Index

A

A (HHGate attribute) (HHGate2D attribute) a (IzhIF attribute) (IzhikevichNrn attribute) a0 (AdExIF attribute) (AdThreshIF attribute) (IzhIF attribute) (QIF attribute) abs_refract (RandSpike attribute) (SpikeGen attribute) absoluteAccuracy (MarkovGslSolver attribute) accommodating (IzhikevichNrn attribute) activation() (IntFire method) (IntFireBase method) (SynChan method) activationOut (SynHandlerBase attribute) Adaptor (built-in class) addMsg() (Shell method) addPostSpike() (GraupnerBrunel2012CaPlasticitySynHandler method) (STDPSynHandler method) addSpike() (SpikeStats method), [1] (Synapse method) addTable() (Streamer method) addTables() (Streamer method) aDest() (IzhikevichNrn method)

AdExIF (built-in class) adjacent (Msg attribute) AdThreshIF (built-in class) alpha (GammaRng attribute), [1] (HHGate attribute) (IzhikevichNrn attribute) alphaParms (HHGate attribute) alwaysDiffuse (CubeMesh attribute) aMinus (STDPSynHandler attribute) aMinus0 (STDPSynHandler attribute) analogStimTable (module) analogStimTable() (in module analogStimTable) Annotator (built-in class) anyValue (Arith attribute) aPlus (STDPSynapse attribute) aPlus0 (STDPSynHandler attribute) arg1() (Arith method) arg1Value (Arith attribute) arg1x2() (Arith method) arg2() (Arith method) arg3() (Arith method) Arith (built-in class) assign_clocks() (in module compartment_net_no_array) assignIntCa() (NMDAChan method) axial (CompartmentBase attribute) axialOut (CompartmentBase attribute)

B

B (CaConcBase attribute) (HHGate attribute) (HHGate2D attribute) b (IzhIF attribute) (IzhikevichNrn attribute) b0 (AdExIF attribute) (IzhIF attribute) badStoichiometry (SteadyState attribute) basal() (CaConcBase method) baseClass (Cinfo attribute) baseDt (Clock attribute) baseLevel (PulseGen attribute), [1]

bDest() (IzhikevichNrn method) beta (HHGate attribute) (IzhikevichNrn attribute) bidirectionalPlasticity (module) BinomialRng (built-in class) bistable (GraupnerBrunel2012CaPlasticitySynHandler attribute) buffer (DifShell attribute) bufferSize (PostMaster attribute) buildDefaultMesh() (ChemCompt method) buildMeshJunctions() (Dsolve method) buildNeuroMeshJunctions() (Dsolve method) buildSegmentTree() (Neuron method) buildXreacs() (Stoich method)

C

C (DifShell attribute) c (Function attribute) (IzhikevichNrn attribute) c0 (IzhIF attribute) Ca (CaConcBase attribute) (GraupnerBrunel2012CaPlasticitySynHandler attribute) Ca_base (CaConcBase attribute) caAdvance (HSolve attribute) CaBasal (CaConcBase attribute) cable() (CompartmentBase method) CaConc (built-in class) CaConcBase (built-in class) caDiv (HSolve attribute) CaInit (GraupnerBrunel2012CaPlasticitySynHandler attribute) caMax (HSolve attribute) caMin (HSolve attribute) CaPost (GraupnerBrunel2012CaPlasticitySynHandler attribute) CaPre (GraupnerBrunel2012CaPlasticitySynHandler attribute) cDest() (IzhikevichNrn method) ceiling (CaConcBase attribute) Ceq (DifShell attribute) ChanBase (built-in class) changeFuncExpression (module) channel (ChanBase attribute) (CompartmentBase attribute) (IzhikevichNrn attribute) (MarkovRateTable attribute) (MarkovSolverBase attribute) channel1 (GapJunction attribute) channel1Out (GapJunction attribute) channel2 (GapJunction attribute) channel2Out (GapJunction attribute) channelDistribution (Neuron attribute) channelOut (ChanBase attribute) ChemCompt (built-in class) chemDoseResponse (module) childOut (Neutral attribute) children (Neutral attribute) chunkSize (HDF5WriterBase attribute) ci() (Nernst method) Cin (Nernst attribute) Cinfo (built-in class) className (Neutral attribute) clear() (SparseMsg method) clearVec() (TableBase method) Clock (built-in class) clockControl (Clock attribute) close() (HDF5WriterBase method) Cm (CompartmentBase attribute) CM (Neuron attribute) CMg (MgBlock attribute) (NMDAChan attribute) co() (Nernst method) color (Annotator attribute) columnIndex (Stoich attribute) command (PIDController attribute) (VClamp attribute) commandIn() (PIDController method) (VClamp method) compareVec() (TableBase method) compareXplot() (TableBase method) Compartment (built-in class) compartment (Dsolve attribute) (Ksolve attribute) (Stoich attribute)

compartment_net (module) compartment_net_no_array (module) CompartmentBase (built-in class) compartmentLengthInLambdas (Neuron attribute) compartments (Neuron attribute) compartmentsFromExpression (Neuron attribute) compression (HDF5WriterBase attribute) compressor (HDF5WriterBase attribute) conc (PoolBase attribute) concen() (HHChannel2D method) (HHChannelBase method) concen2() (HHChannel2D method) concentrationOut (DifShell attribute) concInit (PoolBase attribute) concK1 (CplxEnzBase attribute) concOut (CaConcBase attribute) condFraction (NMDAChan attribute) connect_spikegen() (in module intfire) connect_two_intfires() (in module intfire) convergenceCriterion (SteadyState attribute) convert_Genesis2Sbml (module) Coordinates (MeshEntry attribute) coords (CubeMesh attribute) (CylMesh attribute) copy() (Shell method) count (PulseGen attribute), [1] Cout (Nernst attribute) cplx (CplxEnzBase attribute) cplxDest() (CplxEnzBase method) CplxEnzBase (built-in class) cplxOut (CplxEnzBase attribute) create() (Shell method) create_cell() (in module randomspike) create_compartment() (in module traub_naf) create_model() (in module twocells) create_naf_proto() (in module traub_naf) create_network() (in module compartment_net) create_population() (in module compartment_net) (in module compartment_net_no_array) createGate() (HHChannelBase method) createSpine() (in module multiComptSigNeur) (in module testSigNeur) createSquid() (in module cubeMeshSigNeur) (in module multiComptSigNeur) (in module testSigNeur) crossComptNeuroMesh (module) crossComptSimpleReac (module) crossComptSimpleReacGSSA (module) cspaceSteadyState (module) CubeMesh (built-in class) cubeMeshSigNeur (module) current (VClamp attribute) current() (CaConcBase method) currentFraction() (CaConcBase method) currentOut (VClamp attribute) currentStep (Clock attribute) currentTime (Clock attribute) cylinder (SymCompartment attribute) cylinderDiffusion (module) cylinderMotor (module) cylinderOut (SymCompartment attribute) CylMesh (built-in class)

D

D (DifShell attribute) d (IzhIF attribute) (IzhikevichNrn attribute) dDest() (IzhikevichNrn method) decrease() (CaConcBase method) decrement() (Pool method) defaultTick (Clock attribute) delay (PulseGen attribute), [1] (Synapse attribute) delayD (GraupnerBrunel2012CaPlasticitySynHandler attribute) delayIn() (PulseGen method), [1] delete() (Shell method) deltaThresh (ExIF attribute) dendVoxelsOnCompartment (NeuroMesh attribute) derivative (Func attribute) (Function attribute) (PIDController attribute) derivativeOut (Func attribute) (Function attribute) dest (Finfo attribute) destFields (Neutral attribute) destFieldsOnE1 (Msg attribute) destFieldsOnE2 (Msg attribute) DiagonalMsg (built-in class) diameter (CaConcBase attribute) (CompartmentBase attribute) (DifShell attribute) DiffAmp (built-in class) diffConst (PoolBase attribute) diffEqSolution (module) diffLength (CylMesh attribute) (NeuroMesh attribute)

diffScale (Dsolve attribute) diffSpinyNeuron (module) DiffusionArea (MeshEntry attribute) DiffusionScaling (MeshEntry attribute) diffVol1 (Dsolve attribute) diffVol2 (Dsolve attribute) DifShell (built-in class) dimensions (MeshEntry attribute) dirpath (Annotator attribute) displace() (CompartmentBase method) distal (SymCompartment attribute) distalOut (SymCompartment attribute), [1], [2] divs (HHGate attribute) do_iclamp() (in module traub_naf) do_vclamp() (in module traub_naf) docs (Cinfo attribute) (Finfo attribute) doLoop (StimulusTable attribute) doubleAttr (HDF5WriterBase attribute) doubleVecAttr (HDF5WriterBase attribute) Dsolve (built-in class) dsolve (Stoich attribute) dt (HSolve attribute) (Neutral attribute) dts (Clock attribute) dx (CubeMesh attribute) (Interpol2D attribute) dy (CubeMesh attribute) (Interpol2D attribute) dz (CubeMesh attribute)

E

E (Nernst attribute) e1 (Msg attribute) e2 (Msg attribute) e_previous (PIDController attribute) edgeTriggered (SpikeGen attribute) eigenvalues (SteadyState attribute) Ek (ChanBase attribute) elecComptList (NeuroMesh attribute) (PsdMesh attribute) (SpineMesh attribute) elecComptMap (NeuroMesh attribute) (PsdMesh attribute) (SpineMesh attribute) electrotonicDistanceFromSoma (Neuron attribute) Em (CompartmentBase attribute) (Neuron attribute) endVoxelInCompt (NeuroMesh attribute) (PsdMesh attribute) (SpineMesh attribute)

Enz (built-in class) enz (CplxEnzBase attribute) EnzBase (built-in class) enzDest() (CplxEnzBase method) (EnzBase method) enzOut (CplxEnzBase attribute) Eout (Nernst attribute) epsAbs (Ksolve attribute) epsRel (Ksolve attribute) eqTauPump() (DifShell method) error (PIDController attribute) estimatedDt (Ksolve attribute) eventOut (TimeTable attribute) example() (in module function) (in module randomspike) ExIF (built-in class) ExponentialRng (built-in class) expr (Func attribute) (Function attribute) extCa (NMDAChan attribute)

F

fieldIndex (Neutral attribute) fieldName (Finfo attribute) filename (HDF5WriterBase attribute) (TimeTable attribute) filterXreacs() (Stoich method) findChemSteadyState (module) fInflux() (DifShell method) Finfo (built-in class) finished (Clock attribute) firstDelay (PulseGen attribute), [1] firstLevel (PulseGen attribute), [1] firstWidth (PulseGen attribute), [1] floor (CaConcBase attribute) flush() (HDF5WriterBase method)

flushLimit (HDF5DataWriter attribute) fluxFromIn() (DifShell method) fluxFromOut() (DifShell method) format (Streamer attribute) (Table attribute) (Table2 attribute) fOutflux() (DifShell method) Func (built-in class) func (module) funcInputToPools (module) funcRateHarmonicOsc (module) funcReacLotkaVolterra (module) function (Arith attribute) Function (built-in class) function (module)

G

gain (DiffAmp attribute) (PIDController attribute) (VClamp attribute) gainDest() (PIDController method) gainIn() (DiffAmp method) gamma (IzhikevichNrn attribute) gammaD (GraupnerBrunel2012CaPlasticitySynHandler attribute) gammaP (GraupnerBrunel2012CaPlasticitySynHandler attribute) GammaRng (built-in class), [1] GapJunction (built-in class) gapjunction (module) gapjunction_demo() (in module gapjunction) Gbar (ChanBase attribute) gbar (MarkovChannel attribute) generate_poisson_times() (in module timetable) geometricalDistanceFromSoma (Neuron attribute) geometryPolicy (NeuroMesh attribute) getA() (HHGate method) (HHGate2D method) (IzhIF method) (IzhikevichNrn method) getA0() (AdExIF method) (AdThreshIF method) (IzhIF method) (QIF method) getAbs_refract() (RandSpike method) (SpikeGen method) getAbsoluteAccuracy() (MarkovGslSolver method) getAccommodating() (IzhikevichNrn method) getAdjacent() (Msg method) getAlpha() (GammaRng method), [1] (HHGate method) (IzhikevichNrn method) getAlphaParms() (HHGate method) getAlwaysDiffuse() (CubeMesh method) getAMinus() (STDPSynHandler method) getAMinus0() (STDPSynHandler method) getAnyValue() (Arith method) getAPlus() (STDPSynapse method) getAPlus0() (STDPSynHandler method) getArg1Value() (Arith method) getB() (CaConcBase method) (HHGate method) (HHGate2D method) (IzhIF method) (IzhikevichNrn method) getB0() (AdExIF method) (IzhIF method) getBadStoichiometry() (SteadyState method) getBaseClass() (Cinfo method) getBaseDt() (Clock method) getBaseLevel() (PulseGen method), [1] getBeta() (HHGate method) (IzhikevichNrn method) getBistable() (GraupnerBrunel2012CaPlasticitySynHandler method) getBufferSize() (PostMaster method) getC() (DifShell method) (Function method) (IzhikevichNrn method) getC0() (IzhIF method) getCa() (CaConcBase method) (GraupnerBrunel2012CaPlasticitySynHandler method) getCa_base() (CaConcBase method) getCaAdvance() (HSolve method) getCaBasal() (CaConcBase method) getCaDiv() (HSolve method) getCaInit() (GraupnerBrunel2012CaPlasticitySynHandler method) getCaMax() (HSolve method) getCaMin() (HSolve method) getCaPost() (GraupnerBrunel2012CaPlasticitySynHandler method) getCaPre() (GraupnerBrunel2012CaPlasticitySynHandler method) getCeiling() (CaConcBase method) getCeq() (DifShell method) getChannelDistribution() (Neuron method) getChildren() (Neutral method) getChunkSize() (HDF5WriterBase method) getCin() (Nernst method) getClassName() (Neutral method) getCm() (CompartmentBase method) getCM() (Neuron method) getCMg() (MgBlock method) (NMDAChan method) getColor() (Annotator method) getColumnIndex() (Stoich method) getCommand() (PIDController method) (VClamp method) getCompartment() (Dsolve method) (Ksolve method) (Stoich method) getCompartmentLengthInLambdas() (Neuron method) getCompartments() (Neuron method) getCompartmentsFromExpression() (Neuron method) getCompression() (HDF5WriterBase method) getCompressor() (HDF5WriterBase method) getConc() (PoolBase method) getConcInit() (PoolBase method) getConcK1() (CplxEnzBase method) getCondFraction() (NMDAChan method) getConvergenceCriterion() (SteadyState method) getCoordinates() (MeshEntry method) getCoords() (CubeMesh method) (CylMesh method) getCount() (PulseGen method), [1] getCout() (Nernst method) getCurrent() (VClamp method) getCurrentStep() (Clock method) getCurrentTime() (Clock method) getD() (DifShell method) (IzhIF method) (IzhikevichNrn method) getDefaultTick() (Clock method) getDelay() (PulseGen method), [1] (Synapse method) getDelayD() (GraupnerBrunel2012CaPlasticitySynHandler method) getDeltaThresh() (ExIF method) getDendVoxelsOnCompartment() (NeuroMesh method) getDerivative() (Func method) (Function method) (PIDController method) getDest() (Finfo method) getDestFields() (Neutral method) getDestFieldsOnE1() (Msg method) getDestFieldsOnE2() (Msg method) getDiameter() (CaConcBase method) (CompartmentBase method) (DifShell method) getDiffConst() (PoolBase method) getDiffLength() (CylMesh method) (NeuroMesh method) getDiffScale() (Dsolve method) getDiffusionArea() (MeshEntry method) getDiffusionScaling() (MeshEntry method) getDiffVol1() (Dsolve method) getDiffVol2() (Dsolve method) getDimensions() (MeshEntry method) getDirpath() (Annotator method) getDivs() (HHGate method) getDocs() (Cinfo method) (Finfo method) getDoLoop() (StimulusTable method) getDoubleAttr() (HDF5WriterBase method) getDoubleVecAttr() (HDF5WriterBase method) getDsolve() (Stoich method) getDt() (HSolve method) (Neutral method) getDts() (Clock method) getDx() (CubeMesh method) (Interpol2D method) getDy() (CubeMesh method) (Interpol2D method) getDz() (CubeMesh method) getE() (Nernst method) getE1() (Msg method) getE2() (Msg method) getE_previous() (PIDController method) getEdgeTriggered() (SpikeGen method) getEigenvalues() (SteadyState method) getEk() (ChanBase method) getElecComptList() (NeuroMesh method) (PsdMesh method) (SpineMesh method) getElecComptMap() (NeuroMesh method) (PsdMesh method) (SpineMesh method) getElectrotonicDistanceFromSoma() (Neuron method) getEm() (CompartmentBase method) (Neuron method) getEndVoxelInCompt() (NeuroMesh method) (PsdMesh method) (SpineMesh method) getEpsAbs() (Ksolve method) getEpsRel() (Ksolve method) getError() (PIDController method) getEstimatedDt() (Ksolve method) getExpr() (Func method) (Function method) getExtCa() (NMDAChan method) getFieldIndex() (Neutral method) getFieldName() (Finfo method) getFilename() (HDF5WriterBase method) (TimeTable method) getFirstDelay() (PulseGen method), [1] getFirstLevel() (PulseGen method), [1] getFirstWidth() (PulseGen method), [1] getFloor() (CaConcBase method) getFlushLimit() (HDF5DataWriter method) getFormat() (Streamer method) (Table method) (Table2 method) getFunction() (Arith method) getGain() (DiffAmp method) (PIDController method) (VClamp method) getGamma() (IzhikevichNrn method) getGammaD() (GraupnerBrunel2012CaPlasticitySynHandler method) getGammaP() (GraupnerBrunel2012CaPlasticitySynHandler method) getGbar() (ChanBase method) (MarkovChannel method) getGeometricalDistanceFromSoma() (Neuron method) getGeometryPolicy() (NeuroMesh method) getGk() (ChanBase method) (GapJunction method) getHasFired() (IntFireBase method) (RandSpike method) (SpikeGen method) getHeadDiameter() (Spine method) getHeadLength() (Spine method) getHeadVolume() (Spine method) getHistory() (SeqSynHandler method) getHistoryTime() (SeqSynHandler method) getI1() (OneToAllMsg method) (SingleMsg method) getI2() (SingleMsg method) getICa() (NMDAChan method) getIcon() (Annotator method) getIdValue() (Neutral method) getIk() (ChanBase method) getIm() (CompartmentBase method) (IzhikevichNrn method) getIndependent() (Function method) getIndex() (Neutral method) getInitialState() (MarkovChannel method) (MarkovSolverBase method) getInitString() (PyRun method) getInitU() (IzhikevichNrn method) getInitVm() (CompartmentBase method) (IzhikevichNrn method) getInject() (CompartmentBase method) (IzhikevichNrn method) getInnerArea() (DifShell method) getInputOffset() (Adaptor method) getInputVar() (PyRun method) getInstant() (HHChannel2D method) (HHChannelBase method) getIntCa() (NMDAChan method) getIntCaOffset() (NMDAChan method) getIntCaScale() (NMDAChan method) getIntegral() (PIDController method) getInternalDt() (MarkovGslSolver method) getInvdx() (MarkovSolverBase method) (VectorTable method) getInvdy() (MarkovSolverBase method) getIsA() (Neutral method) getIsInitialized() (MarkovGslSolver method) (SteadyState method) getIsOpen() (HDF5WriterBase method) getIsRunning() (Clock method) getIsToroid() (CubeMesh method) getK1() (CplxEnzBase method) getK2() (CplxEnzBase method) getK3() (CplxEnzBase method) getKb() (ReacBase method) getKcat() (EnzBase method) getKernel() (SeqSynHandler method) getKernelEquation() (SeqSynHandler method) getKernelWidth() (SeqSynHandler method) getKf() (ReacBase method) getKm() (EnzBase method) getKMg_A() (MgBlock method) (NMDAChan method) getKMg_B() (MgBlock method) (NMDAChan method) getKsolve() (Stoich method) getLabels() (MarkovChannel method) getLastEventTime() (IntFireBase method) getLeak() (DifShell method) getLength() (CaConcBase method) (CompartmentBase method) (DifShell method) getLevel() (PulseGen method), [1] getLigandConc() (MarkovChannel method) (MarkovRateTable method) getLongAttr() (HDF5WriterBase method) getLongVecAttr() (HDF5WriterBase method) getLookupindex() (VectorTable method) getLookupvalue() (VectorTable method) getLoopTime() (StimulusTable method) getMatrixEntry() (Stoich method) getMax() (HHGate method) (UniformRng method) getMaxIter() (SteadyState method) getMe() (Neutral method) getMean() (ExponentialRng method) (NormalRng method) (PoissonRng method) (RandGenerator method) (Stats method) getMeshToSpace() (CubeMesh method) getMeshType() (MeshEntry method) getMethod() (ExponentialRng method) (Ksolve method) (MarkovGslSolver method) (NormalRng method) (TimeTable method) getMin() (HHGate method) (UniformRng method) getMInfinity() (HHGate method) getMode() (Func method) (Function method) (HDF5WriterBase method) (PyRun method) (VClamp method) getModeltype() (Annotator method) getModulation() (ChanBase method) getMolWt() (Species method) getMotorConst() (PoolBase method) getMsgDestFunctions() (Neutral method) getMsgDests() (Neutral method) getMsgIn() (Neutral method) getMsgOut() (Neutral method) getMyNode() (PostMaster method) getN() (BinomialRng method) (PoolBase method) getName() (Neutral method) (Table method) (Table2 method) getNeighbors() (MeshEntry method) (Neutral method) getNeuronVoxel() (PsdMesh method) (SpineMesh method) getNInit() (PoolBase method) getNIter() (SteadyState method) getNNegEigenvalues() (SteadyState method) getNoiseSD() (GraupnerBrunel2012CaPlasticitySynHandler method) getNoisy() (GraupnerBrunel2012CaPlasticitySynHandler method) getNormalizeWeights() (SynChan method) getNotes() (Annotator method) getNPosEigenvalues() (SteadyState method) getNsteps() (Clock method) getNum() (Stats method) getNumAllPools() (Stoich method) getNumAllVoxels() (Dsolve method) (Gsolve method) (Ksolve method) getNumBranches() (Neuron method) getNumBufPools() (Stoich method) getNumColumns() (SparseMsg method) getNumCompartments() (Neuron method) getNumData() (Neutral method) getNumDiffCompts() (CylMesh method) (NeuroMesh method) getNumDimensions() (ChemCompt method) getNumEntries() (SparseMsg method) getNumEventInput() (NSDFWriter method) getNumField() (Neutral method) getNumFire() (Gsolve method) getNumGateX() (HHChannel2D method) (HHChannelBase method) getNumGateY() (HHChannel2D method) (HHChannelBase method)

getNumGateZ() (HHChannel2D method) (HHChannelBase method) getNumKb() (ReacBase method) getNumKf() (ReacBase method) getNumKm() (EnzBase method) getNumLocalVoxels() (Gsolve method) (Ksolve method) getNumMesh() (ChemCompt method) getNumNodes() (PostMaster method) getNumOpenStates() (MarkovChannel method) getNumPools() (Dsolve method) (Gsolve method) (Ksolve method) getNumProducts() (ReacBase method) getNumProxyPools() (Stoich method) getNumRates() (Stoich method) getNumRows() (SparseMsg method) getNumSegments() (NeuroMesh method) getNumSpine() (Neuron method) getNumSpines() (Neuron method) getNumStates() (MarkovChannel method) getNumSubstrates() (EnzBase method) (ReacBase method) getNumSynapse() (GraupnerBrunel2012CaPlasticitySynHandler method) (STDPSynHandler method) (SeqSynHandler method) (SimpleSynHandler method), [1] getNumSynapses() (SynHandlerBase method) getNumTables() (Streamer method) getNumTicks() (Clock method) getNumVarPools() (SteadyState method) (Stoich method) getNumVars() (Function method) getNumVoxels() (Dsolve method) getNumX() (Function method) getNVec() (Dsolve method) (Gsolve method) (Ksolve method) getNx() (CubeMesh method) getNy() (CubeMesh method) getNz() (CubeMesh method) getOneVoxelVolume() (ChemCompt method) getOuterArea() (DifShell method) getOutfile() (Streamer method) (Table method) (Table2 method) getOutputOffset() (Adaptor method) getOutputValue() (Adaptor method) (Arith method) (DiffAmp method) (PIDController method) (PulseGen method), [1] (TableBase method) getOutputVar() (PyRun method) getP() (BinomialRng method) getParent() (Neutral method) getParentCompartmentOfSpine() (Neuron method) getParentVoxel() (NeuroMesh method) (SpineMesh method) getPassiveDistribution() (Neuron method) getPath() (Dsolve method) (Neutral method) (Stoich method) getPathDistanceFromSoma() (Neuron method) getPermeability() (NMDAChan method) getPhi() (Neuron method) getPoolIdMap() (Stoich method) getPreserveNumEntries() (CubeMesh method) getProbability() (SparseMsg method) getProxyPools() (Stoich method) getPsdArea() (Spine method) getQ() (MarkovRateTable method) (MarkovSolverBase method) getR0() (CylMesh method) getR1() (CylMesh method) getRa() (CompartmentBase method) getRA() (Neuron method) getRank() (SteadyState method) getRate() (Function method) (RandSpike method) getRatio() (CplxEnzBase method) getRefractoryPeriod() (IntFire method) (IntFireBase method) getRefractT() (RandSpike method) (SpikeGen method) getRelativeAccuracy() (MarkovGslSolver method) getResponseScale() (SeqSynHandler method) getRm() (CompartmentBase method) getRM() (Neuron method) getRmByTau() (IzhikevichNrn method) getRowStart() (Stoich method) getRunString() (PyRun method) getRuntime() (Annotator method) getRunTime() (Clock method) getSample() (RandGenerator method) getSaturation() (DiffAmp method) (PIDController method) getScale() (Adaptor method) (Nernst method) getSdev() (Stats method) getSecondDelay() (PulseGen method), [1] getSecondLevel() (PulseGen method), [1] getSecondWidth() (PulseGen method), [1] getSeed() (HSolve method) (SparseMsg method) getSensed() (PIDController method) (VClamp method) getSeparateSpines() (NeuroMesh method) getSeqActivation() (SeqSynHandler method) getSeqDt() (SeqSynHandler method) getShaftDiameter() (Spine method) getShaftLength() (Spine method) getShapeMode() (DifShell method) getSize() (MarkovRateTable method) (TableBase method) getSolutionStatus() (SteadyState method) getSolver() (Annotator method) getSourceFields() (Neutral method) getSourceFile() (Neuron method) getSpaceToMesh() (CubeMesh method) getSpeciesId() (PoolBase method) getSpineDistribution() (Neuron method) getSpinesFromExpression() (Neuron method) getSpinesOnCompartment() (Neuron method) getSpineVoxelOnDendVoxel() (NeuroMesh method) getSpineVoxelsOnCompartment() (NeuroMesh method) getSrc() (Finfo method) getSrcFieldsOnE1() (Msg method) getSrcFieldsOnE2() (Msg method) getStartTime() (StimulusTable method) getStartVoxelInCompt() (NeuroMesh method) (PsdMesh method) (SpineMesh method) getState() (in module findChemSteadyState) (MarkovChannel method) (MarkovSolverBase method) (TimeTable method) getStateType() (SteadyState method) getStatus() (SteadyState method) (Stoich method) getStencilIndex() (ChemCompt method) getStencilRate() (ChemCompt method) getStepPosition() (StimulusTable method) getStepSize() (StimulusTable method) getStoich() (Dsolve method) (Gsolve method) (Ksolve method) (SteadyState method) getStopTime() (StimulusTable method) getStride() (Clock method) (DiagonalMsg method) getStringAttr() (HDF5WriterBase method) getStringVecAttr() (HDF5WriterBase method) getSubTree() (NeuroMesh method) getSubTreePath() (NeuroMesh method) getSum() (Stats method) getSurface() (CubeMesh method) getTable() (Interpol2D method) (VectorTable method) getTableA() (HHGate method) (HHGate2D method) getTableB() (HHGate method) (HHGate2D method) getTableVector2D() (Interpol2D method) getTarget() (HSolve method) getTau() (CaConcBase method) (HHGate method) (IntFire method) (VClamp method) getTau1() (SynChan method) getTau2() (SynChan method) getTauCa() (GraupnerBrunel2012CaPlasticitySynHandler method) getTauD() (PIDController method) getTauI() (PIDController method) getTauMinus() (STDPSynHandler method) getTauPlus() (STDPSynHandler method) getTauSyn() (GraupnerBrunel2012CaPlasticitySynHandler method) getTauThresh() (AdThreshIF method) getTauW() (AdExIF method) getTd() (VClamp method) getTemperature() (Nernst method) (NMDAChan method) getTextColor() (Annotator method) getTheta() (GammaRng method), [1] (Neuron method) getThetaD() (GraupnerBrunel2012CaPlasticitySynHandler method) getThetaP() (GraupnerBrunel2012CaPlasticitySynHandler method) getThick() (CaConcBase method) getThickness() (DifShell method) (PsdMesh method) getThis() (Mstring method) (Neutral method) getThresh() (IntFire method) (IntFireBase method) getThreshAdaptive() (AdThreshIF method) getThreshJump() (AdThreshIF method) getThreshold() (SpikeGen method) (SpikeStats method), [1] (Table method) (Table2 method) getTi() (VClamp method) getTick() (Neutral method) getTickDt() (Clock method) getTickStep() (Clock method) getTotal() (SteadyState method) getTotalLength() (Spine method) getTotLength() (CylMesh method) getTrigMode() (PulseGen method), [1] getType() (Finfo method) getU() (IzhIF method) (IzhikevichNrn method) getU0() (IzhikevichNrn method) getUInit() (IzhIF method) getUseClockedUpdate() (Gsolve method) getUseConcentration() (HHChannelBase method) getUseInterpolation() (HHGate method) getUseRandInit() (Gsolve method) getUseStreamer() (Table method) (Table2 method) getValence() (DifShell method) (Nernst method) getValue() (Func method) (Function method) (Mstring method) (Variable method) getValueFields() (Neutral method) getValuesFromExpression() (Neuron method) getVar() (Func method) getVariance() (NormalRng method) (RandGenerator method) getVars() (Func method) getVCritical() (QIF method) getVDiv() (HSolve method) getVector() (TableBase method) getVm() (CompartmentBase method) (IntFire method) (IzhikevichNrn method) (MarkovChannel method) (MarkovRateTable method) getVMax() (HSolve method) getVmax() (IzhikevichNrn method) getVMin() (HSolve method) getVolume() (ChemCompt method) (DifShell method) (MeshEntry method), [1] (PoolBase method) getVoxelMidpoint() (ChemCompt method) getVoxelVolume() (ChemCompt method) getVPeak() (ExIF method) (IzhIF method) getVReset() (IntFireBase method) getW() (AdExIF method) getWeight() (Synapse method) getWeightMax() (GraupnerBrunel2012CaPlasticitySynHandler method) (STDPSynHandler method) getWeightMin() (GraupnerBrunel2012CaPlasticitySynHandler method) (STDPSynHandler method) getWeightScale() (GraupnerBrunel2012CaPlasticitySynHandler method) (SeqSynHandler method) getWeightScaleVec() (SeqSynHandler method) getWidth() (PulseGen method), [1] getWindowLength() (Stats method) getWmean() (Stats method) getWnum() (Stats method) getWsdev() (Stats method) getWsum() (Stats method) getX() (Annotator method) (CompartmentBase method) (Func method) (HHChannel2D method) (HHChannelBase method) getX0() (CompartmentBase method) (CubeMesh method) (CylMesh method) getX1() (CubeMesh method) (CylMesh method) getXdivs() (Interpol2D method) (MarkovSolverBase method) (VectorTable method) getXdivsA() (HHGate2D method) getXdivsB() (HHGate2D method) getXindex() (HHChannel2D method) getXmax() (Interpol method) (Interpol2D method) (MarkovSolverBase method) (VectorTable method) getXmaxA() (HHGate2D method) getXmaxB() (HHGate2D method) getXmin() (Interpol method) (Interpol2D method) (MarkovSolverBase method) (VectorTable method) getXminA() (HHGate2D method) getXminB() (HHGate2D method) getXpower() (HHChannel2D method) (HHChannelBase method) getY() (Annotator method) (CompartmentBase method) (Func method) (HHChannel2D method) (HHChannelBase method) (Interpol method) (TableBase method) getY0() (CompartmentBase method) (CubeMesh method) (CylMesh method) getY1() (CubeMesh method) (CylMesh method) getYdivs() (Interpol2D method) (MarkovSolverBase method) getYdivsA() (HHGate2D method) getYdivsB() (HHGate2D method) getYindex() (HHChannel2D method) getYmax() (Interpol2D method) (MarkovSolverBase method) getYmaxA() (HHGate2D method) getYmaxB() (HHGate2D method) getYmin() (Interpol2D method) (MarkovSolverBase method) getYminA() (HHGate2D method) getYminB() (HHGate2D method) getYpower() (HHChannel2D method) (HHChannelBase method) getZ() (Annotator method) (CompartmentBase method) (Func method) (HHChannel2D method) (HHChannelBase method) (Interpol2D method) getZ0() (CompartmentBase method) (CubeMesh method) (CylMesh method) getZ1() (CubeMesh method) (CylMesh method) getZindex() (HHChannel2D method) getZk() (MgBlock method) getZpower() (HHChannel2D method) (HHChannelBase method) ghk (ChanBase attribute) Gk (ChanBase attribute) (GapJunction attribute) GraupnerBrunel2012_STDPfromCaPlasticity (module) GraupnerBrunel2012CaPlasticitySynHandler (built-in class) Group (built-in class) group (Group attribute) Gsolve (built-in class) gssaCylinderDiffusion (module) gssaRDspiny (module)

H

handleAxial() (CompartmentBase method) handleChannel() (CompartmentBase method) (IzhikevichNrn method) handleLigandConc() (MarkovChannel method) (MarkovRateTable method) handleMolWt() (PoolBase method) handleMolWtRequest() (Species method) handleQ() (MarkovGslSolver method) handleRaxial() (CompartmentBase method) handleState() (MarkovChannel method) handleVm() (MarkovRateTable method) (MarkovSolverBase method) hasFired (IntFireBase attribute) (RandSpike attribute) (SpikeGen attribute) HDF5DataWriter (built-in class)

HDF5WriterBase (built-in class) hdfdemo (module) headDiameter (Spine attribute) headLength (Spine attribute) headVolume (Spine attribute) helloMoose (module) HHChannel (built-in class) HHChannel2D (built-in class) HHChannelBase (built-in class) HHGate (built-in class) HHGate2D (built-in class) HigginsGraupnerBrunel2014_LifetimeCaPlasticity (module) hillPump() (DifShell method) history (SeqSynHandler attribute) historyTime (SeqSynHandler attribute) HSolve (built-in class)

I

i1 (OneToAllMsg attribute) (SingleMsg attribute) i2 (SingleMsg attribute) ICa (NMDAChan attribute) ICaOut (NMDAChan attribute) icon (Annotator attribute) idValue (Neutral attribute) Ik (ChanBase attribute) IkOut (ChanBase attribute) Im (CompartmentBase attribute) (IzhikevichNrn attribute) increase() (CaConcBase method) increment() (Pool method) independent (Function attribute) index (Neutral attribute) influx() (DifShell method) init (CompartmentBase attribute) (Gsolve attribute) (Ksolve attribute) init() (MarkovGslSolver method) (MarkovRateTable method) (MarkovSolverBase method) initialState (MarkovChannel attribute) (MarkovSolverBase attribute) initProc() (CompartmentBase method) (Gsolve method) (Ksolve method) initReinit() (CompartmentBase method) (Gsolve method) (Ksolve method) initString (PyRun attribute) initU (IzhikevichNrn attribute) initVm (CompartmentBase attribute) (IzhikevichNrn attribute) inject (CompartmentBase attribute) (IzhikevichNrn attribute) injectMsg() (CompartmentBase method), [1] (IzhikevichNrn method) innerArea (DifShell attribute) innerDif (DifShell attribute) innerDifSourceOut (DifShell attribute)

input() (Adaptor method) (InputVariable method) (Interpol method) (PulseGen method), [1] (Stats method) (Table method) (Table2 method) (Variable method) input_output() (in module pyrun) inputOffset (Adaptor attribute) inputVar (PyRun attribute) InputVariable (built-in class) insertSpines (module) insertSpinesWithoutRdesigneur (module) instant (HHChannel2D attribute) (HHChannelBase attribute) instratesOut (MarkovRateTable attribute) intCa (NMDAChan attribute) intCaOffset (NMDAChan attribute) intCaScale (NMDAChan attribute) integral (PIDController attribute) IntegrateFireZoo (module) internalDt (MarkovGslSolver attribute) Interpol (built-in class) interpol (module) Interpol2D (built-in class) interpol2d (module) interpolation_demo() (in module interpol2d) IntFire (built-in class) intfire (module) IntFireBase (built-in class) invdx (MarkovSolverBase attribute) (VectorTable attribute) invdy (MarkovSolverBase attribute) isA (Neutral attribute) isInitialized (MarkovGslSolver attribute) (SteadyState attribute) isOpen (HDF5WriterBase attribute) isRunning (Clock attribute) isToroid (CubeMesh attribute) IzhIF (built-in class) IzhikevichNrn (built-in class)

K

k1 (CplxEnzBase attribute) k2 (CplxEnzBase attribute) k3 (CplxEnzBase attribute) Kb (ReacBase attribute) kcat (EnzBase attribute) kernel (SeqSynHandler attribute) kernelEquation (SeqSynHandler attribute) kernelWidth (SeqSynHandler attribute)

Kf (ReacBase attribute) Km (EnzBase attribute) KMg_A (MgBlock attribute) (NMDAChan attribute) KMg_B (MgBlock attribute) (NMDAChan attribute) Ksolve (built-in class) ksolve (Stoich attribute)

L

labels (MarkovChannel attribute) lastEventTime (IntFireBase attribute) leak (DifShell attribute) Leakage (built-in class) length (CaConcBase attribute) (CompartmentBase attribute) (DifShell attribute) level (PulseGen attribute), [1] levelIn() (PulseGen method), [1] LIF (built-in class) lif (module) LIFComp (class in lifcomp) (class in multicomp_lif) lifcomp (module) ligandConc (MarkovChannel attribute) (MarkovRateTable attribute)

ligandConc() (MarkovSolverBase method) linearTransform() (TableBase method) loadCspaceModel (module) loadCSV() (TableBase method) loadKineticModel (module) loadSbmlmodel (module) loadXplot() (TableBase method) loadXplotRange() (TableBase method) longAttr (HDF5WriterBase attribute) longVecAttr (HDF5WriterBase attribute) lookup() (Interpol2D method) lookupindex (VectorTable attribute) lookupOut (Interpol attribute) (Interpol2D attribute) lookupReturn2D (Interpol2D attribute) lookupvalue (VectorTable attribute) loopTime (StimulusTable attribute)

M

main() (in module bidirectionalPlasticity) (in module GraupnerBrunel2012_STDPfromCaPlasticity) (in module HigginsGraupnerBrunel2014_LifetimeCaPlasticity) (in module IntegrateFireZoo) (in module RandSpikeStats) (in module STDP) (in module changeFuncExpression) (in module chemDoseResponse) (in module compartment_net) (in module compartment_net_no_array) (in module convert_Genesis2Sbml) (in module crossComptNeuroMesh) (in module crossComptSimpleReac) (in module crossComptSimpleReacGSSA) (in module cspaceSteadyState) (in module cubeMeshSigNeur) (in module cylinderDiffusion) (in module diffEqSolution) (in module diffSpinyNeuron) (in module func) (in module funcInputToPools) (in module funcRateHarmonicOsc) (in module funcReacLotkaVolterra) (in module gapjunction) (in module gssaCylinderDiffusion) (in module gssaRDspiny) (in module hdfdemo) (in module helloMoose) (in module insertSpines) (in module insertSpinesWithoutRdesigneur) (in module interpol) (in module intfire) (in module lifcomp) (in module loadCspaceModel) (in module loadKineticModel) (in module loadSbmlmodel) (in module mapkFB) (in module multiComptSigNeur) (in module multicomp_lif) (in module multiscaleOneCompt) (in module neuronFromDotp) (in module nsdf_vec) (in module onetoonemsg) (in module pulsegen) (in module pulsegen2) (in module pyrun) (in module randomspike) (in module reacDiffBranchingNeuron) (in module reacDiffConcGradient) (in module reacDiffSpinyNeuron) (in module relaxationOsc) (in module repressillator) (in module rxdFuncDiffusion) (in module rxdFuncDiffusionStoch) (in module rxdReacDiffusion) (in module savemodel) (in module scaleVolumes) (in module scriptGssaSolver) (in module scriptKineticModel) (in module scriptKineticSolver) (in module showclocks) (in module showmsg) (in module singlemsgcross) (in module startstop) (in module stimtable) (in module stochasticLotkaVolterra) (in module strongBis) (in module switchKineticSolvers) (in module symcompartment) (in module synapse) (in module synapse_tutorial) (in module tabledemo) (in module testRdesigneur) (in module testSigNeur) (in module testWigglySpines) (in module timetable) (in module transportBranchingNeuron) (in module tweakingParameters) (in module twocells) (in module vclamp) (in module vectors) (in module wildcard)

make_network() (in module recurrentIntFire) (in module recurrentLIF) make_neuron_spike() (in module STDP) make_synapses() (in module compartment_net) (in module compartment_net_no_array) makeChannelPrototypes() (in module neuronFromDotp) makeChemModel() (in module diffSpinyNeuron) (in module gssaRDspiny) (in module reacDiffBranchingNeuron) (in module reacDiffSpinyNeuron) makeModel() (in module chemDoseResponse) (in module TuringOneDim) (in module findChemSteadyState) mapkFB (module) MarkovChannel (built-in class) MarkovGslSolver (built-in class) MarkovRateTable (built-in class) MarkovSolver (built-in class) MarkovSolverBase (built-in class) matrixEntry (Stoich attribute) max (HHGate attribute) (UniformRng attribute) maxIter (SteadyState attribute) me (Neutral attribute) mean (ExponentialRng attribute) (NormalRng attribute) (PoissonRng attribute) (RandGenerator attribute) (Stats attribute) mesh (MeshEntry attribute) MeshEntry (built-in class) meshToSpace (CubeMesh attribute) meshType (MeshEntry attribute) method (ExponentialRng attribute) (Ksolve attribute) (MarkovGslSolver attribute) (NormalRng attribute) (TimeTable attribute) MgBlock (built-in class) min (HHGate attribute) (UniformRng attribute) mInfinity (HHGate attribute) minusIn() (DiffAmp method) mmPump() (DifShell method) mode (Func attribute) (Function attribute) (HDF5WriterBase attribute) (PyRun attribute) (VClamp attribute) modeltype (Annotator attribute) modulation (ChanBase attribute) molWt (Species attribute) molWtOut (Species attribute) motorConst (PoolBase attribute) move() (Shell method) Msg (built-in class) msgDestFunctions (Neutral attribute) msgDests (Neutral attribute) msgIn (Neutral attribute) msgOut (Neutral attribute) Mstring (built-in class) multicomp_lif (module) multiComptSigNeur (module) multiscaleOneCompt (module) myNode (PostMaster attribute)

N

n (BinomialRng attribute) (PoolBase attribute) name (Neutral attribute) (Table attribute) (Table2 attribute) neighbors (MeshEntry attribute) (Neutral attribute) Nernst (built-in class) NeuroMesh (built-in class) Neuron (built-in class) neuronFromDotp (module) neuronVoxel (PsdMesh attribute) (SpineMesh attribute) Neutral (built-in class) nIn() (Pool method) nInit (PoolBase attribute) nIter (SteadyState attribute) NMDAChan (built-in class) nNegEigenvalues (SteadyState attribute) noiseSD (GraupnerBrunel2012CaPlasticitySynHandler attribute) noisy (GraupnerBrunel2012CaPlasticitySynHandler attribute) normalizeWeights (SynChan attribute) NormalRng (built-in class) notes (Annotator attribute) nOut (PoolBase attribute) nPosEigenvalues (SteadyState attribute) nsdf (module) nsdf_vec (module) NSDFWriter (built-in class) nsteps (Clock attribute) num (Stats attribute) numAllPools (Stoich attribute) numAllVoxels (Dsolve attribute) (Gsolve attribute) (Ksolve attribute) numBranches (Neuron attribute) numBufPools (Stoich attribute) numColumns (SparseMsg attribute) numCompartments (Neuron attribute)

numData (Neutral attribute) numDiffCompts (CylMesh attribute) (NeuroMesh attribute) numDimensions (ChemCompt attribute) numEntries (SparseMsg attribute) numField (Neutral attribute) numFire (Gsolve attribute) numKb (ReacBase attribute) numKf (ReacBase attribute) numKm (EnzBase attribute) numLocalVoxels (Gsolve attribute) (Ksolve attribute) numNodes (PostMaster attribute) numOpenStates (MarkovChannel attribute) numPools (Dsolve attribute) (Gsolve attribute) (Ksolve attribute) numProducts (ReacBase attribute) numProxyPools (Stoich attribute) numRates (Stoich attribute) numRows (SparseMsg attribute) numSegments (NeuroMesh attribute) numSpines (Neuron attribute) numStates (MarkovChannel attribute) numSubstrates (EnzBase attribute) (ReacBase attribute) numSynapses (SynHandlerBase attribute) numTables (Streamer attribute) numTicks (Clock attribute) numVarPools (SteadyState attribute) (Stoich attribute) numVars (Function attribute) numVoxels (Dsolve attribute) nVec (Dsolve attribute) (Gsolve attribute) (Ksolve attribute) nx (CubeMesh attribute) ny (CubeMesh attribute) nz (CubeMesh attribute)

O

OneToAllMsg (built-in class) onetoonemsg (module) oneVoxelVolume (ChemCompt attribute) origChannel() (MgBlock method) outerArea (DifShell attribute) outerDif (DifShell attribute) outerDifSourceOut (DifShell attribute) outfile (Streamer attribute) (Table attribute) (Table2 attribute) outflux() (DifShell method) output (Adaptor attribute) (Arith attribute) (DiffAmp attribute) (PIDController attribute) (PulseGen attribute), [1] (PyRun attribute) (RandGenerator attribute) (StimulusTable attribute)

outputOffset (Adaptor attribute) outputValue (Adaptor attribute) (Arith attribute) (DiffAmp attribute) (PIDController attribute) (PulseGen attribute), [1] (TableBase attribute) outputVar (PyRun attribute)

P

p (BinomialRng attribute) p2() (in module testWigglySpines) pairFill() (SparseMsg method) parent (Neutral attribute) parentCompartmentOfSpine (Neuron attribute) parentMsg() (Neutral method) parentVoxel (NeuroMesh attribute) (SpineMesh attribute) passiveDistribution (Neuron attribute) path (Dsolve attribute) (Neutral attribute) (Stoich attribute) pathDistanceFromSoma (Neuron attribute) permeability (NMDAChan attribute) permeabilityOut (ChanBase attribute) phi (Neuron attribute) PIDController (built-in class) plainPlot() (TableBase method) plusIn() (DiffAmp method) PoissonRng (built-in class) Pool (built-in class) pool (Species attribute) PoolBase (built-in class) poolIdMap (Stoich attribute) PostMaster (built-in class) prd (EnzBase attribute) (ReacBase attribute) prdDest() (EnzBase method) (ReacBase method) prdOut (EnzBase attribute) (ReacBase attribute) preserveNumEntries (CubeMesh attribute) probability (SparseMsg attribute) proc (Adaptor attribute) (Arith attribute) (CaConcBase attribute) (ChanBase attribute) (CompartmentBase attribute) (DiffAmp attribute) (Dsolve attribute) (EnzBase attribute) (Func attribute) (Function attribute) (GapJunction attribute) (Gsolve attribute) (HDF5DataWriter attribute) (HSolve attribute) (IntFire attribute) (Interpol attribute) (IzhikevichNrn attribute) (Ksolve attribute) (MarkovGslSolver attribute) (MarkovRateTable attribute) (MarkovSolver attribute) (MarkovSolverBase attribute) (MeshEntry attribute) (NSDFWriter attribute) (PIDController attribute) (PoolBase attribute) (PostMaster attribute) (PulseGen attribute), [1] (PyRun attribute) (RandGenerator attribute) (RandSpike attribute) (ReacBase attribute) (SpikeGen attribute) (Stats attribute) (StimulusTable attribute) (Streamer attribute) (SynHandlerBase attribute) (Table attribute) (Table2 attribute) (TimeTable attribute) (VClamp attribute) (ZombieFunction attribute) proc0 (Clock attribute) proc1 (Clock attribute) proc10 (Clock attribute) proc11 (Clock attribute) proc12 (Clock attribute) proc13 (Clock attribute) proc14 (Clock attribute) proc15 (Clock attribute) proc16 (Clock attribute) proc17 (Clock attribute) proc18 (Clock attribute) proc19 (Clock attribute) proc2 (Clock attribute) proc20 (Clock attribute) proc21 (Clock attribute) proc22 (Clock attribute) proc23 (Clock attribute) proc24 (Clock attribute) proc25 (Clock attribute) proc26 (Clock attribute) proc27 (Clock attribute) proc28 (Clock attribute) proc29 (Clock attribute) proc3 (Clock attribute)

proc30 (Clock attribute) proc31 (Clock attribute) proc4 (Clock attribute) proc5 (Clock attribute) proc6 (Clock attribute) proc7 (Clock attribute) proc8 (Clock attribute) proc9 (Clock attribute) process() (Adaptor method) (Arith method) (CaConcBase method) (ChanBase method) (CompartmentBase method) (DifShell method), [1] (DiffAmp method) (Dsolve method) (EnzBase method) (Func method) (Function method) (GapJunction method) (Gsolve method) (HDF5DataWriter method) (HSolve method) (IntFire method) (Interpol method) (IzhikevichNrn method) (Ksolve method) (MarkovGslSolver method) (MarkovRateTable method) (MarkovSolver method) (MarkovSolverBase method) (MeshEntry method) (NSDFWriter method) (PIDController method) (PoolBase method) (PostMaster method) (PulseGen method), [1] (PyRun method) (RandGenerator method) (RandSpike method) (ReacBase method) (SpikeGen method) (Stats method) (StimulusTable method) (Streamer method) (SynHandlerBase method) (Table method) (Table2 method) (TimeTable method) (VClamp method) (ZombieFunction method) (testSched method) process0 (Clock attribute) process1 (Clock attribute) process10 (Clock attribute) process11 (Clock attribute) process12 (Clock attribute) process13 (Clock attribute) process14 (Clock attribute) process15 (Clock attribute) process16 (Clock attribute) process17 (Clock attribute) process18 (Clock attribute) process19 (Clock attribute) process2 (Clock attribute) process20 (Clock attribute) process21 (Clock attribute) process22 (Clock attribute) process23 (Clock attribute) process24 (Clock attribute) process25 (Clock attribute) process26 (Clock attribute) process27 (Clock attribute) process28 (Clock attribute) process29 (Clock attribute) process3 (Clock attribute) process30 (Clock attribute) process31 (Clock attribute) process4 (Clock attribute) process5 (Clock attribute) process6 (Clock attribute) process7 (Clock attribute) process8 (Clock attribute) process9 (Clock attribute) process_0 (DifShell attribute) process_1 (DifShell attribute) proximal (SymCompartment attribute) proximalOnly (SymCompartment attribute) proximalOut (SymCompartment attribute), [1] proxyPools (Stoich attribute) psdArea (Spine attribute) psdList() (PsdMesh method) psdListOut (NeuroMesh attribute) PsdMesh (built-in class) PulseGen (built-in class), [1] pulsegen (module) pulsegen2 (module) PyRun (built-in class) pyrun (module)

Q

Q (MarkovRateTable attribute) (MarkovSolverBase attribute)

QIF (built-in class) quit() (Shell method)

R

r0 (CylMesh attribute) r1 (CylMesh attribute) Ra (CompartmentBase attribute) RA (Neuron attribute) RandGenerator (built-in class) randInject() (CompartmentBase method) randomInit() (SteadyState method) randomspike (module) RandSpike (built-in class) RandSpikeStats (module) rank (SteadyState attribute) rate (Function attribute) (RandSpike attribute) rateOut (Function attribute) ratio (CplxEnzBase attribute) raxial (CompartmentBase attribute) raxialCylinder() (SymCompartment method) raxialOut (CompartmentBase attribute) raxialSphere() (SymCompartment method), [1] raxialSym() (SymCompartment method), [1], [2] reac (PoolBase attribute) ReacBase (built-in class) reacDest() (PoolBase method) reacDiffBranchingNeuron (module) reacDiffConcGradient (module) reacDiffSpinyNeuron (module) reaction() (DifShell method) read_nsdf() (in module nsdf_vec) recurrentIntFire (module) recurrentLIF (module) refractoryPeriod (IntFire attribute) (IntFireBase attribute) refractT (RandSpike attribute) (SpikeGen attribute) reinit() (Adaptor method) (Arith method) (CaConcBase method) (ChanBase method) (Clock method) (CompartmentBase method) (DifShell method), [1] (DiffAmp method) (Dsolve method) (EnzBase method) (Func method) (Function method) (GapJunction method) (Gsolve method) (HDF5DataWriter method) (HSolve method) (IntFire method) (Interpol method) (IzhikevichNrn method) (Ksolve method) (MarkovGslSolver method) (MarkovRateTable method) (MarkovSolver method) (MarkovSolverBase method) (MeshEntry method) (NSDFWriter method) (PIDController method) (PoolBase method) (PostMaster method) (PulseGen method), [1] (PyRun method) (RandGenerator method) (RandSpike method) (ReacBase method) (SpikeGen method) (Stats method) (StimulusTable method) (Streamer method) (SynHandlerBase method) (Table method) (Table2 method) (TimeTable method) (VClamp method) (ZombieFunction method)

reinit0 (Clock attribute) reinit1 (Clock attribute) reinit10 (Clock attribute) reinit11 (Clock attribute) reinit12 (Clock attribute) reinit13 (Clock attribute) reinit14 (Clock attribute) reinit15 (Clock attribute) reinit16 (Clock attribute) reinit17 (Clock attribute) reinit18 (Clock attribute) reinit19 (Clock attribute) reinit2 (Clock attribute) reinit20 (Clock attribute) reinit21 (Clock attribute) reinit22 (Clock attribute) reinit23 (Clock attribute) reinit24 (Clock attribute) reinit25 (Clock attribute) reinit26 (Clock attribute) reinit27 (Clock attribute) reinit28 (Clock attribute) reinit29 (Clock attribute) reinit3 (Clock attribute) reinit30 (Clock attribute) reinit31 (Clock attribute) reinit4 (Clock attribute) reinit5 (Clock attribute) reinit6 (Clock attribute) reinit7 (Clock attribute) reinit8 (Clock attribute) reinit9 (Clock attribute) relativeAccuracy (MarkovGslSolver attribute) relaxationOsc (module) remesh() (EnzBase method) remeshOut (MeshEntry attribute) remeshReacsOut (MeshEntry attribute) removeTable() (Streamer method) removeTables() (Streamer method) repressillator (module) requestMolWt (PoolBase attribute) requestOut (Adaptor attribute) (Function attribute) (HDF5DataWriter attribute) (Stats attribute) (Table attribute) (Table2 attribute) reset_settle() (in module STDP) resetStencil() (ChemCompt method) resettle() (SteadyState method) responseScale (SeqSynHandler attribute) Rm (CompartmentBase attribute) RM (Neuron attribute) RmByTau (IzhikevichNrn attribute) rowStart (Stoich attribute) run() (PyRun method) (threading_demo.StatusThread method) (threading_demo.WorkerThread method) run_clamp() (in module traub_naf) run_sequence() (in module pyrun) run_sim() (in module traub_naf) runString (PyRun attribute) runtime (Annotator attribute) runTime (Clock attribute) rxdFuncDiffusion (module) rxdFuncDiffusionStoch (module) rxdReacDiffusion (module)

S

sample (RandGenerator attribute) saturation (DiffAmp attribute) (PIDController attribute) savemodel (module) scale (Adaptor attribute) (Nernst attribute) scaleBufsAndRates() (Stoich method) scaleVolumes (module) scriptGssaSolver (module) scriptKineticModel (module) scriptKineticSolver (module) sdev (Stats attribute) secondDelay (PulseGen attribute), [1] secondLevel (PulseGen attribute), [1] secondWidth (PulseGen attribute), [1] seed (HSolve attribute) (SparseMsg attribute) sensed (PIDController attribute) (VClamp attribute) sensedIn() (PIDController method) (VClamp method) separateSpines (NeuroMesh attribute) seqActivation (SeqSynHandler attribute) seqDt (SeqSynHandler attribute) SeqSynHandler (built-in class) set1d() (MarkovRateTable method) set2d() (MarkovRateTable method) setA() (IzhIF method) (IzhikevichNrn method) setA0() (AdExIF method) (AdThreshIF method) (IzhIF method) (QIF method) setAbs_refract() (RandSpike method) (SpikeGen method) setAbsoluteAccuracy() (MarkovGslSolver method) setAccommodating() (IzhikevichNrn method) setAlpha() (GammaRng method), [1] (HHGate method) (IzhikevichNrn method) setAlphaParms() (HHGate method) setAlwaysDiffuse() (CubeMesh method) setAMinus() (STDPSynHandler method) setAMinus0() (STDPSynHandler method) setAnyValue() (Arith method) setAPlus() (STDPSynapse method) setAPlus0() (STDPSynHandler method) setB() (CaConcBase method) (IzhIF method) (IzhikevichNrn method) setB0() (AdExIF method) (IzhIF method) setBaseDt() (Clock method) setBaseLevel() (PulseGen method), [1] setBeta() (HHGate method) (IzhikevichNrn method) setBistable() (GraupnerBrunel2012CaPlasticitySynHandler method) setBufferSize() (PostMaster method) setC() (Function method) (IzhikevichNrn method) setC0() (IzhIF method) setCa() (CaConcBase method) (GraupnerBrunel2012CaPlasticitySynHandler method) setCa_base() (CaConcBase method) setCaAdvance() (HSolve method) setCaBasal() (CaConcBase method) setCaDiv() (HSolve method) setCaInit() (GraupnerBrunel2012CaPlasticitySynHandler method) setCaMax() (HSolve method) setCaMin() (HSolve method) setCaPost() (GraupnerBrunel2012CaPlasticitySynHandler method) setCaPre() (GraupnerBrunel2012CaPlasticitySynHandler method) setCeiling() (CaConcBase method) setCeq() (DifShell method) setChannelDistribution() (Neuron method) setChunkSize() (HDF5WriterBase method) setCin() (Nernst method) setclock() (Shell method) setCm() (CompartmentBase method) setCM() (Neuron method) setCMg() (MgBlock method) (NMDAChan method) setColor() (Annotator method) setCommand() (PIDController method) setCompartment() (Dsolve method) (Ksolve method) (Stoich method) setCompartmentLengthInLambdas() (Neuron method) setCompression() (HDF5WriterBase method) setCompressor() (HDF5WriterBase method) setConc() (PoolBase method) setConcInit() (PoolBase method) setConcK1() (CplxEnzBase method) setCondFraction() (NMDAChan method) setconst() (MarkovRateTable method) setConvergenceCriterion() (SteadyState method) setCoords() (CubeMesh method) (CylMesh method) setCount() (PulseGen method), [1] setCout() (Nernst method) setD() (DifShell method) (IzhIF method) (IzhikevichNrn method) setDelay() (PulseGen method), [1] (Synapse method) setDelayD() (GraupnerBrunel2012CaPlasticitySynHandler method) setDeltaThresh() (ExIF method) setDiameter() (CaConcBase method) (CompartmentBase method) (DifShell method) setDiffConst() (PoolBase method) setDiffLength() (CylMesh method) (NeuroMesh method) setDiffScale() (Dsolve method) setDiffVol1() (Dsolve method) setDiffVol2() (Dsolve method) setDirpath() (Annotator method) setDivs() (HHGate method) setDoLoop() (StimulusTable method) setDoubleAttr() (HDF5WriterBase method) setDoubleVecAttr() (HDF5WriterBase method) setDsolve() (Stoich method) setDt() (HSolve method) setDx() (CubeMesh method) (Interpol2D method) setDy() (CubeMesh method) (Interpol2D method) setDz() (CubeMesh method) setEdgeTriggered() (SpikeGen method) setEk() (ChanBase method) setEm() (CompartmentBase method) (Neuron method) setEntry() (SparseMsg method) setEpsAbs() (Ksolve method) setEpsRel() (Ksolve method) setExpr() (Func method) (Function method) setExtCa() (NMDAChan method) setFilename() (HDF5WriterBase method) (TimeTable method) setFirstDelay() (PulseGen method), [1] setFirstLevel() (PulseGen method), [1] setFirstWidth() (PulseGen method), [1] setFloor() (CaConcBase method) setFlushLimit() (HDF5DataWriter method) setFormat() (Streamer method) (Table method) (Table2 method) setFunction() (Arith method) setGain() (DiffAmp method) (PIDController method) (VClamp method) setGamma() (IzhikevichNrn method) setGammaD() (GraupnerBrunel2012CaPlasticitySynHandler method) setGammaP() (GraupnerBrunel2012CaPlasticitySynHandler method) setGbar() (ChanBase method) (MarkovChannel method) setGeomAndElec() (CompartmentBase method) setGeometryPolicy() (NeuroMesh method) setGk() (ChanBase method) (GapJunction method) setHeadDiameter() (Spine method) setHeadLength() (Spine method) setHeadVolume() (Spine method) setHistoryTime() (SeqSynHandler method) setI1() (OneToAllMsg method) (SingleMsg method) setI2() (SingleMsg method) setIcon() (Annotator method) setIndependent() (Function method) setInitialState() (MarkovChannel method) (MarkovSolverBase method) setInitString() (PyRun method) setInitU() (IzhikevichNrn method) setInitVm() (CompartmentBase method) (IzhikevichNrn method) setInject() (CompartmentBase method) (IzhikevichNrn method) setInnerArea() (DifShell method) setInputOffset() (Adaptor method) setInputVar() (PyRun method) setInstant() (HHChannel2D method) (HHChannelBase method) setIntCa() (NMDAChan method) setIntCaOffset() (NMDAChan method) setIntCaScale() (NMDAChan method) setInternalDt() (MarkovGslSolver method) setIsToroid() (CubeMesh method) setK1() (CplxEnzBase method) setK2() (CplxEnzBase method) setK3() (CplxEnzBase method) setKb() (ReacBase method) setKcat() (EnzBase method) setKernelEquation() (SeqSynHandler method) setKernelWidth() (SeqSynHandler method) setKf() (ReacBase method) setKm() (EnzBase method) setKMg_A() (MgBlock method) (NMDAChan method) setKMg_B() (MgBlock method) (NMDAChan method) setKmK1() (Enz method) setKsolve() (Stoich method) setLabels() (MarkovChannel method) setLeak() (DifShell method) setLength() (CaConcBase method) (CompartmentBase method) (DifShell method) setLevel() (PulseGen method), [1] setLigandConc() (MarkovChannel method) (MarkovRateTable method) setLongAttr() (HDF5WriterBase method) setLongVecAttr() (HDF5WriterBase method) setLoopTime() (StimulusTable method) setMax() (HHGate method) (UniformRng method) setMaxIter() (SteadyState method) setMean() (ExponentialRng method) (NormalRng method) (PoissonRng method) setMeshToSpace() (CubeMesh method) setMethod() (ExponentialRng method) (Ksolve method) (MarkovGslSolver method) (NormalRng method) (TimeTable method) setMin() (HHGate method) (UniformRng method) setMInfinity() (HHGate method) setMode() (Func method) (Function method) (HDF5WriterBase method) (PyRun method) (VClamp method) setModeltype() (Annotator method) setModulation() (ChanBase method) setMolWt() (Species method) setMotorConst() (PoolBase method) setN() (BinomialRng method) (PoolBase method) setName() (Neutral method) (Table method) (Table2 method) setNInit() (PoolBase method) setNoiseSD() (GraupnerBrunel2012CaPlasticitySynHandler method) setNoisy() (GraupnerBrunel2012CaPlasticitySynHandler method) setNormalizeWeights() (SynChan method) setNotes() (Annotator method) setNumAllVoxels() (Gsolve method) (Ksolve method) setNumData() (Neutral method) setNumEventInput() (NSDFWriter method) setNumField() (Neutral method) setNumGateX() (HHChannel2D method) (HHChannelBase method) setNumGateY() (HHChannel2D method) (HHChannelBase method) setNumGateZ() (HHChannel2D method) (HHChannelBase method) setNumKb() (ReacBase method) setNumKf() (ReacBase method) setNumKm() (EnzBase method) setNumMesh() (ChemCompt method) setNumOpenStates() (MarkovChannel method) setNumPools() (Dsolve method) (Gsolve method) (Ksolve method) setNumSpine() (Neuron method) setNumStates() (MarkovChannel method) setNumSynapse() (GraupnerBrunel2012CaPlasticitySynHandler method) (STDPSynHandler method) (SeqSynHandler method) (SimpleSynHandler method), [1] setNumSynapses() (SynHandlerBase method) setNumVars() (Function method) setNumX() (Function method) setNVec() (Dsolve method) (Gsolve method) (Ksolve method) setNx() (CubeMesh method) setNy() (CubeMesh method) setNz() (CubeMesh method) setOneVoxelVolume() (ChemCompt method) setOuterArea() (DifShell method) setOutfile() (Streamer method) (Table method) (Table2 method) setOutputOffset() (Adaptor method) setOutputValue() (Arith method) setOutputVar() (PyRun method) setP() (BinomialRng method) setPassiveDistribution() (Neuron method) setPath() (Dsolve method) (Stoich method) setPermeability() (NMDAChan method) setPhi() (Neuron method) setPreserveNumEntries() (CubeMesh method) setProbability() (SparseMsg method) setPsdArea() (Spine method) setR0() (CylMesh method) setR1() (CylMesh method) setRa() (CompartmentBase method) setRA() (Neuron method) setRandomConnectivity() (SparseMsg method) setRate() (RandSpike method) setRatio() (CplxEnzBase method) setRefractoryPeriod() (IntFire method) (IntFireBase method) setRefractT() (RandSpike method) (SpikeGen method) setRelativeAccuracy() (MarkovGslSolver method) setResponseScale() (SeqSynHandler method) setRm() (CompartmentBase method) setRM() (Neuron method) setRmByTau() (IzhikevichNrn method) setRunString() (PyRun method) setRuntime() (Annotator method) setSaturation() (DiffAmp method) (PIDController method)

setScale() (Adaptor method) (Nernst method) setSecondDelay() (PulseGen method), [1] setSecondLevel() (PulseGen method), [1] setSecondWidth() (PulseGen method), [1] setSeed() (HSolve method) (SparseMsg method) setSeparateSpines() (NeuroMesh method) setSeqDt() (SeqSynHandler method) setShaftDiameter() (Spine method) setShaftLength() (Spine method) setShapeMode() (DifShell method) setSolver() (Annotator method) setSourceFile() (Neuron method) setSpaceToMesh() (CubeMesh method) setSpeciesId() (PoolBase method) setSpineAndPsdDsolve() (Neuron method) setSpineAndPsdMesh() (Neuron method) setSpineDistribution() (Neuron method) setStartTime() (StimulusTable method) setStepPosition() (StimulusTable method) setStepSize() (StimulusTable method) setStoich() (Dsolve method) (Gsolve method) (SteadyState method) setStopTime() (StimulusTable method) setStride() (DiagonalMsg method) setStringAttr() (HDF5WriterBase method) setStringVecAttr() (HDF5WriterBase method) setSubTree() (NeuroMesh method) setSubTreePath() (NeuroMesh method) setSurface() (CubeMesh method) setTable() (Interpol2D method) (VectorTable method) setTableA() (HHGate method) (HHGate2D method) setTableB() (HHGate method) (HHGate2D method) setTableVector2D() (Interpol2D method) setTarget() (HSolve method) setTau() (CaConcBase method) (HHGate method) (IntFire method) (VClamp method) setTau1() (SynChan method) setTau2() (SynChan method) setTauCa() (GraupnerBrunel2012CaPlasticitySynHandler method) setTauD() (PIDController method) setTauI() (PIDController method) setTauMinus() (STDPSynHandler method) setTauPlus() (STDPSynHandler method) setTauSyn() (GraupnerBrunel2012CaPlasticitySynHandler method) setTauThresh() (AdThreshIF method) setTauW() (AdExIF method) setTd() (VClamp method) setTemperature() (Nernst method) (NMDAChan method) setTextColor() (Annotator method) setTheta() (GammaRng method), [1] (Neuron method) setThetaD() (GraupnerBrunel2012CaPlasticitySynHandler method) setThetaP() (GraupnerBrunel2012CaPlasticitySynHandler method) setThick() (CaConcBase method) setThickness() (DifShell method) (PsdMesh method) setThis() (Mstring method) (Neutral method) setThresh() (IntFire method) (IntFireBase method) setThreshAdaptive() (AdThreshIF method) setThreshJump() (AdThreshIF method) setThreshold() (SpikeGen method) (SpikeStats method), [1] (Table method) (Table2 method) setTi() (VClamp method) setTick() (Neutral method) setTickDt() (Clock method) setTickStep() (Clock method) settle() (SteadyState method) setTotal() (SteadyState method) setTotalLength() (Spine method) setTrigMode() (PulseGen method), [1] setU() (IzhIF method) setU0() (IzhikevichNrn method) setUInit() (IzhIF method) setup_electronics() (in module traub_naf) setup_experiment() (in module twocells) setup_model() (in module nsdf) (in module traub_naf) setup_synapse() (in module intfire) setup_two_cells() (in module lifcomp) (in module multicomp_lif) setupAlpha() (HHGate method) setupGate() (HHGate method) setupMatrix() (SteadyState method) setupmodel() (in module lif) setupModel() (in module STDP) setupTau() (HHGate method) setUseClockedUpdate() (Gsolve method) setUseConcentration() (HHChannelBase method) setUseInterpolation() (HHGate method) setUseRandInit() (Gsolve method) setUseStreamer() (Table method) (Table2 method) setValence() (DifShell method) (Nernst method) setValue() (Mstring method) (Variable method) setVar() (Func method) setVariance() (NormalRng method) setVCritical() (QIF method) setVDiv() (HSolve method) setVector() (TableBase method) setVm() (CompartmentBase method) (IntFire method) (IzhikevichNrn method) (MarkovChannel method) (MarkovRateTable method) setVMax() (HSolve method) setVmax() (IzhikevichNrn method) setVMin() (HSolve method) setVolume() (ChemCompt method) (DifShell method) (PoolBase method) setVolumeNotRates() (ChemCompt method) setVPeak() (ExIF method) (IzhIF method) setVReset() (IntFireBase method) setW() (AdExIF method) setWeight() (Synapse method) setWeightMax() (GraupnerBrunel2012CaPlasticitySynHandler method) (STDPSynHandler method) setWeightMin() (GraupnerBrunel2012CaPlasticitySynHandler method) (STDPSynHandler method) setWeightScale() (GraupnerBrunel2012CaPlasticitySynHandler method) (SeqSynHandler method) setWidth() (PulseGen method), [1] setWindowLength() (Stats method) setX() (Annotator method) (CompartmentBase method) (Func method) (HHChannel2D method) (HHChannelBase method) setX0() (CompartmentBase method) (CubeMesh method) (CylMesh method) setX1() (CubeMesh method) (CylMesh method) setXdivs() (Interpol2D method) (MarkovSolverBase method) (VectorTable method) setXdivsA() (HHGate2D method) setXdivsB() (HHGate2D method) setXindex() (HHChannel2D method) setXmax() (Interpol method) (Interpol2D method) (MarkovSolverBase method) (VectorTable method) setXmaxA() (HHGate2D method) setXmaxB() (HHGate2D method) setXmin() (Interpol method) (Interpol2D method) (MarkovSolverBase method) (VectorTable method) setXminA() (HHGate2D method) setXminB() (HHGate2D method) setXpower() (HHChannel2D method) (HHChannelBase method) setY() (Annotator method) (CompartmentBase method) (Func method) (HHChannel2D method) (HHChannelBase method) setY0() (CompartmentBase method) (CubeMesh method) (CylMesh method) setY1() (CubeMesh method) (CylMesh method) setYdivs() (Interpol2D method) (MarkovSolverBase method) setYdivsA() (HHGate2D method) setYdivsB() (HHGate2D method) setYindex() (HHChannel2D method) setYmax() (Interpol2D method) (MarkovSolverBase method) setYmaxA() (HHGate2D method) setYmaxB() (HHGate2D method) setYmin() (Interpol2D method) (MarkovSolverBase method) setYminA() (HHGate2D method) setYminB() (HHGate2D method) setYpower() (HHChannel2D method) (HHChannelBase method) setZ() (Annotator method) (CompartmentBase method) (Func method) (HHChannel2D method) (HHChannelBase method) setZ0() (CompartmentBase method) (CubeMesh method) (CylMesh method) setZ1() (CubeMesh method) (CylMesh method) setZindex() (HHChannel2D method) setZk() (MgBlock method) setZpower() (HHChannel2D method) (HHChannelBase method) shaftDiameter (Spine attribute) shaftLength (Spine attribute) shapeMode (DifShell attribute) Shell (built-in class) showclocks (module) showMatrices() (SteadyState method) showmsg (module) sibling (SymCompartment attribute) SimpleSynHandler (built-in class), [1] single_population() (in module compartment_net_no_array) SingleMsg (built-in class) singlemsgcross (module) size (MarkovRateTable attribute) (TableBase attribute) solutionStatus (SteadyState attribute) solver (Annotator attribute) sourceFields (Neutral attribute) sourceFile (Neuron attribute) spaceToMesh (CubeMesh attribute) SparseMsg (built-in class) Species (built-in class) species (PoolBase attribute) speciesId (PoolBase attribute) sphere (SymCompartment attribute) spike() (Table method) (Table2 method) SpikeGen (built-in class) spikeOut (IntFire attribute) (IntFireBase attribute) (IzhikevichNrn attribute) (RandSpike attribute) (SpikeGen attribute) SpikeStats (built-in class), [1] Spine (built-in class) spineDistribution (Neuron attribute) spineList() (SpineMesh method) spineListOut (NeuroMesh attribute) SpineMesh (built-in class) spinesFromExpression (Neuron attribute) spinesOnCompartment (Neuron attribute) spineVoxelOnDendVoxel (NeuroMesh attribute) spineVoxelsOnCompartment (NeuroMesh attribute) src (Finfo attribute) srcFieldsOnE1 (Msg attribute) srcFieldsOnE2 (Msg attribute) start() (Clock method) startstop (module) startTime (StimulusTable attribute) startVoxelInCompt (NeuroMesh attribute) (PsdMesh attribute) (SpineMesh attribute) state (MarkovChannel attribute) (MarkovSolverBase attribute) (TimeTable attribute) stateOut (MarkovGslSolver attribute) (MarkovSolverBase attribute) stateType (SteadyState attribute) Stats (built-in class) status (SteadyState attribute) (Stoich attribute) StatusThread (class in threading_demo) STDP (module) STDPSynapse (built-in class) STDPSynHandler (built-in class) SteadyState (built-in class) stencilIndex (ChemCompt attribute) stencilRate (ChemCompt attribute) step() (Clock method) stepPosition (StimulusTable attribute) stepSize (StimulusTable attribute) stimtable (module) stimulus_table_demo() (in module stimtable) StimulusTable (built-in class) stochasticLotkaVolterra (module) Stoich (built-in class) stoich (Dsolve attribute) (Gsolve attribute) (Ksolve attribute) (SteadyState attribute) stop() (Clock method) stopTime (StimulusTable attribute) storeInflux() (DifShell method) storeOutflux() (DifShell method) Streamer (built-in class) stride (Clock attribute) (DiagonalMsg attribute) stringAttr (HDF5WriterBase attribute) stringVecAttr (HDF5WriterBase attribute) strongBis (module) sub (EnzBase attribute) (ReacBase attribute) subDest() (EnzBase method) (ReacBase method) subOut (EnzBase attribute) (ReacBase attribute) subTree (NeuroMesh attribute) subTreePath (NeuroMesh attribute) sum (Stats attribute) sumRaxial() (SymCompartment method), [1], [2] sumRaxialOut (SymCompartment attribute), [1], [2] surface (CubeMesh attribute) switchKineticSolvers (module) SymCompartment (built-in class) symcompartment (module) Synapse (built-in class) synapse (module) synapse_tutorial (module) SynChan (built-in class) SynHandlerBase (built-in class)

T

Table (built-in class) table (Interpol2D attribute) (VectorTable attribute) Table2 (built-in class) tableA (HHGate attribute) (HHGate2D attribute) tableB (HHGate attribute) (HHGate2D attribute) TableBase (built-in class) tabledemo (module) tableVector2D (Interpol2D attribute) target (HSolve attribute) tau (CaConcBase attribute) (HHGate attribute) (IntFire attribute) (VClamp attribute) tau1 (SynChan attribute) tau2 (SynChan attribute) tauCa (GraupnerBrunel2012CaPlasticitySynHandler attribute) tauD (PIDController attribute) tauI (PIDController attribute) tauMinus (STDPSynHandler attribute) tauPlus (STDPSynHandler attribute) tauPump() (DifShell method) tauSyn (GraupnerBrunel2012CaPlasticitySynHandler attribute) tauThresh (AdThreshIF attribute) tauW (AdExIF attribute) td (VClamp attribute) Temperature (Nernst attribute) temperature (NMDAChan attribute) test_crossing_single() (in module singlemsgcross) test_one_to_one() (in module onetoonemsg) test_symcompartment() (in module symcompartment) testRdesigneur (module) testSched (built-in class) testSigNeur (module) testWigglySpines (module) textColor (Annotator attribute) theta (GammaRng attribute), [1] (Neuron attribute)

thetaD (GraupnerBrunel2012CaPlasticitySynHandler attribute) thetaP (GraupnerBrunel2012CaPlasticitySynHandler attribute) thick (CaConcBase attribute) thickness (DifShell attribute) (PsdMesh attribute) this (Mstring attribute) (Neutral attribute) threading_demo (module) thresh (IntFire attribute) (IntFireBase attribute) threshAdaptive (AdThreshIF attribute) threshJump (AdThreshIF attribute) threshold (SpikeGen attribute) (SpikeStats attribute), [1] (Table attribute) (Table2 attribute) ti (VClamp attribute) tick (Neutral attribute) tickDt (Clock attribute) tickStep (Clock attribute) TimeTable (built-in class) timetable (module) timetable_file() (in module timetable) timetable_nparray() (in module timetable) total (SteadyState attribute) totalLength (Spine attribute) totLength (CylMesh attribute) transportBranchingNeuron (module) transpose() (SparseMsg method) traub_naf (module) trigger() (PyRun method) trigMode (PulseGen attribute), [1] tripletFill() (SparseMsg method) TuringOneDim (module) tweakAlpha() (HHGate method) tweakingParameters (module) tweakTau() (HHGate method) two_populations() (in module compartment_net_no_array) twocells (module) type (Finfo attribute)

U

u (IzhIF attribute) (IzhikevichNrn attribute) u0 (IzhikevichNrn attribute) uInit (IzhIF attribute) UniformRng (built-in class) unsetEntry() (SparseMsg method) unzombify() (Stoich method)

useClock() (Shell method) useClockedUpdate (Gsolve attribute) useConcentration (HHChannelBase attribute) useInterpolation (HHGate attribute) useRandInit (Gsolve attribute) useStreamer (Table attribute) (Table2 attribute)

V

valence (DifShell attribute) (Nernst attribute) value (Func attribute) (Function attribute) (Mstring attribute) (Variable attribute) valueFields (Neutral attribute) valueOut (Func attribute) (Function attribute) valuesFromExpression (Neuron attribute) var (Func attribute) Variable (built-in class) variance (NormalRng attribute) (RandGenerator attribute) varIn() (Func method) vars (Func attribute) VClamp (built-in class) vclamp (module) vclamp_demo() (in module vclamp) vCritical (QIF attribute) vDiv (HSolve attribute) vector (TableBase attribute) vectors (module) VectorTable (built-in class) Vm (CompartmentBase attribute) (IntFire attribute) (IzhikevichNrn attribute) (MarkovChannel attribute) (MarkovRateTable attribute)

Vm() (ChanBase method), [1] (SpikeGen method) (SpikeStats method), [1] Vm1() (GapJunction method) Vm2() (GapJunction method) vMax (HSolve attribute) Vmax (IzhikevichNrn attribute) vMin (HSolve attribute) VmOut (CompartmentBase attribute) (IzhikevichNrn attribute), [1] volume (ChemCompt attribute) (DifShell attribute) (MeshEntry attribute) (PoolBase attribute) voxelMidpoint (ChemCompt attribute) voxelVol() (Gsolve method) (Ksolve method) voxelVolOut (ChemCompt attribute) voxelVolume (ChemCompt attribute) vPeak (ExIF attribute) (IzhIF attribute) vReset (IntFireBase attribute) Vreset (lifcomp.LIFComp attribute) (multicomp_lif.LIFComp attribute) Vthreshold (lifcomp.LIFComp attribute) (multicomp_lif.LIFComp attribute)

W

w (AdExIF attribute) weight (Synapse attribute) weightMax (GraupnerBrunel2012CaPlasticitySynHandler attribute) (STDPSynHandler attribute) weightMin (GraupnerBrunel2012CaPlasticitySynHandler attribute) (STDPSynHandler attribute) weightScale (GraupnerBrunel2012CaPlasticitySynHandler attribute) (SeqSynHandler attribute) weightScaleVec (SeqSynHandler attribute)

width (PulseGen attribute), [1] widthIn() (PulseGen method), [1] wildcard (module) windowLength (Stats attribute) wmean (Stats attribute) wnum (Stats attribute) WorkerThread (class in threading_demo) write_nsdf() (in module nsdf_vec) wsdev (Stats attribute) wsum (Stats attribute)

X

x (Annotator attribute) (CompartmentBase attribute) (Func attribute) X (HHChannel2D attribute) (HHChannelBase attribute) x0 (CompartmentBase attribute) (CubeMesh attribute) (CylMesh attribute) x1 (CubeMesh attribute) (CylMesh attribute) xCompt (Gsolve attribute) (Ksolve attribute) xComptIn() (Gsolve method) (Ksolve method) xComptOut (Gsolve attribute) (Ksolve attribute) xdivs (Interpol2D attribute) (MarkovSolverBase attribute) (VectorTable attribute) xdivsA (HHGate2D attribute)

xdivsB (HHGate2D attribute) xIn() (Func method) Xindex (HHChannel2D attribute) xmax (Interpol attribute) (Interpol2D attribute) (MarkovSolverBase attribute) (VectorTable attribute) xmaxA (HHGate2D attribute) xmaxB (HHGate2D attribute) xmin (Interpol attribute) (Interpol2D attribute) (MarkovSolverBase attribute) (VectorTable attribute) xminA (HHGate2D attribute) xminB (HHGate2D attribute) xplot() (TableBase method) Xpower (HHChannel2D attribute) (HHChannelBase attribute) xyIn() (Func method) xyzIn() (Func method)

Y

y (Annotator attribute) (CompartmentBase attribute) (Func attribute) Y (HHChannel2D attribute) (HHChannelBase attribute) y (Interpol attribute) (TableBase attribute) y0 (CompartmentBase attribute) (CubeMesh attribute) (CylMesh attribute) y1 (CubeMesh attribute) (CylMesh attribute) ydivs (Interpol2D attribute) (MarkovSolverBase attribute)

ydivsA (HHGate2D attribute) ydivsB (HHGate2D attribute) yIn() (Func method) Yindex (HHChannel2D attribute) ymax (Interpol2D attribute) (MarkovSolverBase attribute) ymaxA (HHGate2D attribute) ymaxB (HHGate2D attribute) ymin (Interpol2D attribute) (MarkovSolverBase attribute) yminA (HHGate2D attribute) yminB (HHGate2D attribute) Ypower (HHChannel2D attribute) (HHChannelBase attribute)

Z

z (Annotator attribute) (CompartmentBase attribute) (Func attribute) Z (HHChannel2D attribute) (HHChannelBase attribute) z (Interpol2D attribute) z0 (CompartmentBase attribute) (CubeMesh attribute) (CylMesh attribute)

z1 (CubeMesh attribute) (CylMesh attribute) zIn() (Func method) Zindex (HHChannel2D attribute) Zk (MgBlock attribute) ZombieCaConc (built-in class) ZombieCompartment (built-in class) ZombieFunction (built-in class) Zpower (HHChannel2D attribute) (HHChannelBase attribute)