessManager, RunControl,Shape plot, Shape Plot, Space Plot, Plotwhat?, GUI tool development

graphics terminology – see GUI: graphicsterminology

greater than operator – see hoc syntax:expressions: operators

greater than or equal to operator – see hocsyntax: expressions: operators

ground – see circuit: element: groundgsyn.mod – see Example 10.5: use-

dependent synaptic plasticityGUI

combining with hoc 141, 324computer display – see GUI: screenconflicts with hoc or other GUI tools 152focus – see focus: cursorgraphics terminology 378implementing a computational model – see

CellBuilder, NetWork Buildermapping to the screen – see GUI: screen:

mapping to the screenmodel 378model coordinates 378

also see GUI: scene coordinatesscene 378scene coordinates 378

making scene and view coordinatesequivalent 395

vs. screen coordinates 394screen 378

mapping to the screen 378also see GUI tool development:

mapping to the screenscreen coordinates 378

vs. scene coordinates – see GUI: scene coordinates: vs. screencoordinates

toolsare implemented in hoc 129, 344Close button 381, 383developing new tools – see GUI tool

developmentwork by constructing hoc programs

129, 344also see NEURON Main Menu GUI

view 378

which view contains the mouse – seeGraph class: view_info()

vs. hoc 128also see user interface: custom GUI,

NEURON Main Menu, standard GUIlibrary

GUI tool developmentbasic pattern – see GUI tool development:

generic starting pointbox – see VBox, HBoxClose button – see GUI: tools: Close buttongeneral issues

allowing multiple instances 380,383–384

destroying 381, 383–384encapsulating 380saving and retrieving 380, 385, 395

also see session file, session file:object_push(), session file:object_pop(), GUI: scenecoordinates: making scene andview coordinates equivalent

generic starting point 387graphical model – see GUI: modelmapping to the screen 386–387

window title 384also see GUI: screen: mapping to the

screen, VBox class: map()mouse events – see mouse: eventspanel – see xpanel()which view contains the mouse – see

Graph class: view_info()

HHamming, R.W. 86HBox 383

also see VBoxhh mechanism 16hiding information – see object-oriented

programming: information hidingHinton plot 180history function – see hoc: history functionhoc 2, 17, 128, 343

adding new mechanisms – see nrniv:adding new mechanisms, mechanisms:user-defined, NMODL

calling an NMODL FUNCTION orPROCEDURE 226

specifying proper instance withsetdata_ 226

can do anything that a GUI tool can 130combining with GUI 141, 324

Index 429






hoc (contd)conflicts with GUI 152efficient simulation – see computational

efficiency: why is NEURON fast?enhancements and extensions 343error handling 348functions – see funcs and procshistory function 347idiomforall nseg*=3 97forall psection() 134load_file("nrngui.hoc") 142,

159also see List class: iteration

immediate mode 347implementing a computational model 130interrupting execution 349

also see hoc: starting and exitingKernighan and Pike 343keywords – see hoc syntax: keywordslibraries 344

also see standard GUI library, standardrun library

oc> prompt 347parse errors – see hoc: error handlingprocedures – see funcs and procsrun-time errors – see hoc: error handlingscalar – see hoc syntax: variables: scalarsscope – see hoc syntax: names, funcs and

procs: local variable, variable: localvs. nonlocal, LOCAL variable,ASSIGNED variable: GLOBAL,NEURON block: GLOBAL,PARAMETER variable: is GLOBAL bydefault

also see object: public members,template: writing a template:public, template: writing atemplate: external

speed – see computational efficiency: whyis NEURON fast?

starting and exiting 346stopping – see hoc: interrupting execution

also see hoc: starting and exitingsyntax – see hoc syntaxtop level of the interpreter 385

also see execute()user-defined variable – see hoc syntax:

namesvs. GUI 128also see hoc syntax, Programmer’s

Reference, good programming style

hoc fileexecuting – see NEURON: starting with a

specific hoc file, nrngui, nrnivalso see load_file(), hoc syntax:

basic input and output: xopen()hoc syntax

basic input and outputfprint() 361fscan() 362getstr() 362print 361printf() 361read() 361ropen() 362sprint() 361wopen() 361xopen() 362

also see load_file()xred() 362

comments 130, 355continuation character 348expressions 354

logical comparison of real values – see hoc syntax:float_epsilon

logical expressions 355operators 354precedence – see hoc syntax:

expressions: operatorsfloat_epsilon 355flow control 356break 100, 357continue 100, 357else 356for 356if 356iterator 356iterator_statement 356quit() 357return 100, 357

also see funcs and procs: returnstop 357while 356

functions – see funcs and procskeywords 350names 350operators – see hoc syntax: expressions:

operators, hoc syntax: pointeroperator

pointer operator 358precedence of operations – see hoc syntax:

expressions: operators

430 Index






procedures – see funcs and procsstatements 355

compound statement 355variables 353

arrays – see hoc syntax: variables:double

built-in constants 353cannot change type 156cannot redefine type 354double 353

also see Vector classobjref – see object reference: objrefscalars 353strdef 354strings – see hoc syntax: variables:

strdefalso see hoc: idiom, Programmer’s

ReferenceHodgkin–Huxley delayed rectifier – see

Example 9.4: a voltage-gated currentHodgkin–Huxley mechanism – see hh

mechanismhypothesis 1, 24

testing 32–33also see model: conceptual

IIClamp class 112

preserving spatial accuracy – see pointprocess: preserving spatial accuracy

iclamp1.mod – see Example 9.3: anintracellular stimulating electrode

IDA 172initialization 187also see numeric integration: adaptive,

DASPK, SUNDIALSidiom – see hoc: idiomif – see hoc syntax: flow control: ifimmediate mode – see hoc: immediate modeimplicit Euler method – see backward Euler

methodinequality operator – see hoc syntax:

expressions: operatorsinformation hiding – see object-oriented

programming: information hidinginheritance – see object-oriented

programming: inheritanceINITIAL block 186, 188, 190, 224

initializing STATE variables – see STATEvariable: initialization

inside NET_RECEIVE block – seeNET_RECEIVE block: INITIAL block

sequence-dependent 186SOLVESTEADYSTATE sparse 189, 243, 258also see initialization: channel model:

kinetic schemealso see initialization, mechanisms:

initialization sequence, mechanisms:user-defined: call order

init() – see initialization: init()initial value problem 48initialization 24, 28, 140

adaptive integration – see numeric integration:adaptive: initialization, CVode class:re_init(), IDA: initialization

active transport – see active transport:initialization

analysis 183ASSIGNED variable – see ASSIGNED

variable: initializationbasic 185

also see initialization:finitialize(), initialization:default

categories 225of a chaotic system – see initialization:

categories: to a desired stateof an oscillating system – see

initialization: categories: to adesired state

overview of custom initialization 185, 188also see initialization: init(): custom

to a desired state 198to a particular resting potential 195to steady state 197also see initialization: basic, initialization:

defaultchannel model 188

Hodgkin–Huxley style 188kinetic scheme 189

also see INITIAL block: SOLVE:STEADYSTATE sparse, ini-tialization: strategies: changing astate variable, initialization:strategies: changing modelparameters, initialization: strate-gies: steady state initialization ofcomplex kinetic schemes

criterion for proper initialization 183custom 152

also see initialization: categories,initialization: strategies,initialization: init(): custom

Index 431






initialization (contd)default 187

also see initialization: init(),initialization: stdinit(),initialization: basic

diffusion – see ion accumulation:initialization

dt – see standard run system: setdt()event delivery system – see standard run

system: event delivery system:initialization, initialization:finitialize()

extracellular mechanism 186fcurrent() – see standard run system:

fcurrent(): in initializationfinitialize() 160, 164, 175,

185–187, 219, 224fixed time step integration – see numeric

integration: fixed time step:initialization

frecord_init() 188init() 160, 164, 187–188

custom 195–198, 204also see initialization: strategies:

changing a state variableinitPlot() 164, 180, 187internal data structures dependent on

topology and geometry 185also see ion accumulation: initialization:

of model geometryion 186, 191–194

accumulation – see ion accumulation:initialization

also see ion mechanism: defaultconcentration, ion_style(),initialization: strategies: changing astate variable

kinetic scheme 183also see INITIAL block: SOLVE:

STEADYSTATE sparse,KINETIC block: CONSERVE: whenis it required for initialization?

linear circuit 183, 186membrane potential – see initialization:

v_init, membrane potential:initialization

NetCon object – see NET_RECEIVEblock: INITIAL block

network 183, 186non-steady state 166object – see template: variable initializationrandom number generator 183

Random.play() 185recording 183

also see initialization:frecord_init(), Vector class:record(): initialization

startsw() 187also see run time, standard run system:

realtimeSTATE variable – see STATE variable:

initializationstate0 – see STATE variable:

initializationstdinit() 160, 164, 180, 187steady state – see initialization: categories: to

steady state, initialization: categories: toa particular resting potential

strategies 225changing a state variable 187–188

also see STATE variable: initialization,ion mechanism: initialization,ion mechanism: defatult concen-tration: specification in hoc

changing an equilibrium potential 195changing model parameters 199groundhog day 199injecting a constant current 196jumping back to move forward 197steady state initialization of complex

kinetic schemes 258also see initialization: init(): custom

synaptic weight vector – see NET_RECEIVEblock: INITIAL block

t 185template – see template: variable initializationv_init 24, 186–188

also see membrane potential: initializationVector.play() 186Vector.record() – see initialization:

frecord_init(), Vector class:record(): initialization

weight vector – see NET_RECEIVE block:INITIAL block

also see RunControl GUI: Init, RunControlGUI: Init & Run, INITIAL block,NET_RECEIVE block: INITIALblock, Graph class: begin(),mechanisms: initialization sequence,mechanisms: user-defined: call order

initialize microstep – see numeric integration:adaptive: initialize microstep

also see standard run system: fadvance():local time step integration

432 Index






initPlot() – see initialization:initPlot()

input and output – see hoc syntax: basic inputand output

input event – see event: externalinsert 111, 133

also see uninsertinsight 32, 34, 86instability – see numeric integration:

instability, KINETIC block: reactionrates: STATE-dependent, and instability

instrumentation 5, 18, 154integrate and fire 83, 88

also see artificial spiking cellintegration – see numeric integrationintensive variable – see variable: intensiveintent – see user’s intentinterpolate microstep – see numeric integration:

adaptive: interpolate microstepalso see standard run system: fadvance():

local time step integrationinterpolation – see Vector class: play():

with interpolationinterpreter – see hocIntFire1 class 290

effect of an input event 292m – see IntFire1 class: membrane state

variableM – see IntFire1 class: membrane state

variable: visualizingmembrane state variable 290

time constant 290visualizing 292, 296

refrac – see IntFire1 class: refractoryperiod

refractory period 294tau – see IntFire1 class: membrane

state variable: time constantalso see artificial spiking cell, Example

10.7: IntFire1, a basic integrateand fire model

IntFire2 class 297approximate firing rate 298bias – see IntFire2 class: synaptic

current state variable: biasconstraint on time constants 298effect of an external event 297, 299firing time

efficient computation 299role of self-events 299

i – see IntFire2 class: synaptic currentstate variable

ib – see IntFire2 class: synaptic currentstate variable: bias

m – see IntFire2 class: membrane statevariable

membrane state variable 297time constant 297

also see IntFire2 class: constrainton time constants

synaptic current state variable 297bias 297time constant 297


taum – see IntFire2 class: membranestate variable: time constant

taus – see IntFire2 class: synapticcurrent state variable: time constant

also see artificial spiking cell, Example10.8: IntFire2, firing rateproportional to input

IntFire4 class 301constraint on time constants 301, 399convergence tolerance 304e – see IntFire4 class: synaptic current

state variables: excitatoryeffect of an external event 301eps – see IntFire4 class: convergence

tolerancefiring time

efficient computation 302role of self-events 303

i1 – see IntFire4 class: synaptic currentstate variables: inhibitory

i2 – see IntFire4 class: synaptic currentstate variables: inhibitory

m – see IntFire4 class: membrane statevariable

membrane state variable 301time constant 301, 399

synaptic current state variablesexcitatory 302inhibitory 302time constants 301, 399


taue – see IntFire4 class: synapticcurrent state variables: time constants

taui1 – see IntFire4 class: synapticcurrent state variables: time constants

taui2 – see IntFire4 class: synapticcurrent state variables: time constants

Index 433






IntFire4 class (contd)taum – see IntFire4 class: synaptic

current state variables: time constants

also see artificial spiking cell, Example10.9: IntFire4, different synaptictime constants

intuition 32–33ion accumulation 199

initialization 200of model geometry 251also see ion mechanism: default

concentration, ion_style(),initialization: strategies: changing astate variable, initialization:strategies: changing modelparameters

kinetic scheme 200also see Example 9.8: calcium diffusion

with buffering, Example 9.9: acalcium pump

under CVODE 88also see active transport, buffer, diffusion,

ion mechanism, ion_style(),equilibrium potential, STATE variable:ion concentration as, Example 9.6:extracellular potassium accumulation

ion channel 13ion concentration – see concentration, ion

accumulation, ion mechanismion mechanism_ion suffix 190automatically created 190, 235default concentration

for user-created ion names 194name 194specification in hoc 194–195

equilibrium potential – see equilibriumpotential: computation

initialization 194, 236also see initialization: ion

ion_style() 194also see ASSIGNED variable, PARAMETER

variable, STATE variable, concentration,initialization: ion

ionic conductance 18also see channel: density

isopotential – see membrane potential:isopotential

iterationcoefficient 61equation 61

of nonlinear equations – see numericintegration: iteration of nonlinearequation

over a List – see List class: iterationover nodes – see range variable: iterating

over nodesover sections – see section: iterating over

sectionsusing iterator – see hoc syntax: flow

control: iteratoriterative development – see good

programming style: iterative developmentiterator – see hoc syntax: flow control:

iteratoriterator_statement – see hoc syntax:

flow control: iterator_statement

JJacobian 239, 243

analytic 114approximate 74, 226, 253, 271computing di/dv elements 168, 189, 262nearly singular 244user-supplied 226

judgment 1, 30, 34, 85also see accuracy, detail, qualitative results

Kk-mole – see units: k-molek_ion – see ion mechanism: automatically

createdk3st.mod – see Example 9.7: kinetic

scheme for a voltage-gated currentkd.mod – see Example 9.4: a voltage-gated

currentKeep Lines – see Graph GUI: primary menu:

Keep LinesKernighan, B.W. – see hoc: Kernighan and

Pikekext.mod – see Example 9.6: extracellular

potassium accumulationkeyboard

Alt key – see Graph class: menu_tool()Control C – see hoc: interrupting executionControl D – see hoc: starting and exitingControl key – see Graph class:

menu_tool()Shift key – see Graph class:

menu_tool()keywords – see hoc syntax: keywords,

NMODLki – see potassium, ion mechanism

434 Index






ki0_k_ion – see potassium, ionmechanism: default concentration:specification in hoc

KINETIC block 243, 252, 259–> (sink reaction indicator) 261~ (tilde) 238<–> (reaction indicator) 238<< (explicit flux) 253and CVODE 88b_flux 238COMPARTMENT 247, 253–254CONSERVE 243–244

when is it required for initialization?244, 252, 258

dependent variableis a STATE variable 184also see KINETIC block: reactants:

ASSIGNED or PARAMETERvariables as

f_flux 238initialization – see initialization: channel

model: kinetic scheme, INITIALblock: SOLVE: STEADYSTATEsparse

LONGITUDINAL_DIFFUSION 253radial diffusion – see Example 9.8: calcium

diffusion with bufferingreactants 238ASSIGNED or PARAMETER variables as

242also see KINETIC block: dependent

variable: is a STATE variablereaction rates 238STATE-dependent, and instability 239voltage-sensitive 239

reaction statement 238also see Crank–Nicholson method: local

error: kinetic scheme, BREAKPOINTblock: SOLVE: sparse

kinetic scheme 36–37compartment size 41also see scale factor, NMODL: units

conversion factor, KINETIC block:COMPARTMENT

conservation rules 39also see scale factor, NMODL: units

conversion factor, KINETIC block:COMPARTMENT

equivalent differential equations 38initialization – see initialization: channel

model: kinetic scheme, initialization:strategies: changing a state variable,

initialization: strategies: changingmodel parameters, KINETIC block:CONSERVE: when is it required forinitialization?

reactants – see KINETIC block: reactantsreaction rates – see KINETIC block:

reaction ratesalso see KINETIC block

Kirchhoff’s current law 44also see charge: conservation, equation:

current balanceko – see potassium, ion mechanismko0_k_ion – see potassium, ion


L� – see length constantL 13, 94, 132

calculation from 3-D data – see 3-Dspecification of geometry: calculationof L, diam, area(), and ri()

change flag 168default value 103specifying

stylized specification 1043-D specification – see 3-D specification

of geometry: calculation of L,diam, area(), and ri()

updating from 3-D data 109also see length

lambda_f() 123leak current – see pas mechanism, leak.modleak.mod – see Example 9.1: a passive

“leak” currentlegacy code – see troubleshooting: legacy

codelength 3, 94

arc – see rangealso see L

length constant 13–14AC 122DC 121also see d_lambda rule

less than operator – see hoc syntax:expressions: operators

less than or equal to operator – see hocsyntax: expressions: operators

linear algebra 65LINEAR block 223

dependent variableis a STATE variable 184

Index 435






linear circuit 56, 74, 87computational efficiency 167initialization – see initialization: linear circuitalso see system equations: matrix form:

linear circuitlinear taper – see range variable: linear taperLinearCircuitBuilder

for gap junctions 272linearity – see channel: linear, channel: gating

model: HH-typeLinearMechanism class 101list

of objects – see List classof sections – see SectionList class

List class 373append() 335, 373count() 325, 330, 373iteration 373object stack 374object() 325, 330, 373remove_all() 330remove() 375

List objectmanaging network cells with 327managing network connections with 279, 327

load_file() 124, 362also see hoc syntax: basic input and output:

xopen(), hoc: idiom:load_file("nrngui.hoc")

loc() – see point process: loc()local – see hoc syntax: names, funcs and

procs: local variable, LOCAL variablealso see object: public members: vs. private

members, template: writing a template:public

local absolute error – see absolute error: locallocal error – see numerical error: locallocal relative error – see relative error: locallocal time step – see numeric integration:

adaptive: local time stepLOCAL variable

declared outside an equation blockinitial value 251scope and persistence 251also see NEURON block: GLOBAL

declared within an equation blockscope and persistence 227

local variable – see hoc syntax: names, funcsand procs: local variable, LOCAL variable

also see object: public members: vs. privatemembers, template: writing a template:public

logical comparison of real values – see hocsyntax: float_epsilon

logical comparison operators – see hocsyntax: expressions: operators

logical expressions – see hoc syntax:expressions: logical expressions

logical operators – see hoc syntax:expressions: operators

LONGITUDINAL_DIFFUSION – seeKINETIC block:LONGITUDINAL_DIFFUSION

longitudinal diffusion – see diffusion: kineticscheme: longitudinal, KINETIC block:LONGITUDINAL_DIFFUSION

loop statement – see NMODL: FROM . . . TO . . . (loop statement)

also see hoc syntax: flow control: for,hoc syntax: flow control: while

Mmapping to the screen – see GUI: screen:

mapping to the screenMarkov process

kinetic scheme 238mass 50

also see materialmass balance – see material: conservationmaterial 36

amount 36, 42concentration 36conservation 36, 238, 242–244, 259density 36

mechanismsadding new – see mechanisms: user-definedinitialization sequence 186involving delay – see standard run system:

event delivery system: implementingdeferred computation

user-defined 113call order 186also see nrniv: adding new

mechanisms, NMODLalso see distributed mechanism, point process

membrane area 51also see area(), surface area

membrane capacitance 15, 53, 91also see cm, specific membrane capacitance

membrane conductance – see specificmembrane conductance

membrane currentcapacitive 53, 122ionic 53, 122

436 Index






accuracy 169positive current convention 51

membrane potential 20–21, 49, 54, 94initialization 186–188

also see initialization: v_init,initialization: categories,initialization: strategies

isopotential 53also see v, membrane state variable

membrane resistance 16, 121membrane state variable – see IntFire1

class: membrane state variable,IntFire2 class: membrane statevariable, IntFire4 class: membranestate variable

membrane time constant 122and attenuation of fast signals 123

METHOD – see BREAKPOINT block: SOLVEmicroelectrode – see electrodeMicroEMACS 362

also see em, emacsmicrostep – see numeric integration: adaptive:

advance microstep, numeric integration:adaptive: initialize microstep, numericintegration: adaptive: interpolatemicrostep

miscellaneous_add() – seeNEURONMainMenu class:miscellaneous_add()

mistakeprogramming – see hoc: error handling

mknrndll – see NMODL: translator:mknrndll

mod file 207, 345compiling

under MSWindows – see NMODL:translator: mknrndll

under UNIX/Linux – see NMODL:translator: nrnivmodl

also see NMODLmodel

3-D 110also see 3-D specification of geometry

ball and stick 34compartmental 92, 96computational 1, 5, 33

analysis 24essential steps 128implementation 34, 98

also see computational model: implementing with hoc

model specification 16

conceptual 1, 3, 28, 33, 36, 118correspondence between conceptual and

computational 128, 130also see discrepancy: between conceptual

model and compartmental modelnetwork – see network modelpurpose – see judgment, user’s intentsimulation control – see simulation controlstylized 104

also see stylized specification of geometrytesting 141

also see topology: checkingMOdel Description Language – see MODLmodel coordinates – see GUI: model

coordinatesvs. screen coordinates – see GUI: scene

coordinates: vs. screen coordinatesmodel description language – see NMODLmodel properties

specifying 98also see anatomical properties:

specifying, biophysical properties:specifying

model specification 5, 16, 154as virtual experimental preparation 154vs. user interface – see good programming

style: separating model specificationfrom user interface

also see model properties: specifyingmodeling 73, 79

empirically-based 32, 61rationale 33

modified Euler method 271also see backward Euler method

modifying standard functions and procedures– see standard run library: redefiningfunctions and procedures, standard GUIlibrary: redefining functions andprocedures

MODL 208vs. NMODL 208, 210

modlunit 216, 231also see units: checking

modular programming – see good programming style: modularprogramming

modulus operator – see hoc syntax:expressions: operators

mole – see units: molemole equivalents 39morphometric data – see quantitative

morphometric data

Index 437






mousebutton – see mouse: eventscursor – see focus: cursorevents 379

Alt, Control, or Shift key – see Graphclass: menu_tool()

cursor coordinates 380, 392handling 380, 392also see Graph class: menu_tool()

which view contains the mouse – seeGraph class: view_info()

movie – see Vector: moviemultiplication operator – see hoc syntax:

expressions: operators

Nn3d() – see 3-D specification of geometry:

n3d()na_ion – see ion mechanism: automatically

creatednai – see ion mechanismnai0_na_ion – see ion mechanism: default

concentration: specification in hocnao – see ion mechanismnao0_na_ion – see ion mechanism: default

concentration: specification in hocNational Biomedical Simulation Resource

project 208Nernst equation – see initialization: ion,

ion_style()Nernst potential – see equilibrium potential,

initialization: ion, ion_style()net_event() – see NET_RECEIVE block:

net_event()net_move() – see NET_RECEIVE block:

net_move()NET_RECEIVE block 275, 278

arguments are call by reference 283flag – see event: flaghandling abrupt changes and discontinuities

262INITIAL block 186, 224, 283

also see NetCon class: weight vectornet_event() 292, 299, 303net_move() 289, 299net_send() 289, 295state_discontinuity() 262also see Examples 10.3–10.9

net_send() – see NET_RECEIVE block:net_send()

NetConand standard run system 166

NetCon class 272, 274delay 274event() 263record() 335source variable 274states – see NetCon class: weight vectorstream-specificity 274, 279target 275threshold 274weight 274weight vector 275

initialization 283NetCon object

as a channel for a stream of events 289initialization – see NET_RECEIVE block:

INITIAL blocknetcvode.cpp 166NetGUI class – see NetWork BuilderNetReadyCellGUI

bringing up a NetReadyCellGUI 322cell names – see NetWork Builder: cells:

nameschanging cell parameters – see NetWork

Builder: caveatsNetWork Builder

adjusting model parameters 318bringing up a NetWork Builder 313buttons

Create 318, 323Delays – see NetWork Builder:

specifying delays and weightsHoc File – see NetWork Builder:

exporting reusable codeLocate – see NetWork Builder: cells:

creatingShow Cell Map – see NetWork Builder:

cells: Cell MapSpikePlot 318Src–> Tar – see NetWork Builder: setting

up network architectureWeights – see NetWork Builder:

specifying delays and weightscanvas 314

dragging 315caveats 322cells

Cell Map 324connecting – see NetWork Builder:

setting up network architecture,NetWork Builder: specifying delaysand weights

creating 314

438 Index






names 314, 323also see NetWork Builder: cells: Cell Map

types – see NetWork Builder: palette of celltypes, ArtCellGUI, NetReadyCellGUI

changing a network – see NetWork Builder:caveats

changing cell parameters – see NetWorkBuilder: caveats

creating an instance of a network – seeNetWork Builder: buttons: Create

default section – see NetWork Builder:exporting reusable code: acell_home_

delays and weights – see NetWork Builder:specifying delays and weights

exploiting reusable code 328exporting reusable code 324acell_home_ 326network cell templates 326network instantiation 328network specification interface 327

hints 314network architecture – see NetWork Builder:

setting up network architecturepalette of cell types 314plotting spikes – see NetWork Builder:

buttons: SpikePlotreusable code – see NetWork Builder:

exploiting reusable codesaving a hoc file – see NetWork Builder:

exporting reusable codesetting up network architecture 315specifying delays and weights 316

network modelarchitecture – see convergence, divergence

also see NetCon, List object:managing network connections with

building with GUI – see ArtCellGUI,NetReadyCellGUI, NetWork Builder

connectivity – see NetCon, List object:managing network connections with

creating algorithmically 329initialization – see initialization: network,

NET_RECEIVE block: INITIAL blockneurite 51, 92, 105

also see sectionNEURON

adding new mechanisms – see mechanisms:user-defined, nrniv: adding newmechanisms, NMODL

last change date – see NEURON: startupbanner

starting and exiting 6

starting with a specific hoc file 133startup banner 347version number – see NEURON: startup

banneralso see hoc: starting and exiting

NEURON block 210ARTIFICIAL_CELL 291

also see artificial spiking cell, IntFire1class, IntFire2 class, IntFire4class

ELECTRODE_CURRENT 218effect on extracellular mechanism

218GLOBAL 190, 211

also see ASSIGNED variable: GLOBAL,PARAMETER variable: is GLOBALby default

NONSPECIFIC_CURRENT 211equilibrium potential 223also see active transport: pump current:

countering with a NONSPECIFIC_CURRENT

POINT_PROCESS 215also see point process

POINTER 268also see POINTER variable

RANGE 190, 211, 218also see range, range variable,

ASSIGNED variable: GLOBAL: vs.RANGE, ASSIGNED variable: is arange variable by default,PARAMETER variable: GLOBAL vs.RANGE, STATE variable: isautomatically RANGE

SUFFIX 211also see distributed mechanism

USEION 222, 230effect on initialization sequence 186READ ex (reading an equilibrium

potential) 222READ ix (reading an ionic current)

235, 250READ xi (reading an intracellular

concentration) 230, 250READ xo (reading an extracellular

concentration) 255WRITE ix (writing an ionic current)

222, 230, 233, 255, 259WRITE xi (writing an intracellular

concentration) 193, 250WRITE xo (writing an extracellular

concentration) 193, 235

Index 439






NEURON demonstration program – seeneurondemo

NEURON Main Menu 6adding items – see NEURONMainMenu

class: miscellaneous_add()creating 142, 155

NEURON Main Menu GUIBuild

CellBuilder 6NetWork Builder 313

Fileload session 18Quit 347save session 17, 23

GraphCurrent axis 180Phase Plane 180Shape plot 22State axis 180Voltage axis 21, 180

ToolsMiscellaneous 384Point Processes 19

also see PointProcessGroupManager,PointProcessManager

RunControl 24VariableStepControl 165, 319

also see VariableTimeStep GUINEURON MOdel Description Language – see

NMODLNEURON program group 6neuron.exe 345neurondemo 345NEURONMainMenu classmiscellaneous_add() 384

NEURONMainMenu objectis always NEURONMainMenu[0] 384

NEURON’s interpreter – see hocnew – see object: newNMODL 113

abrupt change of a variable – see variable:abrupt change of, NET_RECEIVEblock: handling abrupt changes anddiscontinuities

arraysare not dynamic 250, 255index starts at 0 250STATE variable – see STATE variable:

array in NMODLCOMMENT . . . ENDCOMMENT – see

NMODL: commentscomments 209

declaring variables 211specifying units 212also see NMODL: named blocks:

variable declaration, ASSIGNEDblock, CONSTANT block,PARAMETER block, STATE block,LOCAL variable, NMODL: DEFINE

DEFINE 250dt – see dt: use in NMODLFROM . . . TO . . . (loop statement) 252function – see FUNCTION blockFUNCTION_TABLE 244loop statement – see NMODL: FROM . . .

TO . . . (loop statement)mknrndll – see NMODL: translator:

mknrndllnamed blocks 208ASSIGNED – see ASSIGNED blockBREAKPOINT – see BREAKPOINT blockCONSTANT – see CONSTANT blockDERIVATIVE – see DERIVATIVE blockequation definition 208

also see BREAKPOINT block,DERIVATIVE block, FUNC-TION block, INITIAL block,KINETIC block, PROCEDUREblock

FUNCTION – see FUNCTION blockgeneral form 210INITIAL – see INITIAL blockKINETIC – see KINETIC blockNEURON – see NEURON blockNONLINEAR – see NONLINEAR blockPARAMETER – see PARAMETER blockPROCEDURE – see PROCEDURE blockvariable declaration 208

also see ASSIGNED block, PARAME-TER block, STATE block, LOCALvariable

nocmodl – see NMODL: translator:nocmodl

nrnivmodl – see NMODL: translator:nrnivmodl

procedure – see PROCEDURE blockt – see t: use in NMODLtranslator 207, 209, 239–240, 244mknrndll 186, 191, 346

also see nrnmech.dllnmodl 211nocmodl 192, 211, 346nocmodl.exe 211nrnivmodl 186, 191, 345

440 Index






units conversion factor 216, 231, 237,250–251, 259

parentheses 216–217also see UNITS block: units scaling,

scale factorUNITSOFF . . . UNITSON 227user-defined variable 210VERBATIM . . . ENDVERBATIM 209vs. MODL – see MODL: vs. NMODLalso see mod file

nmodl – see NMODL: translator: nmodlnocmodl – see NMODL: translator:

nocmodlnocmodl.exe – see NMODL: translator:

nocmodl.exenode

circuit – see circuit: nodeequation – see equation: current balance,

Kirchhoff’s current lawsection – see section: nodes

“nonbiological” model – see artificial spikingcell, integrate and fire

NONLINEAR block 223dependent variable

is a STATE variable 184nonlinearity – see system: nonlinear, channel:

nonlinearnoninteractive simulations – see GUI: vs. hocNONSPECIFIC_CURRENT – see NEURON

block: NONSPECIFIC_CURRENTnormalized distance along a section – see rangeNOT operator – see hoc syntax: expressions:

operatorsnotation

chemical reaction – see kinetic schemecircuit – see circuit

nrngui 6, 133loads GUI and standard run library 142

nrniv 133, 345adding new mechanisms 345

also see mechanisms: user-defined,NMODL

also see nrnguinrniv.exe 345

also see nrniv, neuron.exenrnivmodl – see NMODL: translator:

nrnivmodlnrnmech.dll 346

also see mknrndllnrnunits.lib 212, 231

also see units: databasenseg 95, 132

effect on spatial accuracy and resolution 96effect on range variable – see range

variable: effect of changing nseg,range variable: inhomogeneous:reassert after changing nseg

may reposition internally attached sectionsand point processes 102, 112

vs. number of 3-D points 106why triple nseg? 97why use odd values? 97also see spatial grid, discretization, segment

nstep_steprun – see standard run system:setdt(), RunControl GUI: Pointsplotted/ms

NULLobject – see object: NULLobjectnumarg() – see funcs and procs:

arguments: numarg()numeric integration 28, 56, 62, 86

accuracy – see accuracy, numericintegration: order of accuracy

adaptive 72, 87, 224, 226, 236, 243,260–261, 263

advance microstep 173and events – see event: times: with

adaptive integration, standard runsystem: event delivery system:adaptive integration and, standardrun system: fadvance(): globaltime step integration, standard runsystem: fadvance(): local timestep integration

and the standard run system – seestandard run system: event deliverysystem: adaptive integration and,standard run system: fadvance():global time step integration, standardrun system: fadvance(): localtime step integration

error control – see numerical error: controlglobal time step 81–82, 88

also see standard run system: fad-vance(): global time step inte-gration, VariableTimeStepGUI–global vs. local time steps

global variable time step – see numericintegration: adaptive: global time step

GUI control – see VariableTimeStep GUIinitialization 187

also see CVode class: re_init(),initialization

initialize microstep 173interpolate microstep 173

Index 441






numeric integration (contd)interpolation formulas 174local time step 74, 80–82, 88, 166

also see standard run system: fad-vance(): local time step inte-gration, standard run system:event time queue, standard runsystem: cell time queue, CVodeclass: record(),VariableTimeStep GUI–globalvs. local time steps

local variable time step – see numericintegration: adaptive: local time step

microstep – see numeric integration:adaptive: advance microstep,numeric integration: adaptive:initialize microstep, numericintegration: adaptive: interpolatemicrostep

switching to fixed time step 88toggling on and off – see

VariableTimeStep GUI: togglingadaptive integration on and off

with discrete events – see standard runsystem: event delivery system:adaptive integration and, standardrun system: fadvance(): globaltime step integration, standard runsystem: fadvance(): local timestep integration, event: times: withadaptive integration

also see CVODE, CVODES, DASPK,IDA, SUNDIALS, standard runsystem: fadvance(): global timestep integration, standard runsystem: fadvance(): local timestep integration

analytic integration of channel states 72,165, 170

central difference method – see Crank–Nicholson method

error – see accuracy, numerical error,numeric integration: order of accuracy

explicit 63, 86, 243also see forward Euler method

fixed time step 75, 86, 225, 236, 263event aggregation 81, 166, 171,

218, 260also see event: times: with adaptive

integrationinitialization 186

also see initializationswitching to adaptive 88

also see backward Euler method, forwardEuler method, Crank–Nicholsonmethod, standard run system:fadvance(): fixed time step

implicit 63, 86–87, 243also see backward Euler method, Crank–

Nicholson methodinitialization – see numeric integration:

adaptive: initialization, numericintegration: fixed time step:initialization, initialization

instability 62, 64also see numeric integration: stability

iteration of nonlinear equations 70, 87NEURON’s default method – see backward

Euler methodorder of accuracy 71, 75, 83

first 226, 243also see backward Euler method,

forward Euler methodsecond 225, 246

also see Crank–Nicholson method, spatial accuracy: second order

variable 226also see numeric integration: adaptive,

CVODE, DASPKprecision – see numeric integration: order

of accuracystability 74, 86, 91

effect of signal sources 66, 86also see system equations: effect of

signal sourcesalso see numeric integration: instability,

system: stiff, backward Eulermethod, forward Euler method,Crank–Nicholson method

summary 86numeric solution – see numeric integrationnumerical error 83

absolute – see absolute errorcaused by changing nseg – see nseg: may

reposition internally attached sectionsand point processes

chaotic system 84control 62, 79

also see absolute error: local: tolerance,relative error: local: tolerance

criterion – see absolute error: local:tolerance, relative error: local:tolerance

cumulative – see numerical error: globalglobal 76, 83

442 Index






integrated 166also see numerical error: global

local 64, 68, 75, 83, 171also see absolute error: local, relative

error: localmessage – see error message, hoc: error

handlingoscillations 67, 70programming – see hoc: error handlingrelative – see relative errorroundoff 65, 97spatial 56, 60, 96

also see spatial accuracytemporal 56

effect of spatial discretization 60, 119also see temporal accuracy

tolerance – see absolute error: local:tolerance, relative error: local: tolerance

total – see numerical error: globalalso see parameters: sensitivity to, accuracy:

physiological, accuracy: qualitativenumerical oscillations – see numerical error:

oscillations, numeric integration:instability

Nyquist sampling theorem 59

Oobject 363

array 372as an argument – see funcs and procs:

arguments: objects and objrefscalling a method – see object: public

members: accessing from hoccollection – see object: array, List classcreating 365destroying 365dot notation – see object: public members:

dot notationincorporating into plotting system – see

standard run system: plotting system:incorporating Graphs and objects

initializing variables – see template:variable initialization

list – see List classmethods 366, 368

calling – see object: public members:accessing from hoc

namehow generated 370vs. object reference 370

new 365notifying at every step – see standard run

system: plotting system: notifyingGraphs and objects

NULLobject 365, 371, 372using the NULLobject 372

objref – see object reference: objrefpassing to a func or proc – see funcs

and procs: arguments: objects andobjrefs

private vs. public – see object: publicmembers: vs. private members,template: writing a template: public

public membersaccessing from hoc 366dot notation 366vs. private members 366also see template: writing a template:

publicreference – see object reference, object:

reference countreference count 366, 370, 383set – see object: array, List classspecifying attributes – see template: writing,

object: public members: dot notationstack – see List class: object stackstate 363, 366this – see object reference: thisvs. class 363vs. object reference 364also see object reference, class, template,

object-oriented programmingobject name – see object: nameobject name vs. object reference – see object

reference: vs. object nameobject reference 112, 364

as an argument – see funcs and procs:arguments: objects and objrefs

cannot be redefined as scalar, double, orstring 365

count – see object: reference countdeclaring 364objectvar 364

also see object reference: cannot redefineas scalar, double, or string

objref 112, 365also see object reference: cannot redefine

as scalar, double, or stringpassing to a func or proc – see funcs

and procs: arguments: objects andobjrefs

points to an object 364, 366this 383vs. object 364vs. object name 370

object variable – see object reference:objectvar

Index 443






object_pop() – see session file:object_pop()

object_push() – see session file:object_push()

object-oriented programmingencapsulating code 375information hiding 363inheritance 327, 363, 376

also see class: base class, class: subclasspolymorphism 181, 363, 376

also see class: base class, class: subclassalso see object, object reference, class,

templateobjectvar – see object reference:

objectvarobjref – see object reference: objrefoc 346

also see nrnivocbox_ – see session file: ocbox_Ohm’s law 52online Programmer’s Reference – see

Programmer’s Referenceoperators – see hoc syntax: expressions:

operatorsoperator precedence – see hoc syntax:

expressions: operatorsoptimization 30OR operator – see hoc syntax: expressions:

operatorsordinary differential equation – see equation:

differential: ordinaryoscillating system – see initialization:

categories: to a desired stateoscillations – see numerical error: oscillationsoscilloscope 23oxymoron 306

Ppanel – see xpanel()PARAMETER block 212

assigning default PARAMETER values 212default value of state0 190

also see STATE variable: state0,STATE block: START

specifying minimum and maximum limits212

PARAMETER variable 184, 212abrupt change of – see variable: abrupt change

of, NET_RECEIVE block: handlingabrupt changes and discontinuities

default value – see PARAMETER block:assigning default PARAMETER values

GLOBAL vs. RANGE 212, 235, 256also see NEURON block: RANGE

is GLOBAL by default 254also see NEURON block: GLOBAL

RANGE 218specifying minimum and maximum

limits – see PARAMETER block:specifying minimum and maximumlimits

time-dependent 161, 263visibility at the hoc level 212when to use for an equilbrium potential

223also see ASSIGNED variable, STATE

variable, ion_style()parameters

biophysical 15–16geometric 13–14sensitivity to 84also see PARAMETER variable

parent section – see section: parentparentheses – see hoc syntax: expressions:

operators, NMODL: units conversionfactor: parentheses, UNITS block: unitsscaling

parse errors – see hoc: error handlingpartial differential equation – see equation:

differential: partialpas mechanism 15e_pas 16g_pas 16

passive cylindrical cable – see cable: passivecylindrical

passive leak current – see Example 9.1: apassive “leak” current

PFWM 16is implemented in C 344saving and retrieving session files – see

session file: saving: from PFWM,session file: loading: from PFWM

physical distance – see distancephysical system 33

representing by a model 33–34physiological accuracy – see accuracy:

physiologicalpiecewise linear approximation – see range

variable: estimating by linearinterpolation between nodes

piecewise linear function – see function:piecewise linear

Pike, R. – see hoc: Kernighan and Pikeplain text file 130

444 Index






plasticitysynaptic – see synaptic plasticity

Plot what? GUI 228, 233also see variable browser

Plot() – see standard run system: Plot()plot lists – see standard run system: plotting

system: fast_flush_list, standardrun system: plotting system:flush_list, standard run system:plotting system: graphLists

plotting spike trains – see spike trains:recording and plotting, NetWork Builder:buttons: SpikePlot

plotting system – see standard run system:plotting system

point process 18, 112, 214, 217adding new – see mechanisms: user-

defined, NMODLattaching – see point process: insertingchanging location with hoc code – see

point process: loc()creating 112destroying 112effect of nseg on location 112inserting 112loc() 113preserving spatial accuracy 97specifying attributes 112vs. distributed mechanism 113also see NEURON block:

POINT_PROCESS, artificial spikingcell, NEURON block:ARTIFICIAL_CELL

Point Process Viewer GUI 217POINTER – see POINTER variable, NEURON

block: POINTER, setpointerpointer – see hoc syntax: pointer operator,

NEURON block: POINTER, POINTERvariable

pointer operator – see hoc syntax: pointeroperator

Pointer class 359POINTER variable 268

effect on Jacobian – see Jacobian:approximate

also see NEURON block: POINTER,setpointer, variable: local vs.nonlocal

PointProcessGroupManagerbringing up a PointProcessGroupManager

319PointProcessManager 18

configuring asAlphaSynapse 19

creating 19, 148location 20, 27

changing 27parameters 20

PointProcessManager GUISelectPointProcess 19Show

Shape 27Points plotted/ms – see RunControl GUI:

Points plotted/mspolymorphism – see object-oriented

programming: polymorphismpotassium

concentration – see Example 9.6:extracellular potassium accumulation

current – see Example 9.4: a voltage-gatedcurrent, Example 9.5: a calcium-activated, voltage-gated current

also see ion mechanismpotential

reversal – see equilibrium potentialalso see membrane potential, voltage

precedence of operations – see hoc syntax:expressions: operators

prediction 33print – see hoc syntax: basic input and

output: printPrint & File Window Manager – see PFWMprintf() – see hoc syntax: basic input and

output: printf()private vs. public – see object: public

members: vs. private members, template:writing a template: public

proc – see funcs and procsPROCEDURE

calling from hoc – see hoc: calling anNMODL FUNCTION or PROCEDURE

also see PROCEDURE block, BREAKPOINTblock: and PROCEDUREs

procedure – see funcs and procs, PROCEDUREPROCEDURE block 232

arguments are call by value 283program organization – see good

programming style: program organizationProgrammer’s Reference 343programming – see hoc

good practices – see good programming stylemistake – see hoc: error handling

project management 154also see good programming style

Index 445






proper initialization – see initialization:criterion for proper initialization

psection() 103pt3d – see 3-D specification of geometrypt3d data – see 3-D specification of geometry:

3-D informationpt3d list – see 3-D specification of geometry:

3-D informationpt3dadd() – see 3-D specification of

geometry: pt3dadd()public – see object: public members,

template: writing a template: publicpump

calcium – see calcium: pumpalso see active transport

purpose of computing – see insightpurpose of the model – see user’s intentpush_section() 100

Qqualitative results 67

also see accuracy, judgmentquantitative morphometric data 98, 105, 126,

144bad diameter values – see diameter: zero or

narrow diameteralso see 3-D specification of geometry

queuecell time – see standard run system: event

delivery system: cell time queueevent time – see standard run system: event

delivery system: event time queueQuiet – see RunControl GUI: Quietquit() – see hoc syntax: flow control:

quit()quitting NEURON – see NEURON: exiting,

hoc syntax: flow control: quit()

RRa 13, 15, 94

default value 16, 103also see cytoplasmic resistivity

radial diffusion – see diffusion: radialramp clamp – see voltage clamp: ramp clampRandom classplay()

initialization – see initialization:Random.play()

random number generatorinitialization – see initialization: random

number generator

RANGE – see NEURON block: RANGE, range,range variable

range 93RANGE variable – see range variablerange variable 93

dot notation – see section: currentlyaccessed: dot notation

effect of changing nseg 115–117estimating by linear interpolation between

nodes 97inhomogeneous

reassert after changing nseg 116in which section? – see section: currently

accessediterating over nodes 114linear taper 115linear variation along a section – see range

variable: linear taperrangevar(x) returns value at nearest

internal node 94also see range, NEURON block: RANGE,

ASSIGNED variable: is a rangevariable by default, PARAMETERvariable: RANGE, STATE variable: isautomatically RANGE

raster plot – see spike trains: recording andplotting, NetWork Builder: buttons:SpikePlot

rate constant 37rate functions – see BREAKPOINT block: and

rate functions, KINETIC block: reactionrates: voltage-sensitive

re_init() – see CVode class: re_init()reactants – see KINETIC block: reactantsreaction – see kinetic scheme

chemical – see kinetic schemerates – see KINETIC block: reaction ratesreactants – see KINETIC block: reactantsscheme – see kinetic scheme, KINETIC

blockstatement – see KINETIC block: reaction

statementalso see KINETIC block: <–> (reaction

indicator)READ – see NEURON block: USEIONread() – see hoc syntax: basic input and

output: read()reading an ion concentration – see NEURON

block: USEIONreading and writing files – see hoc syntax:

basic input and output

446 Index






real model neuron – see oxymoronrealtime – see standard run system:

realtimerecording – see CVode class: record(),

NetCon class: record(), Vectorclass: record()

recording spike trains – see NetCon class:record(), spike trains: recording andplotting, NetWork Builder: buttons:SpikePlot

recursion – see funcs and procs: recursionredefining standard functions and

procedures – see standard run library:redefining functions and procedures,standard GUI library: redefiningfunctions and procedures

reference count – see object: reference count

refractory period – see IntFire1 class:refractory period

relative errorlocal 75, 79

tolerance 75also see absolute error: local, numerical

error: localalso see absolute error

relative local error – see relative error: localrelative tolerance – see relative error: local:

toleranceremainder operator – see hoc syntax:

expressions: operatorsresistance

axial – see axial resistancealso see ri(), Ra, cytoplasmic resistivity

electrode – see electrode: resistancemembrane – see specific membrane

resistanceresistivity – see cytoplasmic resistivity, Raresistor – see circuit: element: resistorrestore() – see SaveState class:

restore()restricted diffusion – see Example 9.6:

extracellular potassium accumulationreturn – see hoc syntax: flow control:

returnalso see funcs and procs: return

returned value – see funcs and procs:return

reusable code – see good programming style:exploiting reusable code

reversal potential – see equilibrium potential

ri()calculation of – see stylized specification of

geometry: calculation of area() andri(), 3-D specification of geometry:calculation of L, diam, area(), andri()

effect of creating a Shape – see Shapeobject: creating: effect on diam,area(), and ri()


infinite 107, 115also see diameter: zero or narrow

diameteralso see axial resistance

rise time 122Rm – see specific membrane resistanceroot section – see section: root sectionropen() – see hoc syntax: basic input and

output: ropen()roundoff error – see numerical error:

roundoffrun control – see RunControl GUI, simulation

control, standard run systemrun time 98, 158, 171

also see RunControl GUI: Real Time,standard run system: realtime,initialization: startsw()

run time system – see standard run systemrun-time errors – see hoc: error handlingrun() – see standard run system: run()RunControl 21

creating 24, 151, 157RunControl GUI

Continue for 158–159, 162also see standard run system:

continuerun()Continue til 158–159, 162

also see standard run system:continuerun()

dt 24, 158also see RunControl GUI: Points

plotted/ms, standard run system:setdt()

Init 24, 158–159Init & Run 24, 152, 158–159, 163

also see standard run system: run()Points plotted/ms 24, 158–159, 162

also see standard run system: setdt(),standard run system: step()

Index 447






RunControl GUI (contd)Quiet 158–159, 162

also see standard run system:stdrun_quiet

Real Time 158, 163also see standard run system:

continuerun(), standard runsystem: realtime

Single Step 158–159, 162also see standard run system: step()

Stop 158, 162–163also see standard run system: stoprun

t 24, 158Tstop 24, 152, 158, 163

also see standard run system: tstopRunge-Kutta method

stability 243running a simulation 26runtime

error – see hoc: error handlingsystem – see standard run systemalso see run time

Ssacred runes – see equation: sacred runessampling theorem – see Nyquist sampling

theoremSaveState classfread() 198fwrite() 198restore() 199save() 198also see initialization: categories: to a

desired statescalar – see hoc syntax: variables: scalarsscale factor 43

also see NMODL: units conversion factor,UNITS block: units scaling

scene – see GUI: scenescene coordinates – see GUI: scene coordinatesscene coordinates vs. screen coordinates – see

GUI: scene coordinates: vs. screencoordinates

screen – see GUI: screenscreen coordinates – see GUI: screen

coordinatesSCoP 208, 213scope – see hoc syntax: names, funcs and

procs: local variable, variable: local vs.nonlocal, LOCAL variable, ASSIGNEDvariable: GLOBAL, NEURON block:GLOBAL, PARAMETER variable: isGLOBAL by default

also see object: public members, template:writing a template: public, template:writing a template: external

sealed end – see boundary conditions: sealedend

SEClamppreserving spatial accuracy – see point

process: preserving spatial accuracyalso see voltage clamp

secname() 108second messenger – see Example 10.5: use-

dependent synaptic plasticityalso see calcium

secondorder 86, 169, 180also see Crank–Nicholson method,

backward Euler methodsection 8, 92access – see access, section: currently

accessed: default sectionarc length – see rangearea – see segment: surface areaarray 103as argument or variable – see

SectionRef classattaching – see connectchild 101

connect 0 end to parent 105, 148connecting – see connectcreating – see createcurrently accessed

default section 21, 23, 100, 143–144dot notation 94–95, 99section stack 99

daughter – see section: childdefault parameter values – see cm, diam,

L, Radefault section – see section: currently

accessed: default sectionvs. root section – see section: root

section: vs. default sectiondetaching – see disconnect()diam – see diamdiameter – see diameter, diam, 3-D

specification of geometry: diam3d()disconnecting – see disconnect()equivalent circuit 106–107iterating over nodes – see range variable:

iterating over nodesiterating over sections 108, 123L – see Llength – see Lnodes 96

448 Index






internal vs. terminal 95iterating over – see range variable:

iterating over nodeslocations 95

also see nseg: why use odd values?zero area 74, 97

normalized distance along a section – see rangenseg – see nsegorientation 138, 145, 147parent 101properties

specifying – see section: currently accessed,3-D specification of geometry, stylizedspecification of geometry, biophysicalproperties: specifying

Ra – see Raroot section 8, 101, 134

is 3-D origin of cell 146, 149vs. default section 102, 134

sets – see SectionList classstack – see section: currently accessed:

section stackvariable – see section variable

section variable 93also see L, nseg, Ra

section.h 169SectionList class 138SectionRef class 100segment 95

diameter – see diamsurface area – see area, area()also see compartment, nseg, section: nodes

self-event – see event: self-eventsensitivity – see parameters: sensitivity toseparating biology from numerical issues 92

also see section, range, range variableses file – see session filesession file 16

loadingfrom NEURON Main Menu 18from PFWM 16

object_pop() 388object_push() 388ocbox_ 388

also see VBox class: map()saving

from NEURON Main Menu 17from PFWM 16

setof numbers – see hoc syntax: variables:

double, Vector classof objects – see object: array, List class

of sections – see SectionList class,CellBuilder GUI: Subsets page

setdata_ – see hoc: calling an NMODLFUNCTION or PROCEDURE: specifyingproper instance with setdata_

setdt() – see standard run system:setdt()

setpointer 269also see POINTER variable

Shape objectcreating

effect on diam, area(), and ri() 108Shape plot 9, 103

creating 22, 145effect on diam, area(), and ri()

108Shape Plot 180Shape plot GUI

primary menuSpace Plot 22also see Space Plot

Shape StyleShow Diam 145

shared object – see NMODL: translator:nrnivmodl, nrniv

shell 41Shift key – see Graph class: menu_tool()shunt.mod – see Example 9.2: a localized

shuntsign convention – see membrane current:

positive current convention, axial current:positive current convention, circuit:positive current convention

signalchemical 50, 119electrical 50, 119

signal monitors 20vs. signal sources 20

signal sources 18effect on system equations – see system

equations: effect of signal sources,numeric integration: stability: effect ofsignal sources

load – see system equations: effect of signalsources, numeric integration: stability:effect of signal sources

also see distributed mechanism, pointprocess

simplification 33–35simulation

control – see simulation controlevent-driven – see discrete event simulation

Index 449






simulation (contd)interactive vs. noninteractive – see GUI: vs.

hoctime 24

also see t, elapsed simulation timesimulation control 5, 21, 139, 154

running 26starting 26stopping – see standard run system:

tstop, RunControl GUI: Tstop,RunControl GUI: Stop, hoc:interrupting execution

also see standard run system, goodprogramming style: modularprogramming, good programmingstyle: program organization

Simulation Control Program – see SCoPsimulation environment

utility of 32, 34sink reaction – see KINETIC block: –>(sink

reaction indicator)size – see compartment: size, discretization,

nsegslope conductance – see conductance: slopesodium – see ion mechanismsolution

analytic – see analytic solutioncomputational – see numeric integrationnumeric – see numeric integration

SOLVE – see BREAKPOINT block: SOLVE,INITIAL block: SOLVE:STEADYSTATE sparse

solve.c 169source

current – see current: source, circuit:element: current source

NetCon class: source variablesignal – see signal sourcesvoltage – see circuit: element: voltage source

space 21–22, 25, 32space constant – see �, length constant,

d_lambda rulespace plot 20Space Plot 180

creating 22sparse – see KINETIC block, BREAKPOINT

block: SOLVE: sparse, INITIAL block:SOLVE: STEADYSTATE sparse

spatial accuracy 96checking 97second order 57, 96

preserving 97, 102

also see discretization: spatial, nseg: effecton spatial accuracy and resolution

spatial decay of fast signals 122spatial discretization – see discretization:

spatial, spatial gridspatial error – see numerical error: spatial,

spatial accuracyspatial frequency – see frequency: spatialspatial grid 57

checking 97choosing – see discretization: guidelines,

d_lambda rule, d_X rule, CellBuilderGUI: Geometry page: specifyingstrategy

also see discretization: spatialspatial resolution – see discretization: spatial,

numerical error: spatial, spatial accuracy,spatial grid

specific membrane capacitance 53, 56, 91–92,94

also see cmspecific membrane conductance 56specific membrane resistance 122

also see specific membrane conductancespecifying geometry – see 3-D specification of

geometry, stylized specification ofgeometry

also see geometry, anatomical propertiesspecifying model properties – see model

properties: specifyingspecifying object attributes – see template:

writing, object: public members: dotnotation

specifying section properties – see section:currently accessed, 3-D specification ofgeometry, stylized specification ofgeometry, biophysical properties:specifying

specifying the current section – see section:currently accessed

specifying the spatial grid – see discretization:spatial grid, nseg, spatial grid

specifying topology – see topology: specifyingspeed – see computational efficiencyspeed vs. accuracy – see accuracy: vs. speedspike event – see event: externalspike trains

recording and plotting 335also see NetCon class: record(),

NetWork Builder: buttons: SpikePlotSpikePlot – see NetWork Builder: buttons:

SpikePlot

450 Index






sprint() – see hoc syntax: basic input andoutput: sprint()

squid axon 28also see hh mechanism

stability – see numeric integration: stabilitystack of objects – see List class: object stackstaggered time steps – see Crank–Nicholson

method: staggered time stepsstandard GUI library

changing functions and procedures – seestandard GUI library: redefiningfunctions and procedures

hoc source accompanies NEURON 344loading – see nrngui, hoc: idiom:

load_file("nrngui.hoc")not loading – see nrnivredefining functions and procedures 344

standard run librarychanging functions and procedures – see

standard run library: redefiningfunctions and procedures

hoc source accompanies NEURON 344redefining functions and procedures 344

standard run system 152addplot() 152, 181advance() 160, 181continuerun() 160, 162–163, 181CVODE 164DASPK 165discrete events – see standard run system:


doEvents() 163event delivery system 165

adaptive integration and 171, 179and models with discontinuities – see

variable: abrupt change of, event:times

cell time queue 173also see numeric integration: adaptive:

local time step, standard run sys-tem: fadvance(): global timestep integration, standard run sys-tem: fadvance(): local timestep integration

event time queue 173, 292also see numeric integration: adaptive:

local time step, standard runsystem: fadvance(): globaltime step integration, standard run

system: fadvance(): localtime step integration

event times – see event: times, standardrun system: event time queue

external event – see event: externalimplementing deferred computation 289,

296, 302also see event: self-event

initialization 183, 185–186input event – see event: externalself event – see event: self-eventalso see event, standard run system:


fadvance() 81, 158, 160, 164, 184, 243,263

discrete events – see standard run system:fadvance(): global time stepintegration, standard run system:fadvance(): local time stepintegration

fixed time step 165global time step integration 179local time step integration 166, 173

fast_flushPlot() 181fcurrent() 164, 170, 186

in initialization 188–189, 196finitialize() – see initialization:

finitialize()flushPlot() 162, 180–181graph lists – see standard run system:

plotting system: graphListsGraphs and objects

incorporating – see standard run system:plotting system: incorporatingGraphs and objects

notifying – see standard run system:plotting system: notifying Graphsand objects

init() – see initialization: init()initialization – see initialization, numeric

integration: adaptive: initialize microstepinitPlot() – see initialization:

initPlot()is implemented in hoc 344NetCon – see NetCon: and standard run

systemnstep_steprun – see standard run

system: setdt(), RunControl GUI:Points plotted/ms

Index 451






standard run system (contd)Plot() 162, 180

also see standard run system: stepplot lists – see standard run system: plotting

system: fast_flush_list,standard run system: plotting system:flush_list, standard run system:plotting system: graphLists

plotting system 179fast_flush_list 180flush_list 180graphLists 179incorporating Graphs and objects 181

also see standard run system: plottingsystem: graphLists, standardrun system: addplot()

notifying Graphs and objects 179also see standard run system: plotting

system: graphListsspecial uses 162

realtime 163–164, 187run() 159–160, 163, 179setdt() 161, 164, 187stdinit() – see initialization:

stdinit()stdrun_quiet 163, 180step 158, 162step() 160–162

under CVODE 162steprun() 160, 162steps_per_ms – see standard run system:

setdt(), standard run system: step,RunControl GUI: Points plotted/ms

stoprun 162–163tstop 152, 163, 181also see RunControl GUI, standard run

librarySTART – see STATE block: START, STATE

variable: initializationstarting hoc – see hoc: starting and exiting,

NEURON: starting and exitingstarting NEURON – see NEURON: starting

and exiting, hoc: starting and exitingstartsw() – see initialization: startsw()state 36, 38, 41

as amount of material 36as concentration 36as density 36as probability 36restoring – see SaveState class:

restore(), initialization: categories:to a desired state

saving – see SaveState class: save()STATE block 223

specifying local absolute error tolerance251

START 190also see STATE variable: initialization,

PARAMETER block: default value ofstate0

also see ASSIGNED block, PARAMETERblock

state variable 67, 70, 73as an ASSIGNED variable 185changing after finitialize() – see

initialization: strategies: changing astate variable

custom initialization – see initialization:strategies: changing a state variable

initialization – see STATE variable:initialization, initialization

of a mechanism vs. state variable of amodel 213

vs. STATE variable – see STATE variable:vs. state variable

STATE variable 168, 184, 223abrupt change of – see variable: abrupt

change of, NetCon class: event(),NET_RECEIVE block: handlingabrupt changes and discontinuities

and COMPARTMENT statement – seeKINETIC block: COMPARTMENT

array in NMODL 244conservation – see KINETIC block:

CONSERVEinitialization 224

default vs. explicit 190state0 190, 237

also see PARAMETER block: defaultvalue of state0, STATE block:START

also see initialization, KINETIC block:CONSERVE

ion concentration as 236is automatically RANGE 223

also see NEURON block: RANGEspecifying local absolute error tolerance –

see STATE block: specifying localabsolute error tolerance

vs. state variable 184, 242also see ASSIGNED variable, PARAMETER

variable, ion_style(), statevariable

452 Index






state_discontinuity() – seeCVODE: and model descriptions:state_discontinuity(), variable:abrupt change of, NET_RECEIVE block:state_discontinuity()

state0 – see STATE variable: initialization,INITIAL block

stdgui.hoc – see standard GUI librarystdinit() – see initialization:

stdinit()stdlib.hoc 123, 357, 373

also see standard run systemstdrun.hoc 159

also see standard run system, standard runlibrary

stdrun_quiet – see standard run system:stdrun_quiet

steady stateinitialization – see initialization: steady

state, initialization: non-steady stateof complex kinetic schemes – see

initialization: strategies: steady stateinitialization of complex kineticschemes, INITIAL block: SOLVE:STEADYSTATE sparse

STEADYSTATE – see INITIAL block: SOLVE:STEADYSTATE sparse, initialization

step – see standard run system: stepstep() – see standard run system: step()steprun() – see standard run system:

steprun()stiffness – see system: stiffstoichiometry 39stop – see hoc syntax: flow control: stopstopping hoc – see hoc: interrupting

execution, hoc: starting and exitingstopping NEURON – see NEURON: starting

and exiting, hoc: interrupting executionstoprun – see standard run system: stoprunstorage oscilloscope 23strange shapes – see stylilzed specification of

geometry: strange shapesstrdef – see hoc syntax: variables:

strdefstring – see hoc syntax: variables: strdefString class 373stylized model – see model: stylized, stylized

specification of geometrystylized specification of geometry 103–104,

132calculation of area() and ri() 104diam – see diam

L – see Lreinterpretation as 3-D specification 108strange shapes 144also see 3-D specification of geometry

subclass – see class: subclass, object-orientedprogramming: polymorphism, object-oriented programming: inheritance

subtraction operator – see hoc syntax:expressions: operators

SUFFIX – see NEURON block: SUFFIXSUNDIALS 172

also see CVODES, IDAsurface area 52

also see area(), membrane areasynapse

alpha function – see AlphaSynapse,Exp2Syn, Example 10.4: alphafunction synapse

AlphaSynapse 19AMPAergic – see Example 10.3: synapse

with exponential decayalso see Example 10.6: saturating

synapsesas instrumentation 139conductance change 19

alpha function – see AlphaSynapse,Exp2Syn, Example 10.4: alphafunction synapse

exponentially decaying – see ExpSyn,Example 10.3: synapse withexponential decay

also see Example 10.5: use-dependentsynaptic plasticity, Example 10.6:saturating synapses

electrical – see gap junction, synapse:ephaptic

ephaptic 265graded – see synaptic transmission: gradedplasticity – see synaptic plasticitysaturating – see Example 10.6: saturating

synapsesstrength – see NetCon class: weightweight – see NetCon class: weightalso see AlphaSynapse, ExpSyn,

Exp2Synsynaptic connection – see NetCon classsynaptic convergence – see convergence


synaptic delay – see NetCon class: delaysynaptic divergence – see divergence


Index 453






synaptic latency – see NetCon class: delaysynaptic plasticity 83

stream-specific – see Example 10.5: use-dependent synaptic plasticity, Example10.6: saturating synapses

synaptic strength – see NetCon class: weightsynaptic transmission

delay – see NetCon class: delaygraded 265

conceptual model 266implementation in NMODL 268also see Example 10.1: graded synaptic

transmissionlatency – see NetCon class: delaysaturating – see Example 10.6: saturating

synapsesspike-triggered

computational efficiency in NEURON 275conceptual model 273event-based implementation 273

also see NetCon class,NET_RECEIVE block, event:external, event: self-event,Example 10.3: synapse withexponential decay, Example 10.4:alpha function synapse, Example10.5: use-dependent synapticplasticity, Example 10.6: saturat-ing synapses

weight – see NetCon class: weightalso see gap junction

synaptic weight – see NetCon class: weightsyntax – see hoc syntax, NMODL

also see Programmer’s Referencesyntax error

example 100also see hoc: error handling

systemchaotic – see initialization: categories: to a

desired statecontinuous 55–58, 60, 96

piecewise linear approximation – seerange variable: estimating by linearinterpolation between nodes

discretized 57, 60also see discretization

linear 65, 71, 86nonlinear 71, 87oscillating – see initialization: categories: to

a desired statestiff 66, 73, 86–87, 169

also see numeric integration: stability

system equationseffect of signal sources 20

also see numeric integration: stability:effect of signal sources

matrix form 73extracellular field 74linear circuit 74also see equation: algebraic

stiff – see system: stiffalso see eigenfunction, eigenvalue

Tt 24, 26


also see t: use in NMODLinitialization – see initialization: tthe independent variable in NEURON 213use in NMODL 213also see time

� – see time constant�m – see membrane time constanttable – see function tabletable_ – see NMODL: FUNCTION_TABLEtapering – see diam: tapering, range variable:

linear taperTaylor’s series 66, 83temperature – see celsiustemplate 363

cannot be redefined 156, 367direct commands 368names cannot redefine hoc keywords 369this – see object reference: thisvariable initialization

default initialization 368init() procedure 368

visibility – see template: writing a template:public, object: public members

writing a template 367begintemplate 367endtemplate 368external 368public 367

also see object: public membersalso see class, object, object-oriented

programmingtemporal accuracy

empty 87also see discretization: temporal

temporal discretization – see discretization:temporal

454 Index






temporal frequency – see frequency: temporaltemporal resolution – see temporal accuracy,

discretization: temporalthis – see object reference: thisthree dimensional specification – see 3-D

specification of geometrytilde – see KINETIC block: ~ (tilde)time 21, 24–26, 32

rise – see rise timealso see t

time constant 48also see membrane time constant

time-dependent variable – see PARAMETERvariable: time-dependent, variable: time-dependent, Vector class: play()

time stepand stability – see numeric integration:

stability, backward Euler method,forward Euler method, Crank–Nicholson method

choosing – see discretization: temporalfixed – see numeric integration: fixed time

stepalso see dt, t, discretization: temporal,

numeric integration: adaptivetime stream – see numeric integration: local

time steptolerance

error – see absolute error: local: tolerance,relative error: local: tolerance

top level of the interpreter – see hoc: top levelof the interpreter

topology 8, 35, 98checking 102–103, 134, 150loops of sections 101specifying 101, 130viewing 103also see branched architecture

topology, subsets, geometry, biophysics 138topology() 102, 150total error – see numerical error: globaltotal ionic current – see membrane current:

ionictransient signals

spatial decay – see spatial decay of fast signalstransmembrane current – see membrane currenttreeset.c 167troubleshooting

conflicts between hoc and GUI – see GUI:conflicts with hoc or other GUI tools

disappearing section 148Graphs don’t work 151

legacy code 142no default section 142no NEURON Main Menu toolbar 142strange shapes – see stylized specification

of geometry: strange shapesTRUE – see hoc syntax: expressions: logical

expressionststop – see standard run system: tstopTstop – see RunControl GUI: Tstop, standard

run system: tstop

Uunaryminus operator – see hoc syntax:

expressions: operatorsunderstanding 32, 33uninsert 153units 36

checking 212, 216, 254also see modlunit

consistency 40, 42–43, 247, 254conversion factor – see scale factor,

NMODL: units conversion factor,UNITS block: units scaling

database 212also see nrnunits.lib

defining new names – see UNITS block:defining new names

dimensionless(1) 250by default 212

e 231also see e: electronic charge vs. units

conversion factorfaraday 231k-mole 231mole 256scaling – see UNITS block: units scalingspecifying 227

also see NMODL: declaring variables:specifying units

UNITS block 222defining new names 222units scaling 231, 250

units scaling – see UNITS block: units scalingUNITSOFF . . . UNITSON – see NMODL:

UNITSOFF . . . UNITSONUNITSON – see NMODL: UNITSOFF . . .

UNITSONuse-dependent synaptic plasticity – see

Example 10.5: use-dependent synapticplasticity, Example 10.6: saturatingsynapses

Index 455






USEION – see NEURON block: USEIONuser-defined mechanisms – see mechanisms:

user-defineduser interface 154

as virtual experimental rig 23, 154custom GUI 22, 29vs. model specification – see good

programming style: separating modelspecification from user interface

user’s intent 81

Vv 21, 94, 168


is a RANGE variable 211also see membrane potential

v_init – see initialization: v_initvariable

abrupt change of 161, 171, 260–262,277–278, 280, 291–292, 294,297–298, 301–302

also see CVODE: and modeldescriptions: at_time(), CVODE:and model descriptions:state_discontinuity(),NetCon class: event(),NET_RECEIVE block: handlingabrupt changes and discontinuities

ASSIGNED – see ASSIGNED variablechanging in mid-run – see variable: abrupt

change of, PARAMETER variable:time-dependent

CONSTANT – see CONSTANTcontinuous – see continuous variabledeclaring in NMODL – see NMODL:

declaring variables, NMODL: namedblocks: variable declaration,ASSIGNED block, CONSTANT block,PARAMETER block, STATE block,LOCAL variable, NMODL: DEFINE

dimensionless – see units: dimensionlessextensive 247global – see variable: local vs. nonlocal,

hoc syntax: names, template: writinga template: external, NEURONblock: GLOBAL, ASSIGNED variable:GLOBAL, PARAMETER variable: isGLOBAL by default

initializing – see initialization, template:variable initialization

intensive 247LOCAL – see LOCAL variablelocal vs. nonlocal 266

also see POINTER variablenames – see hoc syntax: namesobject – see object, object referencePARAMETER – see PARAMETER variablePOINTER – see POINTER variablerange – see range variablescope – see hoc syntax: names, funcs and

procs: local variable, variable: localvs. nonlocal, LOCAL variable,ASSIGNED variable: GLOBAL,NEURON block: GLOBAL,PARAMETER variable: is GLOBAL bydefault

also see object: public members,template: writing a template:public, template: writing atemplate: external

section – see section variablestate – see state variablestate vs. STATE – see STATE variable: vs.

state variableSTATE – see STATE variablestring – see hoc syntax: variables: strdeftime-dependent – see PARAMETER

variable: time-dependent, Vectorclass: play()

user-definedin hoc – see hoc syntax: namesin NMODL – see NMODL: user-defined

variablevariable browser 29

also see Plot what? GUIvariable order integration – see numeric

integration: adaptivevariable order, variable time step

integration – see numeric integration:adaptive

variable time step method – see numericintegration: adaptive

VariableTimeStep GUIbringing up – see NEURON Main Menu:

Tools: VariableStepControlDetails

Local step – see VariableTimeStep GUI:global vs. local time steps

global vs. local time steps 319also see numeric integration: adaptive:

global time step, numericintegration: adaptive: local time step

456 Index






toggling adaptive integration on and off 320Use variable dt checkbox – see

VariableTimeStep GUI: togglingadaptive integration on and off

VBox 383VBox class

intercept() 383map() 383–384, 386

also see session file: ocbox_mapping to the screen

window title 384ref() 383save() 385

Vectormovie 180

Vector classc() 337fill() 337mark() 337play() 77

at specific times 167initialization – see initialization:

Vector.play()under adaptive integration 78under fixed time step integration 78with interpolation 78, 161, 167, 263

record() 171, 187at specific times 167initialization 187

also see initialization:frecord_init()

also see CVode class: record()VERBATIM – see NMODL: VERBATIM . . .

ENDVERBATIMverification 28version number – see NEURON: startup bannervext – see extracellular mechanism:

vextview – see GUI: viewvirtual experimental preparation – see model

specification: as “virtual experimentalpreparation”

virtual experimental rig – see user interface: asvirtual experimental rig

visibility – see template: writing a template:public, object: public members

Vm 20also see membrane potential, v

voltage 44

gradient 50membrane – see membrane potential, v

voltage clampand stability – see numeric integration:

stability: effect of signal sources,system equations: effect of signalsources

currentaccuracy 169

preserving spatial accuracy – see pointprocess: preserving spatial accuracy

ramp clamp 77voltage-gated current – see channel: voltage-

gatedvolume – see compartment: size

Wweight – see NetCon class: weightweight vector – see NetCon class: weight

vectorwhat are the names of things? 29which view contains the mouse? – see Graph

class: view_info()while – see hoc syntax: flow control: whilewhy is NEURON fast? – see computational

efficiency: why is NEURON fast?window title – see GUI tool development:

mapping to the screen: window titlewopen() – see hoc syntax: basic input and

output: wopen()WRITE – see NEURON block: USEIONwriting an ion concentration – see NEURON

block: USEIONwriting files – see hoc syntax: basic input and

output

Xx-expression – see standard run system:

plotting system: graphListsxopen() – see hoc syntax: basic input and

output: xopen()xpanel() 334, 395xpvalue() 395xred() – see hoc syntax: basic input and

output: xred()xvalue() 334, 395

Zzero area node – see section: nodes: zero area

Index 457






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