Index

A

A (HHGate attribute) (HHGate2D attribute) a (IzhikevichNrn 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) addSpike() (SpikeStats method) (Synapse method) aDest() (IzhikevichNrn method) adjacent (Msg attribute) alpha (HHGate attribute) (IzhikevichNrn attribute) alphaParms (HHGate attribute)

alwaysDiffuse (CubeMesh attribute) analogStimTable (module) analogStimTable() (in module analogStimTable) Annotator (built-in class) anyValue (Arith attribute) arg1() (Arith method) (MathFunc method) arg1Value (Arith attribute) arg1x2() (Arith method) arg2() (Arith method) (MathFunc method) arg3() (Arith method) (MathFunc method) arg4() (MathFunc method) Arith (built-in class) axial (CompartmentBase attribute) axialOut (CompartmentBase attribute)

B

B (CaConcBase attribute) (HHGate attribute) (HHGate2D attribute) b (IzhikevichNrn attribute) badStoichiometry (SteadyState attribute) basal() (CaConcBase method) baseClass (Cinfo attribute) baseDt (Clock attribute) baseLevel (PulseGen attribute) bDest() (IzhikevichNrn method)

beta (HHGate attribute) (IzhikevichNrn attribute) buffer (DifShell attribute) bufferSize (PostMaster attribute) BufPool (built-in class) buildDefaultMesh() (ChemCompt method) buildNeuroMeshJunctions() (Dsolve method) buildXreacs() (Stoich method)

C

C (DifShell attribute) c (Function attribute) (IzhikevichNrn attribute) C (RC attribute) Ca (CaConcBase 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) caMax (HSolve attribute) caMin (HSolve attribute) cDest() (IzhikevichNrn method) ce() (in module moose) ceiling (CaConcBase attribute) cell (NeuroMesh attribute) cellPortion() (NeuroMesh method) Ceq (DifShell attribute) ChanBase (built-in class) channel (ChanBase attribute) (CompartmentBase attribute) (IzhikevichNrn attribute) (MarkovRateTable attribute) (MarkovSolverBase attribute) channel1 (GapJunction attribute) channel1Out (GapJunction attribute) channel2 (GapJunction attribute) channel2Out (GapJunction 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) CMg (MgBlock 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) CompartmentBase (built-in class) 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) connect() (in module moose) (moose.melement method) convergenceCriterion (SteadyState attribute) Coordinates (MeshEntry attribute) coords (CubeMesh attribute) (CylMesh attribute) copy() (in module moose) (Shell method) count (PulseGen attribute) Cout (Nernst attribute) cplx (CplxEnzBase attribute) cplxDest() (CplxEnzBase method) CplxEnzBase (built-in class) cplxOut (CplxEnzBase attribute) create() (Shell method) create_1comp_neuron() (in module ionchannel) create_cell() (in module randomspike) create_k_proto() (in module ionchannel) create_model() (in module twocells) create_na_proto() (in module ionchannel) createGate() (HHChannelBase method) crossComptNeuroMesh (module) crossComptOscillator (module) crossComptSimpleReac (module) CubeMesh (built-in class) current (VClamp attribute) current() (CaConcBase method) current_step_test() (in module ionchannel) currentFraction() (CaConcBase method) currentOut (VClamp attribute) currentStep (Clock attribute) currentTime (Clock attribute) cylinder (SymCompartment attribute) cylinderDiffusion (module) cylinderOut (SymCompartment attribute) CylMesh (built-in class)

D

D (DifShell attribute) d (IzhikevichNrn attribute) dataIndex (moose.ElementField attribute) dDest() (IzhikevichNrn method) decrease() (CaConcBase method) decrement() (Pool method) delay (PulseGen attribute) (Synapse attribute) delayIn() (PulseGen method) delete() (in module moose) (Shell method) (moose.vec method) derivative (Func attribute) (Function attribute) (PIDController attribute) derivativeOut (Func attribute) (Function attribute) dest (Finfo attribute) DestField (class in moose) destFields (Neutral attribute) destFieldsOnE1 (Msg attribute) destFieldsOnE2 (Msg attribute) DiagonalMsg (built-in class) diameter (CompartmentBase attribute) (DifShell attribute) DiffAmp (built-in class) diffConst (PoolBase attribute) diffEqSolution (module)

diffLength (CylMesh attribute) (NeuroMesh attribute) DiffusionArea (MeshEntry attribute) DiffusionScaling (MeshEntry attribute) DifShell (built-in class) dimensions (MeshEntry attribute) distal (SymCompartment attribute) distalOut (SymCompartment attribute), [1], [2] divs (HHGate attribute) doc() (in module moose) 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) elecComptMap (NeuroMesh attribute) element() (in module moose) ElementField (class in moose) Em (CompartmentBase attribute) endVoxelInCompt (NeuroMesh 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) EREST_ACT (in module ionchannel) error (PIDController attribute) estimatedDt (Ksolve attribute) eventOut (TimeTable attribute) example() (in module function) (in module hdfdemo) (in module randomspike) (in module tabledemo) ExcInhNet (class in ExcInhNet_HigginsGraupnerBrunel2014) (class in ExcInhNet_Ostojic2014_Brunel2000) ExcInhNet_HigginsGraupnerBrunel2014 (module) ExcInhNet_Ostojic2014_Brunel2000 (module) ExcInhNetBase (class in ExcInhNet_HigginsGraupnerBrunel2014) (class in ExcInhNet_Ostojic2014_Brunel2000) exists() (in module moose) expr (Func attribute) (Function attribute)

F

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) firstLevel (PulseGen attribute) firstWidth (PulseGen attribute) floor (CaConcBase attribute) flush() (HDF5WriterBase method)

flushLimit (HDF5DataWriter attribute) fluxFromIn() (DifShell method) fluxFromOut() (DifShell method) fOutflux() (DifShell method) Func (built-in class) FuncBase (built-in class) FuncPool (built-in class) funcRateHarmonicOsc (module) funcReacLotkaVolterra (module) function (Arith attribute) Function (built-in class) function (MathFunc attribute) (module)

G

gain (DiffAmp attribute) (PIDController attribute) (VClamp attribute) gainDest() (PIDController method) gainIn() (DiffAmp method) gamma (IzhikevichNrn attribute) GapJunction (built-in class) Gbar (ChanBase attribute) gbar (MarkovChannel attribute) geometryPolicy (NeuroMesh attribute) getA() (HHGate method) (HHGate2D method) (IzhikevichNrn method) getAbs_refract() (RandSpike method) (SpikeGen method) getAbsoluteAccuracy() (MarkovGslSolver method) getAccommodating() (IzhikevichNrn method) getAdjacent() (Msg method) getAlpha() (HHGate method) (IzhikevichNrn method) getAlphaParms() (HHGate method) getAlwaysDiffuse() (CubeMesh method) getAnyValue() (Arith method) getArg1Value() (Arith method) getB() (CaConcBase method) (HHGate method) (HHGate2D method) (IzhikevichNrn method) getBadStoichiometry() (SteadyState method) getBaseClass() (Cinfo method) getBaseDt() (Clock method) getBaseLevel() (PulseGen method) getBeta() (HHGate method) (IzhikevichNrn method) getBufferSize() (PostMaster method) getC() (DifShell method) (Function method) (IzhikevichNrn method) (RC method) getCa() (CaConcBase method) getCa_base() (CaConcBase method) getCaAdvance() (HSolve method) getCaBasal() (CaConcBase method) getCaDiv() (HSolve method) getCaMax() (HSolve method) getCaMin() (HSolve method) getCeiling() (CaConcBase method) getCell() (NeuroMesh method) getCeq() (DifShell method) getChildren() (Neutral method) getChunkSize() (HDF5WriterBase method) getCin() (Nernst method) getClassName() (Neutral method) getCm() (CompartmentBase method) getCMg() (MgBlock method) getColor() (Annotator method) getColumnIndex() (Stoich method) getCommand() (PIDController method) (VClamp method) getCompartment() (Dsolve method) (Ksolve method) (Stoich method) getCompression() (HDF5WriterBase method) getCompressor() (HDF5WriterBase method) getConc() (PoolBase method) getConcInit() (PoolBase method) getConcK1() (CplxEnzBase method) getConvergenceCriterion() (SteadyState method) getCoordinates() (MeshEntry method) getCoords() (CubeMesh method) (CylMesh method) getCount() (PulseGen method) getCout() (Nernst method) getCurrent() (VClamp method) getCurrentStep() (Clock method) getCurrentTime() (Clock method) getCwe() (in module moose) getD() (DifShell method) (IzhikevichNrn method) getDataIndex() (moose.melement method) getDelay() (PulseGen method) (Synapse method) getDerivative() (Func method) (Function method) (PIDController method) getDest() (Finfo method) getDestFields() (Neutral method) getDestFieldsOnE1() (Msg method) getDestFieldsOnE2() (Msg method) getDiameter() (CompartmentBase method) (DifShell method) getDiffConst() (PoolBase method) getDiffLength() (CylMesh method) (NeuroMesh method) getDiffusionArea() (MeshEntry method) getDiffusionScaling() (MeshEntry method) getDimensions() (MeshEntry 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) getElecComptMap() (NeuroMesh method) getEm() (CompartmentBase method) getEndVoxelInCompt() (NeuroMesh method) getEpsAbs() (Ksolve method) getEpsRel() (Ksolve method) getError() (PIDController method) getEstimatedDt() (Ksolve method) getExpr() (Func method) (Function method) getField() (in module moose) (moose.melement method) getFieldDict() (in module moose) getFieldIndex() (moose.melement method) getFieldName() (Finfo method) getFieldNames() (in module moose) (moose.melement method) getFieldType() (moose.melement method) getFilename() (HDF5WriterBase method) (TimeTable method) getFirstDelay() (PulseGen method) getFirstLevel() (PulseGen method) getFirstWidth() (PulseGen method) getFloor() (CaConcBase method) getFlushLimit() (HDF5DataWriter method) getFunction() (Arith method) (MathFunc method) getGain() (DiffAmp method) (PIDController method) (VClamp method) getGamma() (IzhikevichNrn method) getGbar() (ChanBase method) (MarkovChannel method) getGeometryPolicy() (NeuroMesh method) getGk() (ChanBase method) (GapJunction method) getHasFired() (IntFireBase method) (RandSpike method) (SpikeGen method) getI1() (OneToAllMsg method) (SingleMsg method) getI2() (SingleMsg method) getIcon() (Annotator method) getId() (moose.melement method) getIk() (ChanBase method) getIm() (CompartmentBase method) (IzhikevichNrn method) getIndependent() (Function method) getInitialState() (MarkovChannel method) (MarkovSolverBase method) getInitU() (IzhikevichNrn method) getInitVm() (CompartmentBase method) (IzhikevichNrn method) getInject() (CompartmentBase method) (IzhikevichNrn method) (RC method) getInnerArea() (DifShell method) getInputOffset() (Adaptor method) getInstant() (HHChannel2D method) (HHChannelBase method) getIntegral() (PIDController method) getInternalDt() (MarkovGslSolver method) getInvdx() (MarkovSolverBase method) (VectorTable method) getInvdy() (MarkovSolverBase 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) getKf() (ReacBase method) getKm() (EnzBase method) getKMg_A() (MgBlock method) getKMg_B() (MgBlock method) getKsolve() (Stoich method) getLabels() (MarkovChannel method) getLeak() (DifShell method) getLength() (CompartmentBase method) (DifShell method) getLevel() (PulseGen method) getLigandConc() (MarkovChannel method) (MarkovRateTable method) getLongAttr() (HDF5WriterBase method) getLongVecAttr() (HDF5WriterBase method) getLookupField() (moose.melement method) getLookupindex() (VectorTable method) getLookupvalue() (VectorTable method) getLoopTime() (StimulusTable method) getMathML() (MathFunc method) getMatrixEntry() (Stoich method) getMax() (HHGate method) getMaxIter() (SteadyState method) getMe() (Neutral method) getMean() (Stats method) getMeshToSpace() (CubeMesh method) getMeshType() (MeshEntry method) getMethod() (Ksolve method) (MarkovGslSolver method) (TimeTable method) getMin() (HHGate method) getMInfinity() (HHGate method) getMode() (Func method) (Function method) (HDF5WriterBase method) (VClamp method) getMolWt() (Species method) getMotorConst() (PoolBase method) getMsgDestFunctions() (Neutral method) getMsgDests() (Neutral method) getMsgIn() (Neutral method) getMsgOut() (Neutral method) getMyNode() (PostMaster method) getN() (PoolBase method) getName() (Neutral method) getNeighbors() (MeshEntry method) (Neutral method) (moose.melement method) getNInit() (PoolBase method) getNIter() (SteadyState method) getNNegEigenvalues() (SteadyState 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) getNumColumns() (SparseMsg method) getNumData() (Neutral method) getNumDiffCompts() (CylMesh method) (NeuroMesh method) getNumDimensions() (ChemCompt method) getNumEntries() (SparseMsg method) getNumField() (Neutral 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) getNumStates() (MarkovChannel method) getNumSubstrates() (EnzBase method) (ReacBase method) getNumSynapse() (SynHandlerBase method) getNumSynapses() (SynHandlerBase method) getNumTicks() (Clock method) getNumVarPools() (SteadyState method) (Stoich 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) getOutputOffset() (Adaptor method) getOutputValue() (Adaptor method) (Arith method) (DiffAmp method) (PIDController method) (PulseGen method) (TableBase method) getParent() (Neutral method) getParentVoxel() (NeuroMesh method) (SpineMesh method) getPath() (Dsolve method) (Neutral method) (Stoich method) (moose.vec method) getPoolIdMap() (Stoich method) getPreserveNumEntries() (CubeMesh method) getProbability() (SparseMsg method) getProxyPools() (Stoich method) getQ() (MarkovRateTable method) (MarkovSolverBase method) getR() (RC method) getR0() (CylMesh method) getR1() (CylMesh method) getRa() (CompartmentBase 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) getResult() (FuncBase method) (MathFunc method) getRm() (CompartmentBase method) getRmByTau() (IzhikevichNrn method) getRowStart() (Stoich method) getRunTime() (Clock method) getSaturation() (DiffAmp method) (PIDController method) getScale() (Adaptor method) (Nernst method) getSdev() (Stats method) getSecondDelay() (PulseGen method) getSecondLevel() (PulseGen method) getSecondWidth() (PulseGen method) getSeed() (HSolve method) (SparseMsg method) getSensed() (PIDController method) (VClamp method) getSeparateSpines() (NeuroMesh method) getShape() (moose.vec method) getShapeMode() (DifShell method) getSize() (MarkovRateTable method) (TableBase method) getSolutionStatus() (SteadyState method) getSourceFields() (Neutral method) getSpaceToMesh() (CubeMesh method) getSpeciesId() (PoolBase method) getSrc() (Finfo method) getSrcFieldsOnE1() (Msg method) getSrcFieldsOnE2() (Msg method) getStartTime() (StimulusTable method) getStartVoxelInCompt() (NeuroMesh method) getState() (in module findChemSteadyState) (MarkovChannel method) (MarkovSolverBase method) (RC method) (TimeTable method) getStateType() (SteadyState method) getStatus() (SteadyState method) getStencilIndex() (ChemCompt method) getStencilRate() (ChemCompt method) getStepPosition() (StimulusTable method) getStepSize() (StimulusTable method) getStoich() (Dsolve method) (Gsolve method) (SteadyState method) getStopTime() (StimulusTable method) getStride() (DiagonalMsg method) getStringAttr() (HDF5WriterBase method) getStringVecAttr() (HDF5WriterBase method) getSubTree() (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) getTauD() (PIDController method) getTauI() (PIDController method) getTd() (VClamp method) getTemperature() (Nernst method) getTextColor() (Annotator method) getThick() (CaConcBase method) getThickness() (DifShell method) (PsdMesh method) getThis() (Mstring method) (Neutral method) getThresh() (IntFire method) (IntFireBase method) getThreshold() (SpikeGen method) (SpikeStats method) (Table method) getTi() (VClamp method) getTick() (Neutral method) getTickDt() (Clock method) getTickStep() (Clock method) getTotal() (SteadyState method) getTotLength() (CylMesh method) getTrigMode() (PulseGen method) getType() (Finfo method) getU() (IzhikevichNrn method) getU0() (IzhikevichNrn method) getUseConcentration() (HHChannelBase method) getUseInterpolation() (HHGate method) getUseRandInit() (Gsolve method) getV0() (RC method) getValence() (DifShell method) (Nernst method) getValue() (Func method) (Function method) (Mstring method) (Variable method) (moose.vec method) getValueFields() (Neutral method) getVar() (Func method) getVars() (Func 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) getWeight() (Synapse method) getWidth() (PulseGen method) 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) Group (built-in class) group (Group attribute) Gsolve (built-in class)

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) helloMoose (module) HHChannel (built-in class) HHChannel2D (built-in class) HHChannelBase (built-in class) HHGate (built-in class) HHGate2D (built-in class) hillPump() (DifShell method) HSolve (built-in class)

I

i1 (OneToAllMsg attribute) (SingleMsg attribute) i2 (SingleMsg attribute) icon (Annotator attribute) Ik (ChanBase attribute) IkOut (ChanBase attribute) Im (CompartmentBase attribute) (IzhikevichNrn attribute) increase() (CaConcBase method) increment() (Pool method) independent (Function attribute) influx() (DifShell method) init (CompartmentBase attribute) (Ksolve attribute) init() (MarkovGslSolver method) (MarkovRateTable method) (MarkovSolverBase method) initialState (MarkovChannel attribute) (MarkovSolverBase attribute) initProc() (CompartmentBase method) (Ksolve method) initReinit() (CompartmentBase method) (Ksolve method) initU (IzhikevichNrn attribute) initVm (CompartmentBase attribute) (IzhikevichNrn attribute) inject (CompartmentBase attribute) (IzhikevichNrn attribute) (RC attribute) injectIn() (RC method) injectMsg() (CompartmentBase method), [1] (IzhikevichNrn method) innerArea (DifShell attribute) innerDif (DifShell attribute)

innerDifSourceOut (DifShell attribute) input() (Adaptor method) (FuncBase method) (FuncPool method) (Interpol method) (PulseGen method) (Stats method) (Table method) (ZombieFuncPool method) input_output() (in module pyrun) inputOffset (Adaptor attribute) instant (HHChannel2D attribute) (HHChannelBase attribute) instratesOut (MarkovRateTable attribute) integral (PIDController attribute) IntegrateFireZoo (module) internalDt (MarkovGslSolver attribute) Interpol (built-in class) Interpol2D (built-in class) IntFire (built-in class) IntFireBase (built-in class) invdx (MarkovSolverBase attribute) (VectorTable attribute) invdy (MarkovSolverBase attribute) ionchannel (module) isInitialized (MarkovGslSolver attribute) (SteadyState attribute) isOpen (HDF5WriterBase attribute) isRunning (Clock attribute) isRunning() (in module moose) isToroid (CubeMesh attribute) IzhikevichNrn (built-in class)

K

k1 (CplxEnzBase attribute) k2 (CplxEnzBase attribute) k3 (CplxEnzBase attribute) K_n_params (in module ionchannel) Kb (ReacBase attribute) kcat (EnzBase attribute)

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

L

labels (MarkovChannel attribute) le() (in module moose) leak (DifShell attribute) Leakage (built-in class) length (CompartmentBase attribute) (DifShell attribute) level (PulseGen attribute) levelIn() (PulseGen method) LIF (built-in class) ligandConc (MarkovChannel attribute) (MarkovRateTable attribute) ligandConc() (MarkovSolverBase method) linearTransform() (TableBase method) loadCSV() (TableBase method) loadModel() (in module moose)

loadRunSTGNeuroML_L123() (in module STG_net) loadXplot() (TableBase method) loadXplotRange() (TableBase method) longAttr (HDF5WriterBase attribute) longVecAttr (HDF5WriterBase attribute) lookup() (Interpol2D method) LookupField (class in moose) lookupindex (VectorTable attribute) lookupOut (Interpol attribute) (Interpol2D attribute) lookupReturn2D (Interpol2D attribute) lookupvalue (VectorTable attribute) loopTime (StimulusTable attribute)

M

main() (in module chemDoseResponse) (in module IntegrateFireZoo) (in module STDP) (in module crossComptNeuroMesh) (in module crossComptOscillator) (in module crossComptSimpleReac) (in module diffEqSolution) (in module findChemSteadyState) (in module funcRateHarmonicOsc) (in module funcReacLotkaVolterra) (in module helloMoose) (in module mapkFB) (in module multiscaleOneCompt) (in module reacDiffBranchingNeuron) (in module reacDiffSpinyNeuron) (in module relaxationOsc) (in module repressillator) (in module scaleVolumes), [1] (in module slowFbOsc) (in module startstop) (in module strongBis) (in module switchKineticSolvers) (in module transportBranchingNeuron) (in module tweakingParameters) make_neuron_spike() (in module STDP) makeChemModel() (in module reacDiffBranchingNeuron) (in module reacDiffSpinyNeuron) makeModel() (in module chemDoseResponse) (in module TuringOneDim) (in module cylinderDiffusion) (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) MathFunc (built-in class) mathML (MathFunc attribute) matrixEntry (Stoich attribute) max (HHGate attribute) maxIter (SteadyState attribute) me (Neutral attribute) mean (Stats attribute) melement (class in moose) mesh (MeshEntry attribute) MeshEntry (built-in class) meshToSpace (CubeMesh attribute) meshType (MeshEntry attribute)

method (Ksolve attribute) (MarkovGslSolver attribute) (TimeTable attribute) MgBlock (built-in class) min (HHGate attribute) mInfinity (HHGate attribute) minusIn() (DiffAmp method) MMenz (built-in class) mmPump() (DifShell method) mode (Func attribute) (Function attribute) (HDF5WriterBase attribute) (VClamp attribute) modulator() (SynChan method) molWt (Species attribute) molWtOut (Species attribute) moose (module) motorConst (PoolBase attribute) move() (in module moose) (Shell method) Msg (built-in class) msgDestFunctions (Neutral attribute) msgDests (Neutral attribute) msgIn (Neutral attribute) msgOut (Neutral attribute) Mstring (built-in class) multiscaleOneCompt (module) myNode (PostMaster attribute)

N

n (PoolBase attribute) Na_h_params (in module ionchannel) Na_m_params (in module ionchannel) name (moose.ElementField attribute) (Neutral attribute) neighbors (MeshEntry attribute) (Neutral attribute) Nernst (built-in class) NeuroMesh (built-in class) Neuron (built-in class) Neutral (built-in class) nInit (PoolBase attribute) nIter (SteadyState attribute) nNegEigenvalues (SteadyState attribute) normalizeWeights (SynChan attribute) notes (Annotator attribute) nOut (PoolBase attribute) nPosEigenvalues (SteadyState attribute) nsteps (Clock attribute) num (moose.ElementField attribute) (Stats attribute) numAllPools (Stoich attribute) numAllVoxels (Dsolve attribute) (Gsolve attribute) (Ksolve attribute) numColumns (SparseMsg attribute) numData (Neutral attribute) numDiffCompts (CylMesh attribute) (NeuroMesh attribute) numDimensions (ChemCompt attribute)

numEntries (SparseMsg attribute) numField (Neutral 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) numStates (MarkovChannel attribute) numSubstrates (EnzBase attribute) (ReacBase attribute) numSynapses (SynHandlerBase attribute) numTicks (Clock attribute) numVarPools (SteadyState attribute) (Stoich 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) OneToOneDataIndexMsg (built-in class) OneToOneMsg (built-in class) oneVoxelVolume (ChemCompt attribute) origChannel() (MgBlock method) outerArea (DifShell attribute) outerDif (DifShell attribute)

outerDifSourceOut (DifShell attribute) outflux() (DifShell method) output (Adaptor attribute) (Arith attribute) (DiffAmp attribute) (FuncBase attribute) (MathFunc attribute) (PIDController attribute) (PulseGen attribute) (RC attribute) (StimulusTable attribute) outputOffset (Adaptor attribute) outputValue (Adaptor attribute) (Arith attribute) (DiffAmp attribute) (PIDController attribute) (PulseGen attribute) (TableBase attribute) owner (moose.ElementField attribute)

P

pairFill() (SparseMsg method) parent (Neutral attribute) parentMsg() (Neutral method) parentVoxel (NeuroMesh attribute) (SpineMesh attribute) path (Dsolve attribute) (Neutral attribute) (Stoich attribute) (moose.ElementField attribute) permeabilityOut (ChanBase attribute) PIDController (built-in class) plainPlot() (TableBase method) plusIn() (DiffAmp method) 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) (FuncBase 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) (MathFunc attribute) (MeshEntry attribute) (PIDController attribute) (PoolBase attribute) (PostMaster attribute) (PulseGen attribute) (RC attribute) (RandSpike attribute) (ReacBase attribute) (SpikeGen attribute) (Stats attribute) (StimulusTable attribute) (SynHandlerBase attribute) (Table attribute) (TimeTable attribute) (VClamp 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) (FuncBase 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) (MathFunc method) (MeshEntry method) (PIDController method) (PoolBase method) (PostMaster method) (PulseGen method) (RC method) (RandSpike method) (ReacBase method) (SpikeGen method) (Stats method) (StimulusTable method) (SynHandlerBase method) (Table method) (TimeTable method) (VClamp 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) propagationBis (module) proximal (SymCompartment attribute) proximalOnly (SymCompartment attribute) proximalOut (SymCompartment attribute), [1] proxyPools (Stoich attribute) psdList() (PsdMesh method) psdListOut (NeuroMesh attribute) PsdMesh (built-in class) PulseGen (built-in class) pwe() (in module moose) pyrun (module)

Q

Q (MarkovRateTable attribute) (MarkovSolverBase attribute)

quit() (in module moose) (Shell method)

R

R (RC attribute) r0 (CylMesh attribute) r1 (CylMesh attribute) Ra (CompartmentBase attribute) rand() (in module moose) randInject() (CompartmentBase method) randomInit() (SteadyState method) randomspike (module) RandSpike (built-in class) rank (SteadyState attribute) rate (Function attribute) (RandSpike attribute) rate_from_spiketrain() (in module ExcInhNet_HigginsGraupnerBrunel2014) (in module ExcInhNet_Ostojic2014_Brunel2000) rateOut (Function attribute) ratio (CplxEnzBase attribute) raxial (CompartmentBase attribute) raxialCylinder() (SymCompartment method) raxialOut (CompartmentBase attribute) raxialSphere() (SymCompartment method), [1] raxialSym() (SymCompartment method), [1], [2] RC (built-in class) Reac (built-in class) reac (PoolBase attribute) ReacBase (built-in class) reacDest() (PoolBase method) reacDiffBranchingNeuron (module) reacDiffSpinyNeuron (module) reaction() (DifShell method) readSBML() (in module moose) 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) (FuncBase 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) (MathFunc method) (MeshEntry method) (PIDController method) (PoolBase method) (PostMaster method) (PulseGen method) (RC method) (RandSpike method) (ReacBase method) (SpikeGen method) (Stats method) (StimulusTable method) (SynHandlerBase method) (Table method) (TimeTable method) (VClamp method) (in module moose) 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) repressillator (module) requestMolWt (PoolBase attribute) requestOut (Adaptor attribute) (Function attribute) (HDF5DataWriter attribute) (Stats attribute) (Table attribute) reset_settle() (in module STDP) resetStencil() (ChemCompt method) resettle() (SteadyState method) result (FuncBase attribute) (MathFunc attribute) Rm (CompartmentBase attribute) RmByTau (IzhikevichNrn attribute) rowStart (Stoich attribute) run_sequence() (in module pyrun) runTime (Clock attribute)

S

saturation (DiffAmp attribute) (PIDController attribute) saveModel() (in module moose) scale (Adaptor attribute) (Nernst attribute) scaleVolumes (module), [1] sdev (Stats attribute) secondDelay (PulseGen attribute) secondLevel (PulseGen attribute) secondWidth (PulseGen attribute) seed (HSolve attribute) (SparseMsg attribute) seed() (in module moose) sensed (PIDController attribute) (VClamp attribute) sensedIn() (PIDController method) (VClamp method) separateSpines (NeuroMesh attribute) set1d() (MarkovRateTable method) set2d() (MarkovRateTable method) setA() (IzhikevichNrn method) setAbs_refract() (RandSpike method) (SpikeGen method) setAbsoluteAccuracy() (MarkovGslSolver method) setAccommodating() (IzhikevichNrn method) setAlpha() (HHGate method) (IzhikevichNrn method) setAlphaParms() (HHGate method) setAlwaysDiffuse() (CubeMesh method) setAnyValue() (Arith method) setB() (CaConcBase method) (IzhikevichNrn method) setBaseDt() (Clock method) setBaseLevel() (PulseGen method) setBeta() (HHGate method) (IzhikevichNrn method) setBufferSize() (PostMaster method) setC() (Function method) (IzhikevichNrn method) (RC method) setCa() (CaConcBase method) setCa_base() (CaConcBase method) setCaAdvance() (HSolve method) setCaBasal() (CaConcBase method) setCaDiv() (HSolve method) setCaMax() (HSolve method) setCaMin() (HSolve method) setCeiling() (CaConcBase method) setCell() (NeuroMesh method) setCeq() (DifShell method) setChunkSize() (HDF5WriterBase method) setCin() (Nernst method) setClock() (in module moose) setclock() (Shell method) setCm() (CompartmentBase method) setCMg() (MgBlock method) setColor() (Annotator method) setCommand() (PIDController method) setCompartment() (Dsolve method) (Ksolve method) (Stoich method) setCompression() (HDF5WriterBase method) setCompressor() (HDF5WriterBase method) setConc() (PoolBase method) setConcInit() (PoolBase method) setConcK1() (CplxEnzBase method) setconst() (MarkovRateTable method) setConvergenceCriterion() (SteadyState method) setCoords() (CubeMesh method) (CylMesh method) setCount() (PulseGen method) setCout() (Nernst method) setCwe() (in module moose) setD() (DifShell method) (IzhikevichNrn method) setDelay() (PulseGen method) (Synapse method) setDestField() (moose.melement method) setDiameter() (CompartmentBase method) (DifShell method) setDiffConst() (PoolBase method) setDiffLength() (CylMesh method) (NeuroMesh 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) setEntry() (SparseMsg method) setEpsAbs() (Ksolve method) setEpsRel() (Ksolve method) setExpr() (Func method) (Function method) setField() (moose.melement method) (moose.vec method) setFilename() (HDF5WriterBase method) (TimeTable method) setFirstDelay() (PulseGen method) setFirstLevel() (PulseGen method) setFirstWidth() (PulseGen method) setFloor() (CaConcBase method) setFlushLimit() (HDF5DataWriter method) setFunction() (Arith method) (MathFunc method) setGain() (DiffAmp method) (PIDController method) (VClamp method) setGamma() (IzhikevichNrn method) setGbar() (ChanBase method) (MarkovChannel method) setGeometryPolicy() (NeuroMesh method) setGk() (ChanBase method) (GapJunction method) setI1() (OneToAllMsg method) (SingleMsg method) setI2() (SingleMsg method) setIcon() (Annotator method) setIndependent() (Function method) setInitialState() (MarkovChannel method) (MarkovSolverBase method) setInitU() (IzhikevichNrn method) setInitVm() (CompartmentBase method) (IzhikevichNrn method) setInject() (CompartmentBase method) (IzhikevichNrn method) (RC method) setInnerArea() (DifShell method) setInputOffset() (Adaptor method) setInstant() (HHChannel2D method) (HHChannelBase method) setInternalDt() (MarkovGslSolver method) setIsToroid() (CubeMesh method) setK1() (CplxEnzBase method) setK2() (CplxEnzBase method) setK3() (CplxEnzBase method) setKb() (ReacBase method) setKcat() (EnzBase method) setKf() (ReacBase method) setKm() (EnzBase method) setKMg_A() (MgBlock method) setKMg_B() (MgBlock method) setKsolve() (Stoich method) setLabels() (MarkovChannel method) setLeak() (DifShell method) setLength() (CompartmentBase method) (DifShell method) setLevel() (PulseGen method) setLigandConc() (MarkovChannel method) (MarkovRateTable method) setLongAttr() (HDF5WriterBase method) setLongVecAttr() (HDF5WriterBase method) setLookupField() (moose.melement method) setLoopTime() (StimulusTable method) setMathML() (MathFunc method) setMax() (HHGate method) setMaxIter() (SteadyState method) setMeshToSpace() (CubeMesh method) setMethod() (Ksolve method) (MarkovGslSolver method) (TimeTable method) setMin() (HHGate method) setMInfinity() (HHGate method) setMode() (Func method) (Function method) (HDF5WriterBase method) (VClamp method) setMolWt() (Species method) setMotorConst() (PoolBase method) setN() (PoolBase method) setName() (Neutral method) setNInit() (PoolBase method) setNormalizeWeights() (SynChan method) setNotes() (Annotator method) setNumAllVoxels() (Gsolve method) (Ksolve method) setNumData() (Neutral 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) setNumStates() (MarkovChannel method) setNumSynapse() (SynHandlerBase method) setNumSynapses() (SynHandlerBase method) setNumX() (Function method) setNVec() (Dsolve method) (Gsolve method) (Ksolve method) setNx() (CubeMesh method) setNy() (CubeMesh method) setNz() (CubeMesh method) setOuterArea() (DifShell method) setOutputOffset() (Adaptor method) setOutputValue() (Arith method) setPath() (Dsolve method) (Stoich method) setPreserveNumEntries() (CubeMesh method) setProbability() (SparseMsg method) setR() (RC method) setR0() (CylMesh method) setR1() (CylMesh method) setRa() (CompartmentBase method) setRandomConnectivity() (SparseMsg method) setRate() (RandSpike method) setRatio() (CplxEnzBase method) setRefractoryPeriod() (IntFire method) (IntFireBase method) setRefractT() (RandSpike method) (SpikeGen method) setRelativeAccuracy() (MarkovGslSolver method)

setRm() (CompartmentBase method) setRmByTau() (IzhikevichNrn method) setSaturation() (DiffAmp method) (PIDController method) setScale() (Adaptor method) (Nernst method) setSecondDelay() (PulseGen method) setSecondLevel() (PulseGen method) setSecondWidth() (PulseGen method) setSeed() (HSolve method) (SparseMsg method) setSeparateSpines() (NeuroMesh method) setShapeMode() (DifShell method) setSpaceToMesh() (CubeMesh method) setSpeciesId() (PoolBase 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) 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) setTauD() (PIDController method) setTauI() (PIDController method) setTd() (VClamp method) setTemperature() (Nernst method) setTextColor() (Annotator method) setThick() (CaConcBase method) setThickness() (DifShell method) (PsdMesh method) setThis() (Mstring method) (Neutral method) setThresh() (IntFire method) (IntFireBase method) setThreshold() (SpikeGen method) (SpikeStats method) (Table method) setTi() (VClamp method) setTick() (Neutral method) setTickDt() (Clock method) setTickStep() (Clock method) settle() (SteadyState method) setTotal() (SteadyState method) setTrigMode() (PulseGen method) setU0() (IzhikevichNrn method) setup_experiment() (in module twocells) setupAlpha() (HHGate method) setupGate() (HHGate method) setupMatrix() (SteadyState method) setupModel() (in module STDP) setupTau() (HHGate method) setUseConcentration() (HHChannelBase method) setUseInterpolation() (HHGate method) setUseRandInit() (Gsolve method) setV0() (RC method) setValence() (DifShell method) (Nernst method) setValue() (Mstring method) (Variable method) setVar() (Func method) (Variable 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) setWeight() (Synapse method) setWidth() (PulseGen method) 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) shapeMode (DifShell attribute) Shell (built-in class) showfield() (in module moose) showMatrices() (SteadyState method) showmsg() (in module moose) sibling (SymCompartment attribute) SimpleSynHandler (built-in class) SingleMsg (built-in class) size (MarkovRateTable attribute) (TableBase attribute) slowFbOsc (module) solutionStatus (SteadyState attribute) sourceFields (Neutral attribute) spaceToMesh (CubeMesh attribute) SparseMsg (built-in class) Species (built-in class) species (PoolBase attribute) speciesId (PoolBase attribute) sphere (SymCompartment attribute) spike() (Table method) SpikeGen (built-in class) spikeOut (IntFire attribute) (IntFireBase attribute) (IzhikevichNrn attribute) (RandSpike attribute) (SpikeGen attribute) SpikeStats (built-in class) spineList() (SpineMesh method) spineListOut (NeuroMesh attribute) SpineMesh (built-in class) src (Finfo attribute) srcFieldsOnE1 (Msg attribute) srcFieldsOnE2 (Msg attribute) start() (Clock method) (in module moose) startstop (module) startTime (StimulusTable attribute) startVoxelInCompt (NeuroMesh attribute) state (MarkovChannel attribute) (MarkovSolverBase attribute) (RC attribute) (TimeTable attribute) stateOut (MarkovGslSolver attribute) (MarkovSolverBase attribute) stateType (SteadyState attribute) Stats (built-in class) status (SteadyState attribute) STDP (module) SteadyState (built-in class) stencilIndex (ChemCompt attribute) stencilRate (ChemCompt attribute) step() (Clock method) stepPosition (StimulusTable attribute) stepSize (StimulusTable attribute) STG_net (module) StimulusTable (built-in class) Stoich (built-in class) stoich (Dsolve attribute) (Gsolve attribute) (SteadyState attribute) stop() (Clock method) (in module moose) stopTime (StimulusTable attribute) storeInflux() (DifShell method) storeOutflux() (DifShell method) stride (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) sum (Stats attribute) SumFunc (built-in class) sumRaxial() (SymCompartment method), [1], [2] sumRaxialOut (SymCompartment attribute), [1], [2] surface (CubeMesh attribute) switchKineticSolvers (module) SymCompartment (built-in class) Synapse (built-in class) SynChan (built-in class) SynHandlerBase (built-in class)

T

Table (built-in class) table (Interpol2D attribute) (VectorTable attribute) 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) tauD (PIDController attribute) tauI (PIDController attribute) tauPump() (DifShell method) td (VClamp attribute) Temperature (Nernst attribute) testSched (built-in class) textColor (Annotator attribute) thick (CaConcBase attribute) thickness (DifShell attribute) (PsdMesh attribute)

this (Mstring attribute) (Neutral attribute) thresh (IntFire attribute) (IntFireBase attribute) threshold (SpikeGen attribute) (SpikeStats attribute) (Table attribute) ti (VClamp attribute) tick (Neutral attribute) tickDt (Clock attribute) tickStep (Clock attribute) TimeTable (built-in class) total (SteadyState attribute) totLength (CylMesh attribute) transportBranchingNeuron (module) transpose() (SparseMsg method) trigMode (PulseGen attribute) tripletFill() (SparseMsg method) TuringOneDim (module) tweakAlpha() (HHGate method) tweakingParameters (module) tweakTau() (HHGate method) twocells (module) type (Finfo attribute)

U

u (IzhikevichNrn attribute) u0 (IzhikevichNrn attribute) unsetEntry() (SparseMsg method) unzombify() (Stoich method)

useClock() (in module moose) (Shell method) useConcentration (HHChannelBase attribute) useInterpolation (HHGate attribute) useRandInit (Gsolve attribute)

V

V0 (RC attribute) valence (DifShell attribute) (Nernst attribute) value (Func attribute) (Function attribute) (Mstring attribute) (Variable attribute) valueFields (Neutral attribute) valueOut (Func attribute) (Function attribute) var (Func attribute) Variable (built-in class) varIn() (Func method) vars (Func attribute) VClamp (built-in class) vDiv (HSolve attribute) VDIVS (in module ionchannel) vec (class in moose) (moose.ElementField attribute) vec() (moose.melement method) vector (TableBase attribute) VectorTable (built-in class)

Vm (CompartmentBase attribute) (IntFire attribute) (IzhikevichNrn attribute) (MarkovChannel attribute) (MarkovRateTable attribute) Vm() (ChanBase method), [1] (SpikeGen method) (SpikeStats method) Vm1() (GapJunction method) Vm2() (GapJunction method) vMax (HSolve attribute) VMAX (in module ionchannel) Vmax (IzhikevichNrn attribute) vMin (HSolve attribute) VMIN (in module ionchannel) 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)

W

weight (Synapse attribute) width (PulseGen attribute) widthIn() (PulseGen method) wildcardFind() (in module moose) windowLength (Stats attribute)

wmean (Stats attribute) wnum (Stats attribute) writeSBML() (in module moose) 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 (Ksolve attribute) xComptIn() (Ksolve method) xComptOut (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) ZombieBufPool (built-in class)

ZombieCaConc (built-in class) ZombieCompartment (built-in class) ZombieEnz (built-in class) ZombieFuncPool (built-in class) ZombieHHChannel (built-in class) ZombieMMenz (built-in class) ZombiePool (built-in class) ZombieReac (built-in class) Zpower (HHChannel2D attribute) (HHChannelBase attribute)