Restart at << restart here >> Items in this list that are followed by a !! are not to be flagged as index terms in the text. They are merely placeholders for this index. An item followed by "see otheritem" is implicitly _not_ to be flagged. ?? means I'm not sure yet whether a term needs to be flagged by itself. Items in parens like this (syn itemname) are merely synonyms--reminders to myself that I should search for this term, but flag it as an instance of the preceding term. General comments--applicable to all chapters-- ============================================== use [ ] for units in text, not ( )--be consistent across chapters This means redo chapter 3, which lacks () and [], and chapter 4, which uses (). anatomical properties, but morphometric data artificial spiking neuron model is an oxymoron. Call it "artificial spiking cell" control flow ?? Cytoplasmic resistance Ra should be Cytoplasmic resistivity Ra d-X rule should be d_X rule, and d-lambda rule should be d_lambda rule d_lambda algorithm should be d_lambda rule density mechanism should be distributed mechanism electrical gap junction should be gap junction electrical equivalent circuit should be equivalent circuit Should IClamp etc. be listed as IClamp class? Distinguish between class and instance? Change membrane capacitance to specific membrane capacitance as needed NEURON programming environment vs. NEURON simulation environment. nrn-5.4 etc. change to nrn-x.x where x.x is the version number (e.g. 5.5) object, object variable, and object reference should agree with chapter 13. Point Process, Point process should be point process run time should NOT be runtime field editor, NOT value editor Shape window, shape plot and Shape plot--which to use when? Answer: never use Shape window. Shape plot << is spawned from Main Menu >> Shape Plot << a false color plot mapped onto a Shape >> Space Plot Instead of say daughter child sister sibling Special notation for symbols and subscripts ------------------------------------------- %DELTA means uppercase delta %lambda means lowercase lambda %lambda_AC means lowercase lambda with AC as subscript Hyphen usage ------------ 3-D behind-the-scenes built-in byproduct Ca2+-gated calbindin-positive calcium-activated calcium-bound closely-related compartment-oriented simulation environment computer-generated conductance-change synapse context-dependent Crank-Nicholson method cross-section current-voltage relation CVODE-specific depolarization-activated domain-specific dt-dependent e-fold attenuation empirically-based modeling event-based communication event-driven experimentally-testable fail-safe fan-in fan-out fast-moving first order hands-off policy HH-style HH-type high frequency term implementation-specific goal input-output relationship ligand-bound ligand-gated channel ligand-receptor interaction line-by-line long-time low pass filter mechanism-specific membrane-associated membrane-bound pump mid-run model-generic model-specific moment-to-moment fluctuations multiple line comment NEURON-specific feature NMODL-specific non-capacitive current non-NEURON context non-node location non-plotted cells non-pump current non-steady state non-tree structures nonzero nseg-dependent object-oriented programming off-diagonal term once-only error one-dimensional peak-to-peak pre-existing problem-dependent quasi-equilibrium re-creating re-execute re-initialize re-use real-world sealed end second order self-event sequence-dependent side-effect single line comment smoothly varying spatially-varying spike-triggered synaptic transmission STATE-dependent reaction rates steady state stream-specific plasticity synapse-specific plasticity time-dependent time step time-varying transmitter-receptor interaction tree-structured use-dependent user-defined user-level specification user-settable parameter user-specified user-supplied Jacobian voltage-dependent voltage-independent voltage-gated voltage-sensitive well-chosen well-designed well-matched well-stirred x-axis Common hyphen suspects ---------------------- -activated -based -bound -defined -dependent -driven -gated -sensitive -settable -specific -specified -style -triggered -varying INDEX GLOSSARY BEGINS HERE ========================== ! (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-oriented syntax \ (backslash) ^ (exponentiation operator)--see hoc syntax: expressions: operators ^C (Control C)--see hoc: interrupting execution ^D (Control D)--see hoc: starting and exiting _ (underscore)--see hoc syntax: names _ion--see ion mechanism: _ion suffix *_ion--see ion mechanism: automatically created *i0_*_ion--see ion mechanism: default concentration: specification in hoc *o0_*_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) %%%% %DELTA x also see spatial grid, discretization %DELTA t fixed--see numeric integration: fixed time step also see discretization %lambda--see length constant %lambda_AC--see length constant: AC %lambda_DC--see length constant: DC %tau--see time constant %tau_m--see membrane time constant 3333 3--see nseg: why triple nseg?, spatial accuracy: checking 3-D model--see model: 3-D, 3-D specification of geometry 3-D specification of geometry 3-D information arc3d() calculation of L, diam, area, and ri coordinates absolute vs. relative data--see 3-D specification of geometry: 3-D information also see quantitative morphometric data diam3d() checking also see stylized specification of geometry: diam: checking diameter also see 3-D specification of geometry: diam3d(), 3-D specification of geometry: calculation of L, diam, area, and ri problems n3d() number of 3-D points--see n3d() effect on computational efficiency vs. nseg origin of cell--see section: root section: is 3-D origin of cell points--see 3-D specification of geometry: 3-D information pt3dadd() pt3dclear() x3d(), y3d(), z3d() also see stylized specification of geometry AAAA abrupt change--see variable: abrupt change of, NET_RECEIVE block: handling abrupt changes and discontinuities absolute error local tolerance also see STATE block: specifying local absolute error tolerance also see numerical error: local, relative error: local also see relative error absolute local error--see absolute error: local absolute tolerance--see absolute error: local: tolerance abstraction AC length constant--see length constant: AC access also see section: currently accessed: default section accumulation--see ion accumulation accuracy effect of boundary conditions of ionic currents--see membrane current: ionic: accuracy, standard run system: fcurrent() order--see numeric integration: order of accuracy physiological qualitative quantitative spatial--see spatial accuracy vs. speed temporal--see temporal accuracy also see judgment, discretization, numerical error, parameters: sensitivity to acell_home_--see NetWork Builder: exporting reusable code: acell_home_ action potential ?? membrane ?? propagating ?? also see spike active current--see channel: voltage-gated active transport electrically silent initialization pump transient kinetic scheme--see Example 9.9: a calcium pump pump current countering with a NONSPECIFIC_CURRENT initialization also see NEURON block: NONSPECIFIC_CURRENT pump transient--see active transport: initialization: pump transient also see buffer, diffusion, ion accumulation adaptive integration--see numeric integration: adaptive adaptive time step--see numeric integration: adaptive adding items to NEURON Main Menu--see NEURONMainMenu class: miscellaneous_add() adding new functions to NEURON--see NMODL adding new mechanisms--see mechanisms: user-defined, nrniv: adding new mechanisms, NMODL 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: external aggregation of events to time step boundaries--see numeric integration: fixed time step: event aggregation to time step boundaries algebra !! linear--see linear algebra algebraic equation--see equation: algebraic algebraic difference equation--see equation: difference AlphaSynapse graphical interface--see PointProcessManager GUI parameters onset tau gmax e preserving spatial accuracy--see point process: preserving spatial accuracy also see Example 10.4: alpha function synapse alpha function synapse--see AlphaSynapse, Example 10.4: alpha function synapse Alt key--see Graph class: menu_tool() amount of material--see material: amount ampa.mod--see Example 10.6: saturating synapses AMPAergic synapse--see Example 10.3: synapse with exponential decay also see Example 10.6: saturating synapses amplification factor--see amplifier: gain amplifier feedback--see feedback: amplifier gain headstage also see circuit: element: amplifier analog--see ?? << what the heck is this used for ?? analog system--see ?? << what the heck is this used for ?? analysis initialization--see initialization: analysis analytic solution and discrete event simulation--see discrete event simulation: conditions for anatomical data--see quantitative morphometric data anatomical distance--see distance anatomical properties separating biology from numerical issues also see section, range, range variable specifying--see 3-D specification of geometry, stylized specification of geometry, topology: specifying also see section, geometry, topology AND operator--see hoc syntax: expressions: operators apostrophe--see DERIVATIVE block: ' (apostrophe) append()--see List class: append(), SectionList class: append(), Vector class: append() approximate Jacobian--see Jacobian: approximate approximation of a continuous system by a discrete system piecewise linear--see continuous variable: piecewise linear approximation also see Jacobian: approximate arc length--see range arc3d()--see 3-D specification of geometry: arc3d() architecture--see topology area membrane--see surface area, membrane area surface--see surface area, membrane area zero area nodes--see section: nodes: zero area area() << code >> as an ASSIGNED variable--see ASSIGNED variable: v, celsius, t, dt, diam, and area calculation of--see stylized specification of geometry: calculation of area and ri, 3-D specification of geometry: calculation of L, diam, area, and ri effect of creating a Shape--see Shape object: creating: effect on diam, area, and ri effect of define_shape()--see define_shape(): effect on diam, area, and ri stylized vs. 3-D surface integral arguments--see funcs and procs: arguments also see NET_RECEIVE block, FUNCTION block, PROCEDURE block section as--see SectionRef class trapping--see good programming style: bulletproofing against nonsense arguments arithmetic operators--see hoc syntax: expressions: operators arrays in NMODL--see NMODL: arrays, STATE variable: array in NMODL of numbers--see hoc syntax: variables: double, Vector class of objects--see object: array of sections--see section: array ArtCellGUI bringing up an ArtCellGUI cell names--see NetWork Builder: cells: names changing--see ArtCellGUI: specifying cell types changing cell parameters--see NetWork Builder: caveats also see PointProcessGroupManager specifying cell types also see NEURON Main Menu GUI: Build: NetWork Cell Artificial Cell--see NEURON Main Menu GUI: Build: NetWork Cell, ArtCellGUI artificial cell--see artificial spiking cell artificial neural system ??? also see biological neural system ??? artificial neuron--see artificial spiking cell artificial spiking cell << artificial >> advantages and uses computational efficiency differences from other point processes implemented as point processes IntFire1--see IntFire1 class, Example 10.7: IntFire1, a basic integrate and fire model IntFire2--see IntFire2 class, Example 10.8: IntFire2, firing rate proportional to input IntFire4--see IntFire4 class, Example 10.9: IntFire4, different synaptic time constants NetStim--see NetStim class also see biophysical neuron model, integrate and fire, IntFire1 class, IntFire2 class, IntFire4 class, NetStim class, NEURON block: ARTIFICIAL_CELL artificial spiking neuron--see artificial spiking cell ARTIFICIAL_CELL--see NEURON block: ARTIFICIAL_CELL, artificial spiking cell ASCII file--see plain text file ASSIGNED block also see PARAMETER block, STATE block ASSIGNED panel--see Distributed Mechanism GUI: Viewer: Shape Name ASSIGNED variable << ASSIGNED >> also see PARAMETER variable, STATE variable, ion_style(), state variable: as an ASSIGNED variable abrupt change of--see variable: abrupt change of, NetCon class: event(), NET_RECEIVE block: handling abrupt changes and discontinuities accuracy GLOBAL also see NEURON block: GLOBAL spatial variation vs. RANGE initialization also see initialization is a range variable by default also see NEURON block: RANGE, range variable v, celsius, t, dt, diam, and area assigned variable also see ASSIGNED variable assignment operator--see hoc syntax: expressions: operators assumptions at_time()--see CVODE: and model descriptions: at_time(), variable: abrupt change of atol also see absolute error: local: tolerance attaching a section--see connect attenuation at high frequencies also see membrane time constant: and attenuation of fast signals, spatial decay of fast signals Avogadro's number--see units: mole axial current positive current convention axial resistance infinite also see diameter: zero or narrow diameter also see ri, Ra, cytoplasmic resistivity axon also see squid axon, hh mechanism BBBB b_flux--see KINETIC block: b_flux backward Euler method and LONGITUDINAL_DIFFUSION iteration coefficient local error stability summary of strengths and weaknesses also see modified Euler method, numeric integration: fixed time step backward flux--see flux: backward, KINETIC block: b_flux backslash (\)--see \ (backslash) balance charge--see charge: conservation mass--see material: conservation ball and stick bandpass barbed wire shape--see stylized specification of geometry: strange shapes base class--see class: base class, object-oriented programming: polymorphism, object-oriented programming: inheritance biological neural system ??? also see artificial neural system ??? biological properties vs. purely computational issues << purely numerical issues >> biological relevance ??? << biologically relevant, significant >> biological system ??? biophysical mechanism--see distributed mechanism, point process biophysical model neuron--see biophysical neuron model biophysical neuron model also see artificial spiking cell biophysical properties separating biology from numerical issues also see section, range, range variable specifying also see distributed mechanism, point process blocks--see NMODL: named blocks boundary conditions effect on accuracy--see accuracy: effect of boundary conditions sealed end branch cell also see neurite, section circuit--see circuit: edge branched architecture also see topology branched cable--see cable: branched break--see hoc syntax: flow control: break BREAKPOINT block << BREAKPOINT >> abrupt change of a variable--see variable: abrupt change of, NetCon class: event(), NET_RECEIVE block: handling abrupt changes and discontinuities and computations that must be performed only once per time step and counts, flags, and random numbers and PROCEDUREs and rate functions and variables that depend on the number of executions at_time()--see CVODE: and model descriptions: at_time(), variable: abrupt change of, NET_RECEIVE block: handling abrupt changes and discontinuities currents assigned at end of METHOD--see BREAKPOINT block: SOLVE SOLVE cnexp derivimplicit is not a function call sparse also see STATE variable state_discontinuity()--see CVODE: and model descriptions: state_discontinuity(), variable: abrupt change of, NET_RECEIVE block: handling abrupt changes and discontinuities time-dependent PARAMETER--see variable: time-dependent, Vector class: play() translation of browser--see Plot what?, directory browser, variable browser buffer also see calcium: buffer, active transport, diffusion, ion accumulation buffering with diffusion--See Example 9.8: calcium diffusion with buffering built-in constants--see hoc syntax: variables: built-in constants built-in editor--see em built-in mechanisms--see mechanisms: built-in bulletproofing against nonsense arguments--see good programming style: bulletproofing against nonsense arguments CCCC C code embedding--see NMODL: VERBATIM . . . ENDVERBATIM ca_ion--see ion mechanism: automatically created CABLE cable branched equation--see equation: cable passive cylindrical unbranched cadif.mod--see Example 9.8: calcium diffusion with buffering cagk.mod--see Example 9.5: a calcium-activated, voltage-gated current cai default concentration also see ion mechanism: default concentration: specification in hoc also see calcium: concentration cai0_ca_ion--see cai: default concentration, ion mechanism: default concentration: specification in hoc calcium amount of buffer concentration free also see cai, cao conductance current effect on concentration also see ica ion permeability pump also see Example 9.9: a calcium pump calcium-activated current--see channel: calcium-activated, Example 9.5: a calcium-activated, voltage-gated current calcium pump--see active transport, Example 9.9: a calcium pump call by reference--see funcs and procs: arguments: call by reference, NET_RECEIVE block: arguments are call by reference also see hoc syntax: pointer operator, funcs and procs: arguments: pointer call by value--see funcs and procs: arguments: call by reference vs. call by value, FUNCTION block: arguments are call by value, PROCEDURE block: arguments are call by value call by value vs. call by reference--see funcs and procs: arguments: call by reference, funcs and procs: arguments: call by reference vs. call by value, FUNCTION block: arguments are call by value, PROCEDURE block: arguments are call by value, NET_RECEIVE block: arguments are call by reference also see hoc syntax: pointer operator, funcs and procs: arguments: pointer cao default concentration also see ion mechanism: default concentration: specification in hoc also see calcium: concentration cao0_ca_ion--see cao: default concentration, ion mechanism: default concentration: specification in hoc capacitance !! electrode--see electrode: capacitance compensation--see electrode: capacitance: compensation membrane--see cm, membrane capacitance, specific membrane capacitance capacitor feedback--see feedback: capacitor also see circuit: element: capacitor capacitive current--see i_cap, membrane current: capacitive Cell Map--see NetWork Builder: cells: Cell Map cell time queue--see standard run system: event delivery system: cell time queue CellBuilder bringing up a CellBuilder hoc output exported cell cell class root section also see section: default section spatial grid--see CellBuilder GUI: Geometry page: nseg, d_lambda, or d_X also see spatial accuracy, spatial grid CellBuilder GUI Biophysics page assigning values specifying strategy Continuous Create Geometry page assigning values specifying strategy nseg d_lambda d_X Management page Cell Type Export Import Subsets page all subset making a new subset Topology page Basename base name changing the name of a section making a new section celsius as an ASSIGNED variable--see ASSIGNED variable: v, celsius, t, dt, diam, and area also see Distributed Mechanism GUI: celsius central difference method--see Crank-Nicholson method changing a variable in mid-run--see PARAMETER variable: time-dependent, variable: abrupt change of changing point process location with hoc code--see point process: loc() changing standard functions and procedures--see standard run library: redefining functions and procedures, standard GUI library: redefining functions and procedures channel ?? analytic integration of states--see numeric integration: analytic integration of channel states conductance calcium-activated also see Example 9.5: a calcium-activated, voltage-gated current current accuracy--see membrane current: ionic: accuracy, standard run system: fcurrent() density initialization--see initialization: channel model gating model HH-type also see channel: linear under CVODE ligand-gated also see Example 10.1: graded synaptic transmission, Example 10.5: use-dependent synaptic plasticity, Example 10.6: saturating synapses linear also see channel: gating model: HH-type model also see current model nonlinear under CVODE ohmic--see channel: linear voltage-gated also see Example 9.4: a voltage-gated current, Example 9.5: a calcium-activated, voltage-gated current, Example 9.7: kinetic scheme for a voltage-gated current chaos and numerical error--see numerical error: chaotic system chaotic system--see initialization: categories: to a desired state charge balance--see charge: conservation conservation also see Kirchhoff's current law, gap junction: conservation of charge electronic--see e: electronic charge vs. units conversion factor chemical !! notation--see kinetic scheme reaction--see kinetic scheme signal--see signal: chemical child section--see section: child chord conductance--see conductance: chord circuit analysis edge element amplifier capacitor current source ground resistor voltage source wire equivalent also see section: equivalent circuit linear--see linear circuit node parallel RC positive current convention clamp--see current clamp, voltage clamp class base class also see object-oriented programming: polymorphism, object-oriented programming: inheritance defining a new class--see template: defining an object template subclass also see object-oriented programming: polymorphism, object-oriented programming: inheritance vs. object also see template, object, object-oriented programming class definition--see template, class Close button--see GUI: tools: Close button closed end--see boundary conditions: sealed end closed system cm << code >> default value also see specific membrane capacitance, membrane capacitance Cm--see cm cnexp--see DERIVATIVE block, BREAKPOINT block: SOLVE: cnexp coincidence detection collection of numbers--see hoc syntax: double, Vector class of objects--see object: array, List class of sections--see SectionList class command history--see hoc: history function command potential !! voltage clamp--see voltage clamp: command potential COMMENT . . . ENDCOMMENT--see NMODL: comments comments--see hoc syntax: comments, NMODL: comments also see good programming style: comments comparison of real values--see hoc syntax: float_epsilon COMPARTMENT--see KINETIC block: COMPARTMENT compartment adjacent << neighboring >> size vs. biologically relevant structures vs. conceptual clarity "boxed in by compartments" also see segment compartmental model--see model: compartmental compartmentalization--see discretization complexity compound statement--see hoc syntax: statements: compound statement computational efficiency << cost, overhead >> and STATEs rate tables--see numeric integration: analytic integration of channel states staggered time step--see Crank-Nicholson method: staggered time step tree topology why is NEURON fast? also see d_lambda rule, function table, IntFire2 class: firing time: efficient computation, IntFire4 class: firing time: efficient computation, synaptic transmission: spike triggered: computational efficiency in NEURON, discrete event simulation: computational efficiency computational model--see model: computational computational solution--see numeric solution computer display--see GUI: screen computing purpose--see insight concentration and accuracy default--see ion mechanism: default concentration specification in hoc--see ion mechanism: default concentration: specification in hoc extracellular gradient initialization--see ion mechanism: default concentration, initialization: ion intracellular specification--see initialization: ion, ion mechanism: default concentration: specification in hoc also see ion accumulation, ion mechanism, initialization: ion conceptual clarity conceptual model--see model: conceptual conductance absolute chord also see conductance: slope density also see channel: density ion channel--see channel: conductance membrane--see membrane conductance, specific membrane conductance slope also see conductance: chord conductance-change synapse--see synapse: conductance-change conflicts between hoc and GUI tools--see GUI: conflicts with hoc or other GUI tools connect << code >> preserving spatial accuracy preventing confusion--see section: child: connect 0 end to parent connectivity--see NetCon class, List object: managing network connections with conservation law charge--see charge: conservation, Kirchhoff's current law material--see material: conservation CONSERVE--see KINETIC block: CONSERVE consistency of units--see units: consistency constant !! built-in constant--see hoc syntax: variables: built-in constants length--see length constant membrane time--see membrane time constant rate--see rate constant time--see time constant CONSTANT vs. PARAMETER or LOCAL variable CONSTANT block constant current mechanism also see initialization: strategies: injecting a constant current continuation character--see \ (backslash) continue--see hoc syntax: flow control: continue continuerun()--see standard run system: continuerun() continuous function--see function: continuous continuous system--see system: continuous continuous variable piecewise linear approximation also see range variable: estimating by linear interpolation between nodes Control C--see hoc: interrupting execution Control D--see hoc: starting and exiting Control key--see Graph class: menu_tool() control--see simulation control convergence also see synaptic transmission: spike-triggered conversion factor--see scale factor, NMODL: units conversion factor, UNITS block: units scaling core correspondence between conceptual and computational model--see model: correspondence between conceptual and computational Crank-Nicholson method also see secondorder iteration coefficient local error kinetic scheme second order correct plots staggered time steps summary of strengths and weaknesses unstaggered time steps create << code >> also see section creating an object--see object: creating creating an object reference--see object reference: declaring criterion for proper initialization--see initialization: criterion for proper initialization Ctrl key--see Graph class: menu_tool() current absolute also see current: density axial--see axial current balance--see Kirchhoff's current law balance equation--see equation: current balance, Kirchhoff's current law capacitive--see membrane current: capacitive, i_cap calcium-activated--see channel: calcium-activated clamp current--see current clamp: current, voltage clamp: current density spatial uniformity also see current: absolute electrode ionic--see membrane current: ionic membrane--see membrane current model--see current model sign convention !! electrical circuit--see circuit: positive current convention membrane current--see membrane current: positive current convention source also see circuit: element: current source transmembrane--see membrane current voltage-gated--see channel: voltage-gated current clamp current preserving spatial accuracy--see point process: preserving spatial accuracy also see IClamp class, Example 9.3: an intracellular stimulating electrode current model currently accessed section--see section: currently accessed cursor--see focus: cursor custom GUI--see user interface: custom GUI custom initialization--see initialization: categories, initialization: strategies CVODE << CVODE >> also see numeric integration: adaptive, standard run system: CVODE abrupt changes and discontinuities--see CVODE: and model descriptions, variable: abrupt change of NET_RECEIVE block: handling abrupt changes and discontinuities and LONGIDUDINAL_DIFFUSION and model descriptions at_time() state_discontinuity() also see NET_RECEIVE block: state_discontinuity() as generic term for adaptive integration default error criteria interpolation formulas--see numeric integration: adaptive: interpolation formulas local error step() under--see standard run system: step(): under CVODE CVode class re-init() also see initialization: strategies: changing a state variable record() CVODES also see numeric integration: adaptive, CVODE cytoplasmic resistivity also see Ra DDDD d_lambda also see d_lambda rule, discretization, spatial grid d_lambda rule also see d_lambda, discretization, spatial grid d_X also see d_X rule, discretization, spatial grid d_X rule also see d_X, discretization, spatial grid DASPK also see numeric integration: adaptive, standard run system: DASPK, IDA daughter section--see section: child DC length constant--see length constant: DC declaring an object reference--see object reference: declaring declaring variables--see NMODL: declaring variables default section--see access, section: currently accessed: default section deferred computation--see standard run system: event delivery system: implementing deferred computation DEFINE--see NMODL: DEFINE define_shape() effect on diam, area, and ri defining a new class--see template: writing a template defining a new template--see template: writing a template delayed action--see standard run system: event delivery system: implementing deferred computation Delete--see Graph GUI primary menu: Delete deleting traces--see Graph GUI primary menu: Delete delta function--see function: delta demonstration program--see neurondemo dendritic spine--see spine density current--see current: density channel--see channel: density material--see material: density density mechanism--see distributed mechanism dependent variable--see variable: dependent DERIVATIVE block ' (apostrophe) and CVODE dependent variable is a STATE variable also see initialization: channel model: Hodgkin-Huxley style derivimplicit--see DERIVATIVE block, BREAKPOINT block: SOLVE: derivimplicit detaching a section--see disconnect() detail also see judgment developing new GUI tools--see GUI tool development diam << code >> as an ASSIGNED variable--see ASSIGNED variable: v, celsius, t, dt, diam, and area calculation from 3-D data--see 3-D specification of geometry: calculation of L, diam, area, and ri caution when specifying linear taper checking also see 3-D specification of geometry: diam3d(): checking default value effect of creating a Shape--see Shape: creating: effect on diam, area, and ri effect of define_shape()--see define_shape(): effect on diam, area, and ri specifying !! stylized specification ?? 3-D specification--see 3-D specification of geometry: calculation of L, diam, area, and ri tapering updating from 3-D data diam3d()--see 3-D specification of geometry: diam3d() diameter abrupt change change flag checking--see diam: checking, 3-D specification of geometry: diam3d(): checking linear taper--see diam: caution when specifying linear taper problems--see 3-D specification of geometry: diameter: problems zero or narrow diameter also see axial resistance: infinite, diam: checking, 3-D specification of geometry: diam3d(): checking also see diam, stylized specification of geometry, 3-D specification of geometry: diam3d() difference equation--see equation: difference differential algebraic solver--see DASPK differential equation--see equation: differential diffusion under CVODE kinetic scheme also see Example 9.8: calcium diffusion with buffering longitudinal also see Example 9.8: calcium diffusion with buffering model geometry--see ion accumulation: initialization: of model geometry radial also see Example 9.8: calcium diffusion with buffering restricted--see Example 9.6: extracellular potassium accumulation with buffering--see Example 9.8: calcium diffusion with buffering also see active transport, buffer, ion accumulation dimensionless variable--see units: dimensionless dimensions--see units consistency--see units: consistency inconsistent--see units: consistency directory browser disconnect() discontinuity--see variable: abrupt change of, diameter: abrupt change also see function: discrete discrepancy between conceptual model and computational model also see model: correspondence between conceptual and computational between physical system and conceptual model between prediction and simulation discrete event simulation computational efficiency conditions for also see standard run system: fadvance(): global time step integration, standard run system: fadvance(): local time step integration discrete event system--see standard run system: event delivery system discrete events and adaptive integration--see standard run system: event delivery system: adaptive integration and, standard run system: fadvance(): global time step integration, standard run system: fadvance(): local time step integration discrete input event--see event: external discrete simulation--see discrete event simulation discrete system--see system: discrete ?? there isn't a system: discrete yet discretization guidelines intent and judgment parameter--see nseg rule--see d_lambda rule, d_X rule, discretization: guidelines spatial also see %lambda, length constant, d_lambda, spatial grid, spatial accuracy temporal also see dt, %DELTA t testing--see spatial accuracy: checking, temporal accuracy: checking discretization interval--see %DELTA x, spatial grid display--see GUI: screen distance normalized distance along a section--see range physical distance along a section distributed mechanism adding new--see mechanisms: user-defined, NMODL insert--see insert << code >> vs. point process also see NEURON block: SUFFIX Distributed Mechanism GUI celsius globalRa Manager Homogeneous Spec Inserter Viewer Globals Name Values Shape Name Distributed Mechanism Manager--see Distributed Mechanism GUI: Manager distributed physical system--see system: continuous divergence also see synaptic transmission: spike-triggered divide and conquer--see good programming style: divide and conquer division operator--see hoc syntax: expressions: operators doEvents()--see standard run system: doEvents() dot notation accessing object members--see object: public members: dot notation specifying section properties--see section: currently accessed: dot notation double--see hoc syntax: variables: double dt as an ASSIGNED variable--see ASSIGNED variable: v, celsius, t, dt, diam, and area also see dt: use in NMODL fixed--see numeric integration: fixed time step use in NMODL variable--see numeric integration: adaptive also see standard run system: setdt(), standard run system: fadvance(), RunControl GUI: dt, RunControl GUI: Points plotted/ms EEEE e electronic charge vs. units conversion factor also see NMODL: units conversion factor also see units: e e_pas--see pas mechanism edge--see circuit: edge efficiency--see computational efficiency eigenfunction eigenvalue eigenvector ?? elapsed simulation time also see t electrical synapse--see synapse: electrical, synapse: ephaptic, gap junction electrode capacitance compensation current--see current: electrode intracellular stimulating--see Example 9.3: an intracellular stimulating electrode resistance compensation shunting effect of sharp microelectrode--see Example 9.2: a localized shunt electronic charge--see e: electronic charge vs. units conversion factor electronic instrumentation--see linear circuit electrotonic architecture spurious effect of changing nseg electrotonus else--see hoc syntax: flow control: else em also see emacs, Appendix A2: NEURON's built-in editor emacs << emacs >> blocks of text copying to the kill buffer cutting to the kill buffer marking pasting from the kill buffer buffers cursor movement entering exiting files modes repeating commands kill current command macros repeating commands search and replace send command to OS text deleting inserting formatting windows embedding C code--see NMODL: VERBATIM . . . ENDVERBATIM empty temporal resolution--see temporal accuracy: empty encapsulating code--see object-oriented programming: encapsulating code ENDCOMMENT--see NMODL: comments ENDVERBATIM--see NMODL: VERBATIM . . . ENDVERBATIM enhancing NEURON--see NMODL enzymatic breakdown EOT (^D)--see hoc: starting and exiting ephapse--see synapse: ephaptic, synapse: electrical, gap junction ephaptic synapse--see synapse: ephaptic, synapse: electrical, gap junction equality operator--see hoc syntax: expressions: operators equation algebraic cable characteristic conservation current balance also see Kirchhoff's current law difference differential coupled vs. independent ordinary partial stiff--see system: stiff iteration--see iteration: equation node--see equation: current balance, Kirchhoff's current law sacred runes system--see system equations equilibrium ?? equilibrium potential ASSIGNED vs. PARAMETER--see ASSIGNED variable: when to use for an equilibrium potential computation also see ion_style(), NEURON block: NONSPECIFIC_CURRENT: equilibrium potential initialization--see initialization: ion also see ion_style() equivalent circuit--see circuit: equivalent, section: equivalent circuit Erase--see Graph GUI: primary menu: Erase erasing traces--see Graph GUI: primary menu: Erase error--see numerical error, hoc: error handling, error message error message diam = 0 no accessed section no message for pt3dadd with zero diameter also see hoc: error handling Euler method--see backward Euler method, forward Euler method event << event >> afferent--see event: external delivery delivery system--see standard run system: event delivery system discrete--see discrete event simulation external distinguishing from a self-event flag also see event: external: distinguishing from a self-event handler--see NetCon class: event() input--see event: external logical mouse--see mouse: events queue--see standard run system: event delivery system: cell time queue, standard run system: event delivery system: event time queue self-event distinguishing from an external event--see event: external: distinguishing from a self-event implementing absolute refractory period--see IntFire1 class: refractory period implementing deferred computation--see standard run system: event delivery system: implementing deferred computation implementing transmitter release duration--see Example 10.6: saturating synapses also see event: external, NET_RECEIVE block: net_move(), NET_RECEIVE block: net_send(), IntFire2 class: firing time: role of self-events, IntFire4 class: firing time: role of self-events spike--see event: external stream times notification--see CVODE: and model descriptions: at_time(), NetCon class: event() with adaptive integration also see NetCon class: event() with fixed time step integration--see numeric integration: fixed time step: event aggregation to time step boundaries also see standard run system: event delivery system: event time queue event aggregation to time step boundaries--see numeric integration: fixed time step: event aggregation to time step boundaries event handler--see NetCon class: event() event queue--see standard run system: event delivery system: event time queue event time queue--see standard run system: event delivery system: event time queue event times--see event: times event-driven simulation--see discrete event simulation also see simulation: continuous system event()--see NetCon class: event() << Example >> Example 9.1: a passive "leak" current Example 9.2: a localized shunt Example 9.3: an intracellular stimulating electrode Example 9.4: a voltage-gated current Example 9.5: a calcium-activated, voltage-gated current Example 9.6: extracellular potassium accumulation Example 9.7: kinetic scheme for a voltage-gated current Example 9.8: calcium diffusion with buffering Example 9.9: a calcium pump Example 10.1: graded synaptic transmission Example 10.2: a gap junction Example 10.3: synapse with exponential decay Example 10.4: alpha function synapse Example 10.5: use-dependent synaptic plasticity Example 10.6: saturating synapses Example 10.7: IntFire1, a basic integrate and fire model Example 10.8: IntFire2, firing rate proportional to input Example 10.9: IntFire4, different synaptic time constants exiting hoc--see hoc: starting and exiting exiting NEURON--see NEURON: starting and exiting exocytosis Exp2Syn computational efficiency e tau1 tau2 also see Example 10.4: alpha function synapse explicit Euler method--see forward Euler method explicit flux--see KINETIC block: << (explicit flux) exploiting reusable code--see good programming style: exploiting reusable code exploratory simulations--see GUI: vs. hoc exponentiation operator--see hoc syntax: expressions: operators ExpSyn e tau also see Example 10.3: synapse with exponential decay expsyn1.mod--see Example 10.3: synapse with exponential decay execute() also see hoc: top level of the interpreter extensive variable--see variable: extensive external event--see event: external extracellular field--see extracellular mechanism, system equations: matrix form: extracellular field extracellular mechanism effect of ELECTRODE_CURRENT--see NEURON block: ELECTRODE_CURRENT: effect on extracellular mechanism computational efficiency initialization--see initialization: extracellular mechanism under CVODE vext also see NEURON block: ELECTRODE_CURRENT: effect on extracellular mechanism extracellular potassium accumulation--see Example 9.6: extracellular potassium accumulation FFFF f_flux--see KINETIC block: f_flux F-H space--see Example 9.6: extracellular potassium accumulation factor amplification--see amplifier: gain conversion--see scale factor, NMODL: units conversion factor, UNITS block: units scaling scale--see scale factor, NMODL: units conversion factor, UNITS block: units scaling fadvance.c also see initialization: finitialize() fadvance()--see standard run system: fadvance() FALSE--see hoc syntax: expressions: logical expressions fan-in--see convergence also see synaptic transmission: spike-triggered fan-out--see divergence also see synaptic transmission: spike-triggered faraday--see units: faraday fast signals spatial decay--see spatial decay of fast signals fast_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() feedback amplifier capacitor negative positive field--see extracellular field file hoc file--see hoc file, hoc mod file--see mod file, NMODL reading and writing--see hoc syntax: basic input and output, File class ses file--see session file session file--see session file finitialize()--see initialization: finitialize() fixed %DELTA t--see numeric integration: fixed time step dt--see numeric integration: fixed time step time step--see numeric integration: fixed time step float_epsilon--see hoc syntax: float_epsilon flow control--see hoc syntax: flow control flushPlot()--see standard run system: flushPlot() flush_list--see standard run system: plotting system: flush_list flux backward also see KINETIC block: b_flux forward also see KINETIC block: f_flux also see KINETIC block: << (explicit flux) FOCAL focus cursor for--see hoc syntax: flow control: for for (x) << code >> forall << code >> forsec << code >> forward Euler method also see numerical integration: fixed time step iteration coefficient local error stability forward flux--see flux: forward, KINETIC block: f_flux Fourier theory fprint()--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 accumulation frecord_init()--see initialization: frecord_init() frequency spatial also see spatial accuracy, spatial grid, numerical error: spatial temporal fscan()--see hoc syntax: basic input and output: fscan() funcs and procs << funcs >> $--see funcs and procs: arguments: positional syntax $i--see funcs and procs: arguments: symbolic positional syntax $o--see funcs and procs: arguments: objref $s--see funcs and procs: arguments: strdef &--see hoc syntax: pointer operator arguments call by reference call by reference vs. call by value numarg() object objref pointer also see hoc syntax: pointer operator positional syntax strdef symbolic positional syntax defining local variable also see hoc syntax: names recursion return also see hoc syntax: flow control: return returned value--see funcs and procs: return FUNCTION calling from hoc--see hoc: calling an NMODL FUNCTION or PROCEDURE FUNCTION block arguments are call by value function also see funcs and procs, FUNCTION continuous of space also see range variable of time delta discrete ?? piecewise linear also see continuous variable: piecewise linear approximation rate--see BREAKPOINT block: and rate functions, KINETIC block: reaction rates: voltage sensitive table--see function table function call operator--see hoc syntax: expressions: operators function table also see NMODL: FUNCTION_TABLE FUNCTION_TABLE--see NMODL: FUNCTION_TABLE GGGG g_pas--see pas mechanism gain--see amplifier: gain gap junction computational efficiency conservation of charge also see charge: conservation, equation: current balance, Kirchhoff's current law spurious oscillations under CVODE also see Example 10.2: a gap junction, synapse: electrical, synapse: ephaptic, LinearCircuitBuilder: for gap junctions gap.mod--see Example 10.2: a gap junction gating model--see channel: gating model gating state initialization--see initialization: channel model custom initialization--see initialization: strategies: changing a state variable gating variable -- see gating state Gaussian elimination generic starting point for GUI tool development--see GUI tool development: generic starting point GENESIS geometry artifacts stylized specification reinterpreted as 3-D specification zero diameter specifying--see 3-D specification of geometry, stylized specification of geometry also see CellBuilder GUI: Geometry page zero diameter also see topology, anatomical properties getstr()--see hoc syntax: basic input and output: getstr() GLOBAL--see NEURON block: GLOBAL, ASSIGNED variable: GLOBAL, PARAMETER variable: is GLOBAL by default, global variable also see LOCAL variable: declared outside an equation block: scope and persistence global--see hoc syntax: names, global variable global error--see numerical error: global global time step--see numeric integration: adaptive: global time step global variable also see see hoc syntax: names, NEURON block: GLOBAL, template: writing a template: external globalRa--see Distributed Mechanism GUI: globalRa GMODL good programming style bulletproofing against nonsense arguments comments divide and conquer exploiting reusable code iterative development modular programming control--see simulation control instrumentation--see instrumentation model specification--see model specification program organization separate model specification from user interface testing and revision also see hoc: idiom graded synapse--see synaptic transmission: graded gradient--see concentration: gradient gradsyn.mod--see Example 10.1: graded synaptic transmission Graph automatically updating plots and x axis--see standard run system: addplot() creating Current axis Grapher also see Grapher Phase Plane Shape plot << is spawned from Main Menu >> Shape Plot << a false color plot mapped onto a Shape >> Space Plot State axis Voltage axis incorporating into plotting system--see standard run system: plotting system: incorporating Graphs and objects, standard run system: addplot() raster--see spike train: recording and plotting also see NetWork Builder: buttons: SpikePlot Graph class addexpr() addvar() begin() also see initialization: initPlot(), standard run system: Plot() beginline() erase_all() exec_menu() fast_flush() also see standard run system: fast_flushPlot() flush() also see standard run system: flushPlot() mark() menu_tool() plot() also see standard run system: Plot() save_name() size() view() view_count() view_info() also see standard run system: addplot() Graph GUI primary menu Change Text Color/Brush Crosshair Delete Erase Keep Lines Move Text Pick Vector Plot what? secondary menu NewView Object Name Scene=View Set View Translate View = plot Zoom in/out graph raster--see spike trains: recording and plotting, NetWork Builder: buttons: SpikePlot also see Graph graph lists--see standard run system: plotting system: graphLists graph theory graphical interface--see user interface: custom GUI, NEURON Main Menu graphical tools--see NEURON Main Menu, CellBuilder, Graph, PFWM, PointProcessManager, RunControl, Shape plot, Shape Plot, Space Plot, Plot what?, GUI tool development graphics terminology--see GUI: graphics terminology greater than operator--see hoc syntax: expressions: operators greater than or equal to operator--see hoc syntax: expressions: operators ground--see circuit: element: ground gsyn.mod--see Example 10.5: use-dependent synaptic plasticity GUI << GUI >> combining with hoc computer display--see GUI: screen conflicts with hoc or other GUI tools edit field focus graphics terminology implementing a computational model--see CellBuilder, Channel Builder, Linear Circuit Builder, NetWork Builder mapping to the screen--see GUI: screen: mapping to the screen model model coordinates also see GUI: scene coordinates numeric field checkbox default value spinner scene scene coordinates making scene and view coordinates equivalent also see Graph GUI: secondary menu: Scene=View transforming to screen coordinates--see Graph class: view_info() vs. screen coordinates screen mapping to the screen also see GUI tool development: mapping to the screen screen coordinates vs. scene coordinates--see GUI: scene coordinates: vs. screen coordinates tools are implemented in hoc Close button developing new tools--see GUI tool development work by constructing hoc programs also see NEURON Main Menu GUI view which view contains the mouse--see Graph class: view_info() vs. hoc also see custom GUI, NEURON Main Menu, standard GUI library GUI tool development basic pattern--see GUI tool development: generic starting point box--see VBox, HBox Close button--see GUI: tools: Close button general issues allowing multiple instances destroying encapsulating saving and retrieving also see session file, session file: object_push(), session file: object_pop(), GUI: scene coordinates: making scene and view coordinates equivalent generic starting point graphical model--see GUI: model mapping to the screen window title also see GUI: screen: mapping to the screen, VBox class: map() mouse events--see mouse: events panel--see xpanel() which view contains the mouse--see Graph class: view_info() HHHH Hamming, R.W. HBox also see VBox hh mechanism hiding information--see object-oriented programming: information hiding Hinton plot history function--see hoc: history function hoc << hoc >> adding new mechanisms--see nrniv: adding new mechanisms, mechanisms: user-defined, NMODL calling an NMODL FUNCTION or PROCEDURE specifying proper instance with setdata_ can do anything that a GUI tool can combining with GUI conflicts with GUI efficient simulation--see computational efficiency: why is NEURON fast? enhancements and extensions error handling funcs--see funcs and procs functions--see funcs and procs history function idiom forall nseg *= 3 forall psection() load_file("nrngui.hoc") also see List class: iteration immediate mode implementing a computational model interrupting execution also see hoc: starting and exiting Kernighan and Pike keywords--see hoc syntax: keywords libraries also see standard GUI library, standard run library oc> prompt parse errors--see hoc: error handling procedures--see funcs and procs procs--see funcs and procs run-time errors--see hoc: error handling scalar--see hoc syntax: variables: scalars scope--see hoc syntax: names, funcs and procs: local variable, LOCAL variable, ASSIGNED variable: GLOBAL, NEURON block: GLOBAL, PARAMETER variable: is GLOBAL by default also see template: writing a template: external, object: public members, template: writing a template: public speed--see computational efficiency: why is NEURON fast? starting and exiting stopping--see hoc: interrupting execution also see hoc: starting and exiting syntax--see hoc syntax top level of the interpreter also see execute() user-defined variable--see hoc syntax: names vs. GUI also see hoc syntax, Programmer's Reference, good programming style hoc file executing--see NEURON: starting with a specific hoc file, nrngui, nrniv also see load_file(), hoc syntax: basic input and output: xopen() hoc syntax << hoc syntax >> basic input and output fprint() fscan() getstr() print printf() read() ropen() sprint() wopen() xopen() also see load_file() xred() comments expressions logical comparison of real values--see hoc syntax: float_epsilon logical expressions operators precedence--see hoc syntax: expressions: operators float_epsilon flow control break continue else for if iterator iterator_statement quit() return also see funcs and procs: return stop while funcs--see funcs and procs functions--see funcs and procs keywords names operators--see hoc syntax: expressions: operators, hoc syntax: pointer operator pointer operator precedence of operations--see hoc syntax: expressions: operators procedures--see funcs and procs procs--see funcs and procs statements compound statement variables arrays--see hoc syntax: variables: double built-in constants cannot redefine type double objref--see object reference: objref scalars strdef strings--see hoc syntax: variables: strdef also see hoc: idiom, Programmer's Reference Hodgkin-Huxley delayed rectifier--see Example 9.4: a voltage-gated current Hodgkin-Huxley mechanism--see hh mechanism hypothesis testing also see model: conceptual IIII i_cap << code >> ica << code >> IClamp class preserving spatial accuracy--see point process: preserving spatial accuracy iclamp1.mod--see Example 9.3: an intracellular stimulating electrode IDA initialization also see numeric integration: adaptive, DASPK, SUNDIALS idiom--see hoc: idiom if--see hoc syntax: flow control: if ifsec << code >> immediate mode--see hoc: immediate mode implicit Euler method--see backward Euler method ina << code >> iterative development--see good programming style: iterative development independent variable--see variable: independent inequality operator--see hoc syntax: expressions: operators information hiding--see object-oriented programming: information hiding inheritance--see object-oriented programming: inheritance init()--see initialization: init() initPlot()--see initialization: initPlot() INITIAL block initializing STATE variables--see STATE variable: initialization: default vs. explicit, STATE variable: initialization: state0, STATE block: START inside NET_RECEIVE block--see NET_RECEIVE block: INITIAL block sequence-dependent SOLVE STEADYSTATE sparse also see initialization: channel model: kinetic scheme also see initialization, mechanisms: initialization sequence, mechanisms: user-defined: call order initial condition ?? not in chap 4 but maybe elsewhere initial value problem initialization << initialization >> adaptive integration--see numeric integration: adaptive: initialization, CVode class: re_init(), IDA: initialization active transport--see active transport: initialization analysis ASSIGNED variable--see ASSIGNED variable: initialization basic also see initialization: finitialize(), initialization: default categories overview of custom initialization also see initialization: init(): custom of a chaotic system--see initialization: categories: to a desired state of an oscillating system--see initialization: categories: to a desired state to a desired state to a particular resting potential to steady state also see initialization: basic, initialization: default channel model Hodgkin-Huxley style kinetic scheme also see INITIAL block: SOLVE: STEADYSTATE sparse, initialization: strategies: changing a state variable, initialization: strategies: changing model parameters, initialization: strategies: steady state initialization of complex kinetic schemes criterion for proper initialization custom--see initialization: categories, initialization: strategies also see initialization: init(): custom default 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 fcurrent()--see standard run system: fcurrent(): in initialization finitialize() fixed time step integration--see numeric integration: fixed time step: initialization frecord_init() init() custom also see initialization: strategies: changing a state variable initPlot() internal data structures dependent on topology and geometry also see ion accumulation: initialization: of model geometry ion accumulation--see ion accumulation: initialization also see ion mechanism: default concentration, ion_style(), initialization: strategies: changing a state variable kinetic scheme also see INITIAL block: SOLVE: STEADYSTATE sparse, KINETIC block: CONSERVE: when is it required for initialization? linear circuit membrane potential--see membrane potential: initialization, initialization: v_init NetCon object--see NET_RECEIVE block: INITIAL block network non-steady state--see initialization: categories: to a desired state object--see template: variable initialization random number generator Random.play() recording--see initialization: frecord_init(), Vector class: record(): initialization startsw() also see run time, standard run system: realtime STATE variable--see STATE variable: initialization state0--see STATE variable: initialization stdinit() steady state--see initialization: categories: to steady state, initialization: categories: to a particular resting potential strategies changing a state variable also see STATE variable: initialization, ion mechanism: initialization, ion mechanism: defatult concentration: specification in hoc changing model parameters changing an equilibrium potential groundhog day injecting a constant current jumping back to move forward steady state initialization of complex kinetic schemes also see initialization: init(): custom synaptic weight vector--see NET_RECEIVE block: INITIAL block t template--see template: variable initialization v_init also see membrane potential: initialization Vector.play() Vector.record()--see initialization: frecord_init(), Vector class: record(): initialization weight vector--see NET_RECEIVE block: INITIAL block also see RunControl GUI: Init, RunControl GUI: Init & Run, INITIAL block, NET_RECEIVE block: INITIAL block, Graph class: begin(), mechanisms: initialization sequence, mechanisms: user-defined: initialization sequence initialize microstep--see numeric integration: adaptive: initialize microstep also see standard run system: fadvance(): local time step integration() input and output--see hoc syntax: basic input and output, File class input event--see event: external insert <> also see uninsert insight "insight, not numbers"--see Hamming, R.W. instability--see numeric integration: instability instrumentation displaying results electronic--see linear circuit model parameters also see synapse: as instrumentation integrate and fire also see artificial spiking cell integration--see numeric integration intensive variable--see variable: intensive intent--see user's intent interpolate microstep--see numeric integration: adaptive: interpolate microstep also see standard run system: fadvance(): local time step integration() interpolation--see Vector class: play(): with interpolation interpreter--see hoc IntFire1 class << IntFire1 >> effect of an input event m--see IntFire1 class: membrane state variable M--see IntFire1 class: membrane state variable: visualizing membrane state variable time constant visualizing refrac--see IntFire1 class: refractory period refractory period tau--see IntFire1 class: membrane state variable: time constant also see artificial spiking cell, Example 10.7: IntFire1, a basic integrate and fire model IntFire2 class approximate firing rate bias--see IntFire2 class: synaptic current state variable: bias constraint on time constants effect of an external event firing time efficient computation role of self-events i--see IntFire2 class: synaptic current state variable ib--see IntFire2 class: synaptic current state variable: bias m--see IntFire2 class: membrane state variable membrane state variable time constant also see IntFire2 class: constraint on time constants role of self-events--see IntFire2 class: firing time: role of self-events synaptic current state variable bias time constant also see IntFire2 class: constraint on time constants taum--see IntFire2 class: membrane state variable: time constant taus--see IntFire2 class: synaptic current state variable: time constant also see artificial spiking cell, Example 10.8: IntFire2, firing rate proportional to input IntFire4 class constraint on time constants convergence tolerance effect of an external event eps--see IntFire4 class: convergence tolerance firing time efficient computation role of self-events e--see IntFire4 class: synaptic current state variables: excitatory i1--see IntFire4 class: synaptic current state variables: inhibitory i2--see IntFire4 class: synaptic current state variable: inhibitory m--see IntFire4 class: membrane state variable mathematical analysis--see Appendix A1: Mathematical analysis of IntFire4 membrane state variable time constant synaptic current state variables excitatory inhibitory time constants also see IntFire4 class: constraint on time constants taue--see IntFire4 class: synaptic current state variables: time constants taui1--see IntFire4 class: synaptic current state variables: time constants taui2--see IntFire4 class: synaptic current state variables: time constants taum--see IntFire4 class: membrane state variable: time constant also see artificial spiking cell, Example 10.9: IntFire4, different synaptic time constants intracellular stimulating electrode--see Example 9.3: an intracellular stimulating electrode intuition ion accumulation << ion accumulation >> << as in specific mechanisms of ion accumulation >> initialization of model geometry also see ion mechanism: default concentration, ion_style(), initialization: strategies: changing a state variable, initialization: strategies: changing model parameters kinetic scheme also see Example 9.8: calcium diffusion with buffering, Example 9.9: a calcium pump under CVODE also see active transport, buffer, diffusion, ion mechanism, ion_style(), equilibrium potential, STATE variable: ion concentration as, Example 9.6: extracellular potassium accumulation ion channel also see distributed mechanism ion concentration--see concentration, ion accumulation, ion mechanism ion mechanism _ion suffix automatically created default concentration for user-created ion names name specification in hoc equilibrium potential--see equilibrium potential: computation initialization also see initialization: ion ion_style() also see ASSIGNED variable, PARAMETER variable, STATE variable, concentration, initialization: ion ionic conductance also see channel density ionic current--see membrane current: ionic ionic equilibrium potential--see equilibrium potential isopotential--see membrane potential: isopotential, current: density: spatial uniformity iteration coefficient equation of nonlinear equations--see numeric integration: iteration of nonlinear equation over a List--see List class: iteration over nodes--see range variable: iterating over nodes over sections--see section: iterating over sections using iterator--see hoc syntax: flow control: iterator iterator--see hoc syntax: flow control: iterator iterator_statement--see hoc syntax: flow control: iterator_statement JJJJ Jacobian analytic approximate computing di/dv elements nearly singular user-supplied judgment also see accuracy, detail, qualitative results KKKK k-mole--see units: k-mole k_ion--see ion mechanism: automatically created k3st.mod--see Example 9.7: kinetic scheme for a voltage-gated current kd.mod--see Example 9.4: a voltage-gated current Keep Lines--see Graph GUI: primary menu: Keep Lines keep lines--see Graph GUI: primary menu: Keep Lines Kernighan, B.W.--see hoc: Kernighan and Pike kext.mod--see Example 9.6: extracellular potassium accumulation keyboard Alt key--see Graph class: menu_tool() Control C--see hoc: interrupting execution Control D--see hoc: starting and exiting Control key--see Graph class: menu_tool() Shift key--see Graph class: menu_tool() keywords--see hoc syntax: keywords, NMODL ki default concentration also see ion mechanism: default concentration: specification in hoc ki0_k_ion--see ki: default concentration, ion mechanism: default concentration: specification in hoc KINETIC block << KINETIC >> -> (sink reaction indicator) ~ (tilde) <-> (reaction indicator) << (explicit flux) and CVODE b_flux COMPARTMENT CONSERVE when is it required for initialization? dependent variable is a STATE variable also see KINETIC block: reactants: ASSIGNED or PARAMETER variables as f_flux initialization--see initialization: channel model: kinetic scheme, INITIAL block: SOLVE: STEADYSTATE sparse LONGITUDINAL_DIFFUSION also see backward Euler method: and LONGITUDINAL_DIFFUSION, CVODE: and LONGITUDINAL_DIFFUSION radial diffusion--see Example 9.8: calcium diffusion with buffering reactants ASSIGNED or PARAMETER variables as also see KINETIC block: dependent variable: is a STATE variable reaction rates voltage sensitive KINETIC block STATE-dependent, and instability also see kinetic scheme: reaction rates also see Crank-Nicholson method: local error: kinetic scheme, BREAKPOINT block: SOLVE: sparse kinetic scheme compartment size also see scale factor, NMODL: units conversion factor, KINETIC block: COMPARTMENT conservation rules also see material: conservation, KINETIC block: CONSERVE equivalent differential equations initialization--see initialization: channel model: kinetic scheme, initialization: strategies: changing a state variable, initialization: strategies: changing model parameters, KINETIC block: CONSERVE: when is it required for initialization? reactants--see KINETIC block: reactants reaction rates voltage sensitive also see KINETIC block kinetic states initialization--see initialization: channel model: kinetic scheme, initialization: strategies: changing a state variable, initialization: strategies: changing model parameters, KINETIC block: CONSERVE: when is it required for initialization? Kirchhoff's current law also see charge: conservation, equation: current balance ko default concentration also see ion mechanism: default concentration: specification in hoc ko0_k_ion--see ko: default concentration, ion mechanism: default concentration: specification in hoc LLLL L << code >> calculation from 3-D data--see 3-D specification of geometry: calculation of L, diam, area, and ri change flag default value specifying stylized specification ?? 3-D specification--see 3-D specification of geometry: calculation of L, diam, area, and ri updating from 3-D data also see length lambda_f() leak current also see pas mechanism leak.mod--see Example 9.1: a passive "leak" current legacy code--see troubleshooting: legacy code length arc--see range also see L length constant AC DC also see d_lambda less than operator--see hoc syntax: expressions: operators less than or equal to operator--see hoc syntax: expressions: operators library of mechanisms--see mechanisms: library linear algebra LINEAR block dependent variable is a STATE variable linear circuit also see system equations: matrix form: linear circuit computational efficiency initialization--see initialization: linear circuit under CVODE linear circuit method--see LinearCircuitBuilder LinearCircuitBuilder for gap junctions linearity also see channel: linear, channel: gating model: HH-type linear taper--see range variable: linear taper, diam: caution when specifying linear taper LinearMechanism class list of objects--see List class of sections--see SectionList class List class append() count() iteration object stack object() remove() remove_all() List object managing network cells with managing network connections with also see NetCon load_file() also 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 variable also see object: public members: vs. private members, template: writing a template: public local absolute error--see absolute error: local local error--see numerical error: local local relative error--see relative error: local local time step--see numeric integration: adaptive: local time step LOCAL variable declared outside an equation block initial value scope and persistence also see NEURON block: GLOBAL declared within an equation block scope and persistence local variable--see hoc syntax: names, funcs and procs: local variable, LOCAL variable also see object: public members: vs. private members, template: writing a template: public logical comparison of real values--see hoc syntax: float_epsilon logical comparison operators--see hoc syntax: expressions: operators logical expressions--see hoc syntax: expressions: logical expressions logical operators--see hoc syntax: expressions: operators LONGITUDINAL_DIFFUSION--see KINETIC block: LONGITUDINAL_DIFFUSION longitudinal diffusion--see diffusion: longitudinal, KINETIC block: LONGITUDINAL_DIFFUSION lookup table ?? also see table lookup ?? loop statement--see NMODL: FROM . . . TO . . . (loop statement) also see hoc syntax: flow control: for, hoc syntax: flow control: while MMMM mapping to the screen--see GUI: screen: mapping to the screen mass balance--see material: conservation also see material material amount concentration conservation density Matrix class mechanisms adding new--see mechanisms: user-defined built-in initialization sequence involving delay--see standard run system: event delivery system: implementing deferred computation library user-defined also see nrniv: adding new mechanisms, NMODL initialization sequence also see distributed mechanism, point process membrane area also see area(), surface area membrane capacitance also see cm, specific membrane capacitance membrane conductance also see sepecific membrane conductance membrane current capacitive also see i_cap density vs. absolute ?? ionic accuracy positive current convention membrane potential initialization also see initialization: v_init, initialization: categories, initialization: strategies isopotential also see current: density: spatial uniformity also see v, membrane state variable membrane resistance membrane state variable--see IntFire1 class: membrane state variable, IntFire2 class: membrane state variable, IntFire4 class: membrane state variable membrane time constant and attenuation of fast signals METHOD--see BREAKPOINT block: SOLVE microelectrode--see electrode MicroEMACS also see em, emacs microstep--see numeric integration: adaptive: advance microstep, numeric integration: adaptive: initialize microstep, numeric integration: adaptive: interpolate microstep miscellaneous_add()--see NEURONMainMenu class: miscellaneous_add() mistake !! programming--see hoc: error handling mknrndll--see NMODL: translator: mknrndll model 3-D also see 3-D specification of geometry ball and stick compartmental computational analysis essential steps implementation conceptual correspondence between conceptual and computatonal also see discrepancy: between conceptual model and compartmental model designing description ?? implementation instrumentation--see instrumentation network--see network model parameters also see instrumentation: model parameters purpose--see judgment, user's intent simulation control--see simulation control stylized also see stylized specification of geometry testing << evaluating >> also see topology: checking MOdel Description Language--see MODL model coordinates--see GUI: model coordinates vs. screen coordinates--see GUI: scene coordinates: vs. screen coordinates model description language--see NMODL modeling empirically-based rationale modeling networks--see Chapter 11: Modeling networks model properties !! specifying also see anatomical properties: specifying, biophysical properties: specifying model specification << noun! >> as virtual experimental preparation vs. user interface--see good programming style: separate model specification from user interface also see model properties: specifying mod file compiling under MSWindows--see NMODL: translator: mknrndll under UNIX/Linux--see NMODL: translator: nrnivmodl also see NMODL modified Euler method also see backward Euler method modifying standard functions and procedures--see standard run library: redefining functions and procedures, standard GUI library: redefining functions and procedures MODL vs. NMODL modlunit also see units: checking modular programming--see good programming style: modular programming modulus operator--see hoc syntax: expressions: operators mole--see units: mole mole equivalents morphometric data--see quantitative morphometric data mouse button--see mouse: events cursor--see focus events Alt, Control, or Shift key--see Graph class: menu_tool() cursor coordinates handling also see Graph class: menu_tool() which view contains the mouse--see Graph class: view_info() movie--see Vector: movie multiplication operator--see hoc syntax: expressions: operators NNNN n3d()--see 3-D specification of geometry: n3d() na_ion--see ion mechanism: automatically created nai default concentration also see ion mechanism: default concentration: specification in hoc nai0_na_ion--see nai: default concentration, ion mechanism: default concentration: specification in hoc nao default concentration also see ion mechanism: default concentration: specification in hoc nao0_na_ion--see nao: default concentration, ion mechanism: default concentration: specification in hoc National Biomedical Simulation Resource project (neural modeling is a synonym for computational modeling?) Nernst 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 << NET_RECEIVE >> arguments are call by reference flag--see event: flag handling abrupt changes and discontinuities INITIAL block also see NetCon: weight vector net_event() net_move() net_send() also see Example 10.3: synapse with exponential decay, Example 10.4: alpha function synapse, Example 10.5: use-dependent synaptic plasticity, Example 10.6: saturating synapses, Example 10.7: IntFire1, a basic integrate and fire model, Example 10.8: IntFire2, firing rate proportional to input, Example 10.9: IntFire4, different synaptic time constants NET_RECEIVE procedure--see NET_RECEIVE block net_send()--see NET_RECEIVE block: net_send() NetCon and standard run system NetCon class << NetCon >> delay event() record() source variable states--see NetCon class: weight vector stream-specificity target threshold weight also see NetCon class: weight vector weight vector initialization NetCon object as a channel for a stream of events initialization--see NET_RECEIVE block: INITIAL block also see List object: managing network connections with netcvode.cpp NetGUI class SpikePlot--see NetWork Builder: buttons: SpikePlot implementation << not in this edition >> also see NetWork Builder NetReadyCellGUI bringing up a NetReadyCellGUI cell names--see NetWork Builder: cells: names changing cell parameters--see NetWork Builder: caveats also see biophysical neuron model NetStim class also see artificial spiking cell NetWork Builder << network >> adjusting model parameters bringing up a NetWork Builder buttons Create Delays--see NetWork Builder: specifying delays and weights Hoc File--see NetWork Builder: exporting reusable code Locate--see NetWork Builder: cells: creating Show Cell Map--see NetWork Builder: cells: Cell Map SpikePlot Src -> Tar--see NetWork Builder: cells: connecting Weights--see NetWork Builder: specifying delays and weights canvas dragging caveats cells Cell Map connecting--see NetWork Builder: setting up network architecture, NetWork Builder: specifying delays and weights creating names also see NetWork Builder: cells: Cell Map types--see NetWork Builder: palette of cell types, ArtCellGUI, NetReadyCellGUI changing a network--see NetWork Builder: caveats changing cell parameters--see NetWork Builder: caveats creating an instance of a network--see NetWork 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 also see NetWork Builder: exporting reusable code exporting reusable code acell_home_ network cell templates network instantiation network specification interface also see NetWork Builder: exploiting reusable code hints network architecture--see NetWork Builder: setting up network architecture palette of cell types plotting spikes--see NetWork Builder: buttons: SpikePlot reusable code--see NetWork Builder: exporting reusable code saving a hoc file--see NetWork Builder: exporting reusable code setting up network architecture specifying delays and weights synaptic delays and weights--see NetWork Builder: specifying delays and weights network model architecture--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 initialization--see initialization: network, NET_RECEIVE block: INITIAL block neurite also see section (neuronal modeling is a synonym for computational modeling?) NEURON << NEURON >> adding new mechanisms--see mechanisms: user-defined, nrniv: adding new mechanisms, NMODL last change date--see NEURON: startup banner starting and exiting starting with a specific hoc file startup banner version number--see NEURON: startup banner also see hoc: starting and exiting NEURON block ARTIFICIAL_CELL also see artificial spiking cell, IntFire1 class, IntFire2 class, IntFire4 class, NetStim class ELECTRODE_CURRENT effect on extracellular mechanism GLOBAL also see global variable, ASSIGNED variable: GLOBAL, PARAMETER variable: is GLOBAL by default NONSPECIFIC_CURRENT equilibrium potential also see active transport: countering pump current with a NONSPECIFIC_CURRENT POINT_PROCESS also see point process POINTER also see POINTER variable RANGE also see range, range variable, ASSIGNED variable: GLOBAL: vs. RANGE, ASSIGNED variable: is a range variable by default, PARAMETER variable: GLOBAL vs. RANGE, STATE variable: is automatically RANGE SUFFIX also see distributed mechanism USEION also see mechanisms: initialization sequence effect on initialization order READ ex (reading an equilibrium potential) READ ix (reading an ionic current) READ xi (reading an intracellular concentration) READ xo (reading an extracellular concentration) WRITE ix (writing an ionic current) WRITE xi (writing an intracellular concentration) WRITE xo (writing an extracellular concentration) NEURON demonstration program--see neurondemo NEURON Main Menu << Main Menu >> adding items--see NEURONMainMenu class: miscellaneous_add() creating NEURON Main Menu GUI File load dll load hoc load session save session working dir recent dir Print Quit Build single compartment Cell Builder also see CellBuilder Linear Circuit NetWork Builder NetWork Cell--see ArtCellGUI Tools adding items--see NEURONMainMenu class: miscellaneous_add() Distributed Mechanisms also see Distributed Mechanism GUI Fitting Impedance Miscellaneous Point Processes also see PointProcessManager, PointProcessGroupManager RunControl VariableStepControl also see VariableTimeStep GUI Graph Voltage axis Current axis State axis Shape plot Phase Plane Grapher Vector Save to File Retrieve from File Gather Values Play Display Draw Window Print & File Window Manager Ungrouped Group Manager NEURON MOdel Description Language--see NMODL NEURON program group NEURONMainMenu class miscellaneous_add() NEURONMainMenu object is always NEURONMainMenu[0] NEURON's interpreter--see hoc neuron.exe also see nrniv.exe neurondemo NEURONMainMenu miscellaneous_add() new--see object: new, object: creating NMODL << NMODL >> abrupt change of a variable--see variable: abrupt change of, NET_RECEIVE block: handling abrupt changes and discontinuities arrays are not dynamic index starts at 0 STATE variable--see STATE variable: array in NMODL COMMENT . . . ENDCOMMENT--see NMODL: comments comments declaring variables also see NMODL: named blocks: variable declaration, ASSIGNED block, CONSTANT block, PARAMETER block, STATE block, LOCAL variable, NMODL: DEFINE specifying units DEFINE dt--see dt: use in NMODL FROM . . . TO . . . (loop statement) function--see FUNCTION block FUNCTION_TABLE loop statement--see NMODL: FROM . . . TO . . . (loop statement) mknrndll--see NMODL: translator: mknrndll named blocks ASSIGNED--see ASSIGNED block BREAKPOINT--see BREAKPOINT block CONSTANT--see CONSTANT block DERIVATIVE--see DERIVATIVE block FUNCTION--see FUNCTION block INITIAL--see INITIAL block KINETIC--see KINETIC block NEURON--see NEURON block NONLINEAR--see NONLINEAR block PARAMETER--see PARAMETER block PROCEDURE--see PROCEDURE block equation definition also see BREAKPOINT block, DERIVATIVE block, FUNCTION block, INITIAL block, KINETIC block, PROCEDURE block general form variable declaration also see ASSIGNED block, PARAMETER block, STATE block, LOCAL variable nocmodl--see NMODL: translator: nocmodl nrnivmodl--see NMODL: translator: nrnivmodl procedure--see PROCEDURE block t--see t: use in NMODL translator mknrndll also see nrnmech.dll, NMODL: translator: nrnivmodl nmodl nocmodl nocmodl.exe nrnivmodl also see NMODL: translator: mknrndll units conversion factor parentheses also see UNITS block: units scaling, scale factor user-defined variable VERBATIM . . . ENDVERBATIM vs. MODL--see MODL: vs. NMODL also see mod file nmodl--see NMODL: translator: nmodl nocmodl--see NMODL: translator: nocmodl nocmodl.exe--see NMODL: translator: nocmodl.exe node circuit--see circuit: node equation--see equation: current balance, Kirchhoff's current law section--see section: nodes "nonbiological" model--see artificial spiking cell, integrate and fire NONLINEAR block dependent variable is a STATE variable nonlinearity--see system: nonlinear, channel: nonlinear noninteractive simulations--see GUI: vs. hoc NONSPECIFIC_CURRENT--see NEURON block: NONSPECIFIC_CURRENT normalized distance along a section--see range NOT operator--see hoc syntax: expressions: operators notation chemical reaction--see kinetic scheme circuit--see circuit nrngui loads GUI and standard run library also see NEURON: starting and exiting nrniv adding new mechanisms also see mechanisms: user-defined, NMODL also see nrngui, NEURON: starting and exiting nrniv.exe also see nrniv, neuron.exe nrnivmodl--see NMODL: translator: nrnivmodl nrnmech.dll also see mknrndll nrnunits.lib also see units: database nseg << code >> effect on spatial accuracy and resolution effect on range variable--see range variable: effect of changing nseg, range variable: inhomogeneous: reassert after changing nseg repositions internally attached sections and point processes vs. number of 3-D points why triple nseg? why use odd values? also see spatial grid, discretization, segment nstep_steprun--see standard run system: setdt(), RunControl GUI: Points plotted/ms NULLobject--see object: NULLobject numarg()--see funcs and procs: arguments: numarg() numeric integration << numeric >> accuracy--see accuracy, numeric integration: order of accuracy adaptive also see CVODE, CVODES, DASPK, IDA, SUNDIALS, standard run system: fadvance(): global time step integration, standard run system: fadvance(): local time step integration advance microstep and events--see event: times: with adaptive integration, standard run system: event delivery system: adaptive integration and, standard run system: fadvance(): global time step integration, standard run system: fadvance(): local time step integration and the standard run system--see standard run system: event delivery system: adaptive integration and, standard run system: fadvance(): global time step integration, standard run system: fadvance(): local time step integration error control--see numerical error: control global time step also see standard run system: fadvance(): global time step integration, VariableTimeStep GUI--global vs. local time steps global variable time step--see numeric integration: adaptive: global time step GUI control--see VariableTimeStep GUI initialization also see CVode class: re_init(), initialization initialize microstep interpolate microstep interpolation formulas local time step also see standard run system: fadvance(): local time step integration, standard run system: event time queue, standard run system: cell time queue, CVode class: record(), VariableTimeStep GUI--global vs. local time steps local variable time step--see numeric integration: adaptive: local time step microstep--see numeric integration: adaptive: advance microstep, numeric integration: adaptive: initialize microstep, numeric integration: adaptive: interpolate microstep switching to fixed time step toggling ON and OFF--see VariableTimeStep GUI--toggling adaptive integration ON and OFF with discrete events--see standard run system: event delivery system: adaptive integration and, standard run system: fadvance(): global time step integration, standard run system: fadvance(): local time step integration, event: times: with adaptive integration analytic integration of channel states central difference method--see Crank-Nicholson method error--see accuracy, numerical error, numeric integration: order of accuracy explicit also see forward Euler method fixed time step also see backward Euler method, forward Euler method, Crank-Nicholson method, standard run system: fadvance(): fixed time step event aggregation to time step boundaries also see event: times: with adaptive integration initialization also see initialization switching to adaptive implicit also see backward Euler method, Crank-Nicholson method initialization--see numeric integration: adaptive: initialization, numeric integration: fixed time step: initialization, initialization instability also see numeric integration: stability iteration of nonlinear equations NEURON's default method--see backward Euler method order of accuracy << accuracy precision >> first also see backward Euler method, forward Euler method second also see Crank-Nicholson method, spatial accuracy: second order variable also see numeric integration: adaptive, CVODE, DASPK precision--see numeric integration: order of accuracy stability also see numeric integration: instability, system: stiff, backward Euler method, forward Euler method, Crank-Nicholson method effect of signal sources also see system equations: effect of signal sources summary numeric solution numerical error !! << numerical error >> also see parameters: sensitivity to, accuracy: physiological, accuracy: qualitative absolute--see absolute error caused by changing nseg--see nseg: repositions internally attached sections and point processes chaotic system control also see absolute error: local: tolerance, relative error: local: tolerance criterion--see absolute error: local: tolerance, relative error: local: tolerance cumulative--see numerical error: global global integrated also see numerical error: global local also see absolute error: local, relative error: local message--see error message, hoc: error handling oscillations programming--see hoc: error handling relative--see relative error roundoff spatial also see spatial accuracy temporal effect of spatial discretization also see temporal accuracy tolerance--see absolute error: local: tolerance, relative error: local: tolerance total--see numerical error: global numerical oscillations--see numerical error: oscillations, numeric integration: instability Nyquist sampling theorem OOOO object << object >> array as an argument--see funcs and procs: arguments: object calling a method--see object: public members: accessing from hoc collection--see object: array, List class creating destroying dot notation--see object: public members: dot notation incorporating into plotting system--see standard run system: plotting system: incorporating Graphs and objects initializing variables--see template: variable initialization list--see List class methods calling--see object: public members: accessing from hoc name how generated vs. object reference new NULLobject using the NULLobject notifying at every step--see standard run system: plotting system: notifying Graphs and objects objref--see object reference: objref passing to a func or proc--see funcs and procs: arguments: object private vs. public--see object: public members: vs. private members, template: writing a template: public public members accessing from hoc dot notation vs. private members also see template: writing a template: public reference--see object reference, object: reference count reference count set--see object: array, List class specifying attributes--see template: writing, object: public members: dot notation stack--see List class: object stack state this--see object reference: this vs. class vs. object reference also see object reference, class, template, object-oriented programming polymorphism object name--see object: name object name vs. object reference--see object reference: vs. object name object reference as an argument--see funcs and procs: arguments: objref cannot be redefined as scalar, double, or string count--see object: reference count declaring objectvar also see object reference: cannot redefine as scalar, double, or string objref also see object reference: cannot redefine as scalar, double, or string passing to a func or proc--see funcs and procs: arguments: objref points to an object this vs. object vs. object name object variable--see object reference: objectvar object_pop()--see session file: object_pop() object_push()--see session file: object_push() object-oriented programming class wrapper ?? encapsulating code information hiding inheritance also see class: base class, class: subclass polymorphism also see class: base class, class: subclass also see object, object reference, class, template, object-oriented programming objectvar--see object reference: objectvar objref--see object reference: objref oc also see nrniv ocbox_--see session file: ocbox_ Ohm's law online Programmer's Reference--see Programmer's Reference operators--see hoc syntax: expressions: operators operator precedence--see hoc syntax: expressions: operators OR operator--see hoc syntax: expressions: operators oscillations--see numerical error: oscillations oscillating system--see initialization: categories: to a desired state oscilloscope optimization ordinary differential equation--see equation: differential: ordinary oxymoron PPPP panel--see xpanel() PARAMETER block assigning default PARAMETER values default value of state0 also see STATE variable: state0, STATE block: START specifying minimum and maximum limits PARAMETER panel--see Distributed Mechanism GUI: Viewer: Shape Name PARAMETER variable also see ASSIGNED variable, STATE variable, ion_style() abrupt change of--see variable: abrupt change of, NetCon class: event(), NET_RECEIVE block: handling abrupt changes and discontinuities default value--see PARAMETER block: assigning default PARAMETER values GLOBAL vs. RANGE also see NEURON block: RANGE is global by default also see NEURON block: GLOBAL RANGE specifying minimum and maximum limits--see PARAMETER block: specifying minimum and maximum limits time-dependent visibility at the hoc level when to use for an equilibrium potential parameters also see PARAMETER variable adjusting biophysical geometric sensitivity to parent section--see section: parent parentheses--see NMODL: variable declaration: specification of units, NMODL: units conversion factor: parentheses, UNITS block: units scaling parse errors--see hoc: error handling partial differential equation--see equation: differential: partial pas mechanism e_pas g_pas i_pas passing an object as an argument--see funcs and procs: arguments: object passing an objref as an argument--see funcs and procs: arguments: objref passive cylindrical cable--see cable: passive cylindrical passive leak current--see Example 9.1: a passive "leak" current permeability also see calcium: permeability PFWM creating is implemented in C saving and retrieving session files--see session file: saving: from PFWM, session file: loading: from PFWM PFWM GUI Print To Printer PostScript PS snapshot Idraw Ascii Select Printer Window Titles Printed Window Decorations Printed Land/Port Session Retrieve Save selected Save all VirtualScreen move page layout area resize select virtual screen physical distance--see distance physical system representing by a model physiological ????? standalone or paired with something else or below something else? physiological accuracy--see accuracy: physiological piecewise linear approximation--see range variable: estimating by linear interpolation between nodes piecewise linear function--see function: piecewise linear Pike, R.--see hoc: Kernighan and Pike plain text file plasticity synaptic--see synaptic plasticity Plot what? GUI creating--see Graph GUI: primary menu: Plot what? Plot()--see standard run system: Plot() plot lists--see standard run system: plotting system: fast_flush_list, standard run system: plotting system: flush_list, standard run system: plotting system: graphLists PlotShape plotting spike trains--see spike trains: recording and plotting, NetWork Builder: buttons: SpikePlot plotting system--see standard run system: plotting system point process adding new--see mechanisms: user-defined, NMODL attaching--see point process: inserting changing location with hoc code--see point process: loc() creating destroying effect of nseg on location inserting loc() preserving spatial accuracy specifying attributes vs. distributed mechanism also see PointProcess, NEURON block: POINT_PROCESS, artificial spiking cell, NEURON block: ARTIFICIAL_CELL POINTER--see POINTER variable, NEURON block: POINTER, setpointer pointer--see hoc syntax: pointer operator, NEURON block: POINTER, POINTER variable POINTER variable effect on Jacobian--see Jacobian: approximate also see NEURON block: POINTER, setpointer, variable: local vs. nonlocal Pointer class pointer operator--see hoc syntax: pointer operator PointProcess PointProcessGroupManager bringing up a PointProcessGroupManager PointProcessManager configuring as AlphaSynapse also see PointProcessManager GUI: SelectPointProcess creating location changing also see PointProcessManager GUI: Show: Shape parameters also see PointProcessManager GUI: Show: Parameters PointProcessManager GUI SelectPointProcess AlphaSynapse Show Shape Parameters Points plotted/ms--see RunControl GUI: Points plotted/ms polymorphism--see object-oriented programming: polymorphism potassium concentration also see ki, ko conductance current also see ik potential action--see action potential, spike command--see voltage clamp: command potential reversal--see synapse: conductance-change: reversal potential, equilibrium potential also see membrane potential, voltage precedence of operations--see hoc syntax: expressions: operators precision and judgment prediction print--see hoc syntax: basic input and output: print Print & File Window Manager--see PFWM printf()--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 procs PROCEDURE also see BREAKPOINT block: and PROCEDUREs calling from hoc--see hoc: calling an NMODL FUNCTION or PROCEDURE PROCEDURE block arguments are call by value procedure--see funcs and procs, PROCEDURE Programmer's Reference programming--see hoc good practices--see good programming style mistake--see hoc: error handling program organization--see good programming style: program organization project management also see good programming style proper initialization--see initialization: criterion for proper initialization psection() << code >> pt3d--see 3-D specification of geometry pt3d data--see 3-D specification of geometry: 3-D information pt3d list--see 3-D specification of geometry: 3-D information pt3dadd()--see 3-D specification of geometry: pt3dadd() pt3dclear()--see 3-D specification of geometry: pt3dclear() public--see object: public members, template: writing a template: public pump calcium--see calcium: pump also see active transport purpose of computing--see insight purpose of the model--see user's intent push_section() << code >> QQQQ qualitative results also see accuracy, judgment quantitative morphometric data also see 3-D specification of geometry bad diameter values--see diameter: zero or narrow diameter queue cell time--see standard run system: event delivery system: cell time queue event time--see standard run system: event delivery system: event time queue Quiet--see RunControl GUI: Quiet quit()--see hoc syntax: flow control: quit() quitting NEURON--see NEURON: exiting, hoc syntax: flow control: quit() RRRR Ra << code >> default value also see cytoplasmic resistivity, Distributed Mechanism GUI: globalRa radial diffusion--see diffusion: radial ramp clamp--see voltage clamp: ramp clamp Random class play() initialization--see initialization: Random.play() random number generator initialization--see initialization: random number generator RANGE--see NEURON block: RANGE, range, range variable range RANGE variable--see range variable, ASSIGNED variable: is a range variable by default, PARAMETER variable: RANGE, STATE variable: is automatically RANGE range variable dot notation--see section: currently accessed: dot notation effect of changing nseg estimating by linear interpolation between nodes inhomogeneous reassert after changing nseg in which section?--see section: currently accessed iterating over nodes also see for(x) linear taper linear variation along a section--see range variable: linear taper rangevar(x) returns value at nearest internal node also see range, NEURON block: RANGE, ASSIGNED variable: is a range variable by default, PARAMETER variable: RANGE, STATE variable: is automatically RANGE raster plot--see spike trains: recording and plotting, NetWork Builder: buttons: SpikePlot rate constant rate functions--see BREAKPOINT block: and rate functions, KINETIC block: reaction rates: voltage sensitive re_init()--see CVode class: re_init() reactants--see KINETIC block: reactants reaction--see kinetic scheme chemical--see kinetic scheme rates--see KINETIC block: reaction rates reactants--see KINETIC block: reactants scheme--see kinetic scheme, KINETIC block statement--see KINETIC block: reaction statement also see KINETIC block: <-> (reaction indicator) READ--see NEURON block: USEION read()--see hoc syntax: basic input and output: read() reading an ion concentration--see NEURON block: USEION reading and writing files--see hoc syntax: basic input and output, File class real model neuron--see oxymoron realtime--see standard run system: realtime recording--see CVode class: record(), Vector class: record() recording spike trains--see NetCon class: record(), spike trains: recording and plotting, NetWork Builder: buttons: SpikePlot recursion--see funcs and procs: recursion redefining standard functions and procedures--see standard run library: redefining functions and procedures, standard GUI library: redefining functions and procedures reference count--see object: reference count refractory period--see IntFire1 class: refractory period relative error also see absolute error local also see absolute error: local, numerical error: local tolerance relative local error--see relative error: local relative tolerance--see relative error: local: tolerance remainder operator--see hoc syntax: expressions: operators resistance axial--see axial resistance also see cytoplasmic resistivity, Ra electrode--see electrode: resistance compensation--see electrode: resistance: compensation resistivity--see cytoplasmic resistivity, Ra resistor--see circuit: element: resistor restore()--see SaveState class: restore() restricted diffusion--see Example 9.6: extracellular potassium accumulation return--see hoc syntax: flow control: return also see funcs and procs: return returned value--see funcs and procs: return reusable code--see good programming style: exploiting reusable code reversal potential--see synapse: conductance-change: reversal potential, equilibrium potential, AlphaSynapse: e, ExpSyn: e, Exp2Syn: e ri also see axial resistance calculation of--see stylized specification of geometry: calculation of area and ri, 3-D specification of geometry: calculation of L, diam, area, and ri effect of creating a Shape--see Shape object: creating: effect on diam, area, and ri effect of define_shape()--see define_shape(): effect on diam, area, and ri infinite also see diameter: zero or narrow diameter rise time Rm--see specific membrane resistance root section--see section: root section ropen()--see hoc syntax: basic input and output: ropen() roundoff error--see numerical error: roundoff run control--see RunControl GUI, simulation control, standard run system run time also see RunControl GUI: Real Time, standard run system: realtime, initialization: startsw() run time system--see standard run system run-time errors--see hoc: error handling run()--see standard run system: run() RunControl creating RunControl GUI Continue for also see standard run system: continuerun() Continue til also see standard run system: continuerun() Init Init & Run also see standard run system: run() Points plotted/ms also see standard run system: setdt(), standard run system: step() Quiet also see standard run system: stdrun_quiet Real Time also see standard run system: continuerun(), standard run system: realtime Stop also see standard run system: stoprun Single Step also see standard run system: step Tstop also see standard run system: tstop dt also see RunControlGUI: Points plotted/ms, standard run system: setdt() t Runge-Kutta method stability running a simulation runtime error--see hoc: error handling system--see standard run system also see run time SSSS sacred runes--see equation: sacred runes sampling theorem--see Nyquist sampling theorem SaveState class fread() fwrite() restore() save() also see initialization: categories: to a desired state scalar--see hoc syntax: variables: scalars scale factor also see NMODL: units conversion factor, UNITS block: units scaling scene--see GUI: scene scene coordinates--see GUI: scene coordinates scene coordinates vs. screen coordinates--see GUI: scene coordinates: vs. screen coordinates screen--see GUI: screen screen coordinates--see GUI: screen coordinates screen coordinates vs. scene coordinates--see GUI: scene coordinates: vs. screen coordinates SCoP scope--see hoc: names, funcs and procs: local variable, LOCAL variable, ASSIGNED variable: GLOBAL, NEURON block: GLOBAL, PARAMETER variable: is GLOBAL by default also see template: writing a template: external, template: writing a template: private, object: public members sealed end--see boundary conditions: sealed end SEClamp preserving spatial accuracy--see point process: preserving spatial accuracy series resistance also see voltage clamp SEClamp class secname() second messenger--see Example 10.5: use-dependent synaptic plasticity also see calcium secondorder also see Crank-Nicholson method, backward Euler method section << section >> access--see access, section: currently accessed arc length--see range area--see area() array as argument or variable--see SectionRef class attaching--see connect child connect 0 end to parent connecting--see connect creating--see create currently accessed default section dot notation section stack daughter--see section: child default section !! vs. root section--see section: root section: vs. default section also see section: currently accessed: default default parameter values--see cm, diam, L, Ra detaching--see disconnect() diam--see diam diameter--see diameter, diam, 3-D specification of geometry: diam3d() disconnecting--see disconnect() equivalent circuit iterating over sections also see forall, forsec, ifsec L--see L length--see L nodes internal vs. terminal iterating over--see for (x), range variable: iterating over nodes locations also see nseg: even vs. odd zero area normalized distance along a section--see range nseg--see nseg orientation parent properties !! specifying--see section: currently accessed, 3-D specification of geometry, stylized specification of geometry, biophysical properties: specifying Ra--see Ra root section is 3-D origin of cell vs. default section sets--see SectionList class specifying properties--see section: currently accessed, 3-D specification of geometry, stylized specification of geometry, biophysical properties: specifying stack--see section: currently accessed: section stack variable--see section variable section stack--see section: currently accessed: section stack section variable also see L, nseg, Ra section.h SectionList class append() SectionRef class segment diameter--see diam surface area--see area() also see compartment, nseg, section: nodes self-event--see event: self-event sensitivity--see parameters: sensitivity to separating biology from numerical issues also see section, range, range variable ses file--see session file session file loading from NEURON Main Menu from PFWM ocbox_ also see VBox class: map() object_pop() object_push() saving from NEURON Main Menu from PFWM set of numbers--see hoc syntax: double, Vector class of objects--see object: array, List class of sections--see SectionList class, CellBuilder GUI: Subsets page setdata_--see hoc: calling an NMODL FUNCTION or PROCEDURE: specifying proper instance with setdata_ setdt()--see standard run system: setdt() setpointer also see POINTER variable: setpointer sets of sections--see SectionList class Shape class Shape object creating effect on diam, area, and ri shape plot Shape plot << is spawned from Main Menu >> creating effect on diam, area, and ri Shape plot GUI primary menu 3D Rotate Section Shape Style Show Diam Centroid Schematic Shape Plot Space Plot also see Space Plot Time Plot Plot what? Shape Plot << a false color plot mapped onto a Shape >> shared object--see NMODL: translator: nrnivmodl, nrniv shell Shift key--see Graph class: menu_tool() shunt.mod--see Example 9.2: a localized shunt sign convention--see circuit: positive current convention, membrane current: positive current convention signal chemical electrical signal monitors vs. signal sources signal sources effect on system equations--see system equations: effect of signal sources, numeric integration: stability: effect of signal sources load--see system equations: effect of signal sources, numeric integration: stability: effect of signal sources also see distributed mechanism, point process simplification Simulation Control Program--see SCoP simulation continuous system ?? control--see simulation control event-driven--see discrete event simulation interactive vs. noninteractive--see GUI: vs. hoc time--see t, elapsed simulation time simulation control initialization--see initialization running starting stopping also see standard run system, good programming style: modular programming, good programming style: program organization simulation environment utility of sink reaction--see KINETIC block: -> (sink reaction indicator) size--see compartment: size, discretization, nseg slope conductance--see conductance: slope sodium concentration also see nai, nao conductance current also see ina solution analytic--see analytic solution computational--see numeric solution numeric--see numeric solution SOLVE--see BREAKPOINT block: SOLVE, INITIAL block: SOLVE: STEADYSTATE sparse solve.c source current--see current: source, circuit: element: current source signal--see signal sources space space constant--see %lambda, length constant, d_lambda space plot Space Plot creating Space Plot GUI primary menu -- is this needed?? does anything go here??? sparse--see KINETIC block, BREAKPOINT block: SOLVE: sparse, INITIAL block: SOLVE: STEADYSTATE sparse spatial accuracy checking second order preserving also see discretization: spatial, nseg: effect on spatial accuracy and resolution spatial decay of fast signals spatial discretization--see discretization: spatial, spatial grid spatial error--see numerical error: spatial, spatial accuracy spatial frequency--see frequency: spatial spatial grid also see discretization: spatial choosing--see discretization: guidelines, d_lambda rule, d_X rule, CellBuilder GUI: Geometry page: specifying strategy spatial resolution--see discretization: spatial, numerical error: spatial, spatial accuracy, spatial grid special--see NMODL: translator: nrnivmodl, nrniv specific membrane capacitance also see cm specific membrane conductance also see membrane conductance specific membrane resistance also see specific membrane conductance specifying geometry--see 3-D specification of geometry, stylized specification of geometry also see geometry, anatomical properties specifying model properties--see model properties: specifying specifying object attributes--see template: writing, object: public members: dot notation specifying section properties--see section: currently accessed, 3-D specification of geometry, stylized specification of geometry, 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: specifying speed--see computational efficiency speed vs. accuracy--see accuracy: vs. speed spike also see action potential spike event--see event: external spike trains recording and plotting also see NetCon class: record(), NetWork Builder: buttons: SpikePlot SpikePlot--see NetWork Builder: buttons: SpikePlot spine sprint()--see hoc syntax: basic input and output: sprint() squid axon also see hh mechanism stability--see numeric integration: stability stack of objects--see List class: object stack staggered time steps--see Crank-Nicholson method: staggered time steps standard GUI library << GUI library >> changing functions and procedures--see standard GUI library: redefining functions and procedures hoc source accompanies NEURON loading--see nrngui, hoc: idiom: load_file("nrngui.hoc") not loading--see nrniv redefining functions and procedures also see stdgui.hoc standard run library changing functions and procedures--see standard run library: redefining functions and procedures hoc source accompanies NEURON redefining functions and procedures standard run system << standard run >> addplot() addvar() advance() continuerun() discrete events--see standard run system: fadvance(): global time step integration, standard run system: fadvance(): local time step integration doEvents() event delivery system adaptive integration and and models with discontinuities--see variable: abrupt change of, event: times cell time queue also see numeric integration: adaptive: local time step, standard run system: fadvance(): global time step integration, standard run system: fadvance(): local time step integration event time queue also see numeric integration: adaptive: local time step, standard run system: fadvance(): global time step integration, standard run system: fadvance(): local time step integration event times--see event: times, standard run system: event time queue external event--see event: external implementing deferred computation also see event: self-event initialization input event--see event: external self-event--see event: self-event also see event, standard run system: fadvance(): global time step integration, standard run system: fadvance(): local time step integration fadvance() discrete events--see standard run system: fadvance(): global time step integration, standard run system: fadvance(): local time step integration fixed time step global time step integration local time step integration fast_flushPlot() fcurrent() in initialization finitialize()--see initialization: finitialize() flushPlot() graph lists--see standard run system: plotting system: graphLists Graphs and objects ! incorporating--see standard run system: plotting system: incorporating Graphs and objects notifying--see standard run system: plotting system: notifying Graphs and objects init()--see initialization: init() initialization--see initialization initialize--see initialization, numeric integration: adaptive: initialize microstep also see standard run system: fadvance(): local time step integration() initPlot()--see initialization: initPlot() is implemented in hoc NetCon--see NetCon: and standard run system nstep_steprun--see standard run system: setdt(), RunControl GUI: Points plotted/ms Plot() also see standard run system: step plot 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 fast_flush_list flush_list graphLists incorporating Graphs and objects also see standard run system: plotting system: graphLists, standard run system: addplot() notifying Graphs and objects also see standard run system: plotting system: graphLists special uses realtime run() setdt() stdinit()--see initialization: stdinit() stdrun_quiet step also see standard run system: step() step() under CVODE also see standard run system: step steprun() steps_per_ms--see standard run system: setdt(), standard run system: step, RunControl GUI: Points plotted/ms stoprun tstop also see RunControl GUI, standard run library START see STATE block: START, STATE variable: initialization starting hoc--see hoc: starting and exiting, NEURON: starting and exiting starting NEURON--see NEURON: starting and exiting, hoc: starting and exiting startsw()--see initialization: startsw() state as amount of material as concentration as density as probability restoring--see SaveState class: restore(), initialization: categories: to a desired state saving--see SaveState class: save() STATE block << STATE >> also see ASSIGNED block, PARAMETER block specifying local absolute error tolerance START also see STATE variable: initialization, PARAMETER block: default value of state0 STATE panel--see Distributed Mechanism GUI: Viewer: Shape Name STATE variable also see ASSIGNED variable, PARAMETER variable, ion_style(), state variable abrupt change of--see variable: abrupt change of, NetCon class: event(), NET_RECEIVE block: handling abrupt changes and discontinuities array in NMODL and COMPARTMENT statement--see KINETIC block: COMPARTMENT conservation--see KINETIC block: CONSERVE initialization default vs. explicit state0 also see PARAMETER block: default value of state0, STATE block: START also see initialization, KINETIC block: CONSERVE ion concentration as is automatically RANGE also see NEURON block: RANGE specifying local absolute error tolerance--see STATE block: specifying local absolute error tolerance vs. state variable state variable as an ASSIGNED variable changing after finitialize()--see initialization: strategies: changing a state variable custom initialization--see initialization: strategies: changing a state variable initialization--see STATE variable: initialization, initialization of a mechanism vs. state variable of a model vs. STATE variable--see STATE variable: vs. state variable state_discontinuity()--see CVODE: and model descriptions: state_discontinuity(), variable: abrupt change of, NET_RECEIVE block: state_discontinuity() state0--see STATE variable: initialization, INITIAL block stdgui.hoc also see standard GUI library stdinit()--see initialization: stdinit() stdlib.hoc also see standard run system stdrun.hoc also see standard run system, standard run library stdrun_quiet--see standard run system: stdrun_quiet steady state also see initialization: steady state, initialization: non-steady state, equilibrium ?? initialization of complex kinetic schemes--see initialization: strategies: steady state initialization of complex kinetic schemes, INITIAL block: SOLVE: STEADYSTATE sparse STEADYSTATE--see INITIAL block: SOLVE: STEADYSTATE sparse, initialization step--see standard run system: step step()--see standard run system: step() steprun()--see standard run system: steprun() stiffness--see system: stiff stoichiometry stop--see hoc syntax: flow control: stop stopping hoc--see hoc: interrupting execution, hoc: starting and exiting stopping NEURON--see NEURON: starting and exiting, hoc: interrupting execution stoprun--see standard run system: stoprun storage oscilloscope strange shapes--see stylilzed specification of geometry: strange shapes ?? strdef--see hoc syntax: variables: strdef stream !! of events--see event: stream of values--see Vector class: play() time--see numeric integration: local time step String class string--see hoc syntax: variables: strdef stylized model--see model: stylized, stylized specification of geometry stylized specification of geometry also see 3-D specification of geometry calculation of area and ri diam--see diam L--see L reinterpretation as 3-D specification strange shapes subclass--see class: subclass, object-oriented programming: polymorphism, object-oriented programming: inheritance subtraction operator--see hoc syntax: expressions: operators SUFFIX--see NEURON block: SUFFIX SUNDIALS also see CVODES, IDA surface area also see area(), membrane area synapse << synapse >> alpha function--see AlphaSynapse, Exp2Syn, Example 10.4: alpha function synapse AMPAergic--see Example 10.3: synapse with exponential decay also see Example 10.6: saturating synapses as instrumentation conductance-change alpha function--see AlphaSynapse, Exp2Syn, Example 10.4: alpha function synapse conductance exponentially decaying--see ExpSyn, Example 10.3: synapse with exponential decay reversal potential also see Example 10.5: use-dependent synaptic plasticity, Example 10.6: saturating synapses electrical also see synapse: ephaptic, gap junction ephaptic also see synapse: electrical, gap junction graded--see synaptic transmission: graded plasticity--see synaptic plasticity saturating--see Example 10.6: saturating synapses strength--see NetCon class: weight, NetCon class: weight vector weight--see NetCon class: weight, NetCon class: weight vector also see AlphaSynapse, ExpSyn, Exp2Syn synaptic connection--see NetCon class synaptic convergence--see convergence also see synaptic transmission: spike-triggered synaptic delay--see NetCon class: delay synaptic divergence--see divergence also see synaptic transmission: spike-triggered synaptic latency--see NetCon class: delay synaptic plasticity stream-specific--see Example 10.5: use-dependent synaptic plasticity, Example 10.6: saturating synapses synaptic strength--see NetCon class: weight, NetCon class: weight vector synaptic transmission delay--see NetCon class: delay graded conceptual model implementation in NMODL also see Example 10.1: graded synaptic transmission latency--see NetCon class: delay saturating--see Example 10.6: saturating synapses spike-triggered computational efficiency in NEURON conceptual model event-based implementation also see NetCon class, NET_RECEIVE block, event: external, event: self-event, Example 10.3: synapse with exponential decay, Example 10.4: alpha function synapse, Example 10.5: use-dependent synaptic plasticity, Example 10.6: saturating synapses weight--see NetCon class: weight, NetCon class: weight vector also see gap junction synaptic weight--see NetCon class: weight, NetCon class: weight vector syntax--see hoc syntax, NMODL also see Programmer's Reference syntax error--see hoc: error handling system chaotic--see initialization: categories: to a desired state continuous piecewise linear approximation--see range variable: estimating by linear interpolation between nodes discrete discretized also see discretization electrical ?? linear nonlinear oscillating--see initialization: categories: to a desired state stiff also see numeric integration: stability system equations also see eigenfunction, eigenvalue, eigenvector matrix form extracellular field linear circuit also see equation: algebraic effect of signal sources also see numeric integration: stability: effect of signal sources stiff--see system: stiff TTTT t as an ASSIGNED variable--see ASSIGNED variable: v, celsius, t, dt, diam, and area also see t: use in NMODL initialization--see initialization: t the independent variable in NEURON use in NMODL also see time table !! function--see function table lookup--see function table table_--see NMODL: FUNCTION_TABLE tapering--see diam: tapering, range variable: linear taper Taylor's series temperature--see celsius template cannot be redefined direct commands names cannot redefine hoc keywords this--see object reference: this variable initialization default initialization init() procedure visibility--see template: writing a template: public, object: public members writing a template begintemplate endtemplate external public also see object: public members also see class, object, object-oriented programming temporal accuracy checking empty also see discretization: temporal temporal discretization--see discretization: temporal temporal frequency--see frequency: temporal temporal resolution--see temporal accuracy, discretization: temporal testing and revision--see good programming style: testing and revision this--see object reference: this three dimensional specification--see 3-D specification of geometry threshold ?? tilde--see KINETIC block: ~ (tilde) time current rise--see rise time also see t time constant also see membrane time constant time-dependent variable--see variable: time-dependent, Vector class: play() time step and stability--see numeric integration: stability, backward Euler method, forward Euler method, Crank-Nicholson method choosing current--see time: current fixed--see numeric integration: fixed time step also see dt, %DELTA t, discretization: temporal, numeric integration: adaptive time stream--see numeric integration: local time step tolerance error--see absolute error: local: tolerance, relative error: local: tolerance top level of the interpreter--see hoc: top level of the interpreter topology artifacts ?? checking loops of sections specifying viewing also see branched architecture topology() topology, subsets, geometry, biophysics total ionic current--see membrane current: ionic total error--see numerical error: global transient signals spatial decay--see spatial decay of fast signals transmembrane current--see membrane current treeset.c troubleshooting conflicts between hoc and GUI--see GUI: conflicts with hoc or other GUI tools disappearing section Graphs don't work legacy code no NEURON Main Menu toolbar no default section strange shapes--see stylized specification of geometry: strange shapes TRUE--see hoc syntax: expressions: logical expressions tstop--see standard run system: tstop Tstop--see RunControl GUI: Tstop, standard run system: tstop UUUU unaryminus operator--see hoc syntax: expressions: operators understanding uninsert << code >> UNITS block defining new names units scaling units checking also see modlunit consistency conversion factor--see scale factor, NMODL: units conversion factor, UNITS block: units scaling database also see nrnunits.lib defining new names--see UNITS block: defining new names dimensionless (1) by default disabling checking--see NMODL: UNITSOFF . . . UNITSON e also see e: electronic charge vs. units conversion factor faraday k-mole mole scaling--see UNITS block: units scaling specifying also see NMODL: declaring variables: specifying units units scaling--see UNITS block: units scaling UNITSOFF . . . UNITSON--see NMODL: UNITSOFF . . . UNITSON UNITSON--see NMODL: UNITSOFF . . . UNITSON use-dependent synaptic plasticity--see Example 10.5: use-dependent synaptic plasticity, Example 10.6: saturating synapses USEION--see NEURON block: USEION user-defined mechanisms--see mechanisms: user-defined user interface as virtual experimental rig custom GUI vs. model specification--see good programming practice: separate model specification from user interface user's intent VVVV v as an ASSIGNED variable--see ASSIGNED variable: v, celsius, t, dt, diam, and area is a range variable also see membrane potential v_init--see initialization: v_init variable << variable >> abrupt change of also see CVODE: and model descriptions: at_time(), CVODE: and model descriptions: state_discontinuity(), NetCon class: event(), NET_RECEIVE block: handling abrupt changes and discontinuities ASSIGNED--see ASSIGNED variable changing in mid-run--see variable: abrupt change of, PARAMETER variable: time-dependent CONSTANT--see CONSTANT continuous--see continuous variable declaring in NMODL--see NMODL: declaring variables, NMODL: named blocks: variable declaration, ASSIGNED block, CONSTANT block, PARAMETER block, STATE block, LOCAL variable, NMODL: DEFINE dependent dimensionless--see units: dimensionless extensive global--see global variable independent initializing--see initialization, template: variable initialization intensive LOCAL--see LOCAL variable local vs. nonlocal also see POINTER variable names--see hoc syntax: names object--see object-oriented programming: object reference PARAMETER--see PARAMETER variable POINTER--see POINTER variable range--see range variable scope--see hoc syntax: names, funcs and procs: local variable, global variable, LOCAL variable, ASSIGNED variable: GLOBAL, NEURON block: GLOBAL, PARAMETER variable: is GLOBAL by default section--see section variable state--see state variable state vs. STATE--see STATE variable: vs. state variable STATE--see STATE variable string--see hoc syntax: variables: strdef time-dependent--see PARAMETER variable: time-dependent also see Vector class: play() user-defined in hoc--see hoc: user-defined variable in NMODL--see NMODL: user-defined variable variable browser--see Plot what? GUI variable order integration--see numeric integration: adaptive variable order variable time step integration--see numeric integration: adaptive variable time step method--see numeric integration: adaptive VariableTimeStep GUI bringing up--see NEURON Main Menu: Tools: VariableStepControl Details Local step--see VariableTimeStep GUI: global vs. local time steps global vs. local time steps also see numeric integration: adaptive: global time step, numeric integration: adaptive: local time step toggling adaptive integration ON and OFF Use variable dt checkbox--see VariableTimeStep GUI: toggling adaptive integration ON and OFF VBox VBox class intercept() map() also see session file: ocbox_ mapping to the screen window title ref() save() Vector movie Vector class append() c() fill() mark() play() initialization--see initialization: Vector.play() under adaptive integration under fixed time step integration with interpolation also see variable: time-dependent record() also see CVode class: record() initialization also see initialization: frecord_init() VERBATIM--see NMODL: VERBATIM . . . ENDVERBATIM version number--see NEURON: startup banner vext--see extracellular mechanism: vext view--see GUI: view virtual experimental preparation see model specification: as "virtual experimental preparation" virtual experimental rig--see user interface: as virtual experimental rig visibility--see template: writing a template: public, object: public members Vm--see membrane potential, v voltage membrane--see membrane potential voltage clamp and stability--see numeric integration: stability: effect of signal sources, system equations: effect of signal sources command potential current accuracy preserving spatial accuracy--see point process: preserving spatial accuracy ramp clamp also see SEClamp voltage-gated current--see channel: voltage-gated volume--see compartment: size WWWW weight--see NetCon class: weight weight array--see NetCon class: weight: vector weight vector--see NetCon class: weight: vector what are the names of things? which view contains the mouse--see Graph class: view_info() while--see hoc syntax: flow control: while why is NEURON fast?--see computational efficiency: why is NEURON fast? window title--see GUI tool development: mapping to the screen: window title wopen()--see hoc syntax: basic input and output: wopen() WRITE--see NEURON block: USEION writing an ion concentration--see NEURON block: USEION writing files--see hoc syntax: basic input and output, File class XXXX x3d()--see 3-D specification of geometry: x3d(), y3d(), z3d() x-expression--see standard run system: plotting system: graphLists xopen()--see hoc syntax: basic input and output: xopen() xpanel() xpvalue() xred()--see hoc syntax: basic input and output: xred() xvalue() YYYY y3d()--see 3-D specification of geometry: x3d(), y3d(), z3d() ZZZZ z3d()--see 3-D specification of geometry: x3d(), y3d(), z3d() zero area node--see section: nodes: zero area