All Classes and Interfaces

Class	Description
Annotation	Concise processing directives for downstream applications.
Authors	A reference to an author Note: This element will possibly change when a new set of schema files is adopted for adding references, authors, citations, etc.
Biophysics	Description of biophysical properties of a cell.
Block	Specification for the influence of a blocking species on the conductance of a BlockingSynapse.
BlockingSynapse	A synaptic mechanism whose conductance can be blocked by the presence of a specific species (ion/molecule).
Cable	Definition of a cable.
CableGroup	Definition of a cable group.
CableGroup.Cable	Java class for anonymous complex type.
Cell	Definition of a cell.
Cell.Cables	Java class for anonymous complex type.
Cell.CellBody	Java class for anonymous complex type.
Cell.Segments	Java class for anonymous complex type.
Cell.Spines	Java class for anonymous complex type.
CellInstance	An instance of a cell at a the specified location
Cells	Collection of all cells.
ChannelML	Root element containing the ions used in the mechanism, the unit system of the file (as attribute), and information on channels and/or ion concentration dynamics.
ChannelType	Definition of a voltage/concentration dependent cell membrane conductance
ClosedState	Closed state of a gating complex
ConcDependence	Specification of the factor to use in the concentration dependence of the rate expressions of a gate
ConcFactor	Specification of the time independent scaling factor for a concentration dependent conductance.
ConductanceLaw	Java class for ConductanceLaw.
Connection	A single synaptic connection
Connection.InternalProperties
Connections	The list of cell connections
ConnectivityPattern	Information on the number of target cells connected to source cells, etc.
ConnectivityPattern.AllToAll	Java class for anonymous complex type.
ConnectivityPattern.FixedProbability	Java class for anonymous complex type.
CoreEquationType	Java class for CoreEquationType.
CurrentVoltageRelation	How the current through the channel depends on the conductance of the channel.
DecayingPoolModel	Element for parameters in a decaying pool model of ion concentration (e.g.
DeprecatedAkdEquation	Definition of a type of rate constant equation which takes parameters A, k, d and maps to either exponential, sigmoidal or linoidal.
DeprecatedCoreEquationType	Java class for Deprecated_CoreEquationType.
DeprecatedGenericEquation	Definition of a type of rate constant equation
DeprecatedHHGate	Gate with Hodgkin Huxley like state transitions
DeprecatedIon	Definition of an ion which is involved in this channel mechanism.
DeprecatedIonRole	Java class for Deprecated_IonRole.
DeprecatedKSGate	Gate with kinetic scheme transitions
DeprecatedKSState	Single kinetic scheme state.
DeprecatedOhmic	Signifies an ohmic relation; the current is proportional to the potential difference across the channel.
DeprecatedOhmic.Conductance	Java class for anonymous complex type.
DeprecatedParameter	Generic parameter used in rate equations
DeprecatedRateConstantEqn	Definition of a rate constant equation.
DeprecatedRateConstantEqnChoice	Choice of the various rate constant expressions allowed
DeprecatedRateConstVoltConcDep	Rate constant expressions allowed for voltage and conc dependent channels.
DeprecatedTransition	Deprecated since v1.7.3.
DeprecatedVoltageConcGate	Definition of a mechanics of a gate which depends on voltage and concentration (e.g.
DeprecatedVoltageGate	Definition of a voltage gate.
DoubleExponentialSynapse	A basic synaptic mechanism with a double exponential conductance time course.
ElectricalSynapse	Electrical synaptic coupling as at a gap junction.
FacDep	Facilitating and depressing synaptic parameters.
FacDepSynapse	A synaptic type with facilitating and depressing amplitude.
Feature	The group of things allowed in features.
FixedPoolInfo	(IN PROGRESS, not stable!!!!) In this case the parameter which determines how quickly the internal pool 'fills' is given as a fixed value.
FreePoints	A set of varicosities or synaptic connections.
Gate	Definition of a single voltage/concentration dependent gate
Gate.State	Java class for anonymous complex type.
GatingComplex	Preferred element for defining a gate since v1.7.3.
GlobalSynapticProperties	Information on synapse type and default values for weight, delay, threshold, etc.
GlobalSynapticProperties.SynapseTypeElement
GridArrangement	A regular placement of the cells in a number of dimensions
GridArrangement.Spacing	Java class for anonymous complex type.
GroupDetail	Metadata for each Group.
ImplementationPrefs	These items ideally shouldn't be in a specification which deals with a description of the physiology of the channel.
ImplementationPrefs.TableSettings	Java class for anonymous complex type.
InhomogeneousParam	Definition of a parameter which varies along a cable group.
InhomogeneousParam.Distal	Java class for anonymous complex type.
InhomogeneousParam.Proximal	Java class for anonymous complex type.
InhomogeneousValue	How a value changes over the cable group.
Initialisation	Element added for *testing purposes only*.
InitialMembPotential	This quantity is often required for computational simulations and specifies the potential difference across the membrane at the start of the simulation.
Input	Description of a single electrical input to a number of cells
Inputs	The list of electrical inputs into the cells.
InputSite	Specifies a location on a cell where input is received
InputSitePattern	Information on the number of cells on which to apply inputs.
InputSitePattern.AllCells	Java class for anonymous complex type.
InputSitePattern.PercentageCells	Java class for anonymous complex type.
InputSites	The list of input sites
InputTarget	Specifies the cell group and which cells/segments to apply the stimulation
Instances	Cell Instance position information
IntegrateAndFire	Signifies a current which will cause the cell to behave like an integrate and fire neuron.
IonConcentration	Specification of how an ion concentration alters with time, e.g.
IonProperties	Some properties accociated with an ion type which takes part in the mechanisms on the cell
IonSpecies	Which ion is involved in an ion_concentration mechanism.
LengthUnits	Java class for LengthUnits.
Level3Biophysics	Biophysics of Level3 cell, including specification for allowable synaptic locations.
Level3Cell	Cell with extensions for biophysics, and network functionality
Level3Cells	Set of Level 3 cells
Level3Connectivity	Biophysics of Level3 cell, including specification for allowable synaptic locations.
LocalSynapticProperties	Variables specifying a single synapse
Manifold	A surface.
Mechanism	Definition of placement of a single electrophysiological mechanism (e.g.
MechanismType	Java class for MechanismType.
ModelDBReference	A reference to an entity in ModelDB Note: This element will possibly change when a new set of schema files is adopted for adding references, authors, citations, etc.
Morphology	The main element which details the neuronal morphology.
Morphology.Features	Java class for anonymous complex type.
Morphology.GroupDetails	Java class for anonymous complex type.
Morphology.PropertyDetails	Java class for anonymous complex type.
MultiDecaySynapse	A more complex synaptic mechanism featuring up to 4 exponential components (1 rise and 3 decay).
NamedParameter	Definition of a value for a quantity and the associated groups of cables which have this value.
NetworkML	The main elements which make up a NetworkML compliant document.
NeuroML1Validator
NeuroMLConverter
NeuroMLLevel3	Description of neuronal models, including biophysics and channel mechanisms, and network connections (NeuroML Level 3).
NeuroMLNamespacePrefixMapper
NeuroMorphoRef	A reference to an entity in NeuroMorpho.org Note: This element will possibly change when a new set of schema files is adopted for adding references, authors, citations, etc.
NeuronDBReference	A reference to an entity in NeuronDB Note: This element will possibly change when a new set of schema files is adopted for adding references, authors, citations, etc.
NonSpatialGrid	Specifies a grid of up to 3 dimensions, without any explicit 3D location information.
ObjectFactory	This object contains factory methods for each Java content interface and Java element interface generated in the org.neuroml1.model.bio package.
ObjectFactory	This object contains factory methods for each Java content interface and Java element interface generated in the org.neuroml1.model.channel package.
ObjectFactory	This object contains factory methods for each Java content interface and Java element interface generated in the org.neuroml1.model.meta package.
ObjectFactory	This object contains factory methods for each Java content interface and Java element interface generated in the org.neuroml1.model.morph package.
ObjectFactory	This object contains factory methods for each Java content interface and Java element interface generated in the org.neuroml1.model.network package.
ObjectFactory	This object contains factory methods for each Java content interface and Java element interface generated in the org.neuroml1.model package.
Offset	Java class for Offset complex type.
OpenState	Open state of a gating complex
Parameter	A single parameter which can be used in generic expressions
Parameters	Fixed value parameters which can be used in generic expressions
Path	Possibly branching histological structures.
PerCellConnection	Connection built iteratively from each pre (or post) cell based on a number of parameters
Person	A generic reference to a person, for authorship, etc
Point	A 3D point with optional diameter.
Point3D	A 3D point with no diameter.
Points	A collection of points.
Polygon	A closed structure represented by a list of points where the first point connects with the last point.
Polyhedron	A 3d surface to represent the cell body or histological structure.
Polyhedron.Polygons	Java class for anonymous complex type.
PoolVolumeInfo	Information on the volume of the ion pool
Population	Description of a cell population of the same type
Population.CellTypeElement
PopulationLocation	Description of the 3D positioning of cells in the population, in place of giving explicit locations for each cell
Populations	The list of cell populations
PotentialSynapticLocation	Subset of sections on cell where synaptic connection of a particular type is allowed.
PotentialSynapticLocation.GroupElementPSL2
PotentialSynLoc	Subset of sections on cell where synaptic connection of a particular type is allowed.
PotentialSynLoc.GroupElementPSL1
Projection	Description of how one cell population makes synaptic connections with another
Projection.SourceElement
Projection.TargetElement
Projections	The list of projections from one cell population to another
Properties	A collection of Properties
Property	A Tag/Value/Type tuple.
PropertyDetail	Metadata for each Property.
Publication	A reference to a publication Note: This element will possibly change when a new set of schema files is adopted for adding references, authors, citations, etc.
PulseInput	A single input pulse.
Q10Settings	Q10 scaling affects the tau in the rate equations.
RandomArrangement	A random arrangement of cells in a 3D location.
RandomStim	A random stimulation at a specific frequency.
RandomStimInstance	Instance/site specific random stimulation at a specific frequency.
RateAdjustments	Adjustments necessary to all the rate equations, e.g temperature dependencies, voltage offsets introduced when moving between species, etc.
RectangularBox	A Rectangular Box for locating cells in 3D.
RectangularBox.Size	Java class for anonymous complex type.
Segment	Defines the smallest unit within a possibly branching structure, such as a segment of a dendrite or axon.
SpecAxialResistance	Specific axial resistance of a group of sections
SpecCapacitance	Capacitance per unit area of a group of sections
Sphere	A spherical structure such as a cell body or cell.
Spine	A spine with location, shape, and direction.
SpineShape	Java class for SpineShape.
Status	Status element giving the stability state of files and some extra comments.
StatusValue	Java class for StatusValue.
StdpDep	A synaptic mechanism implementing basic Spike Timing Dependent Plasticity based on Song and Abbott, 2001.
StdpSynapse	A synaptic mechanism implementing basic Spike Timing Dependent Plasticity based on Song and Abbott, 2001 Extends MultiDecaySynapse
SteadyState	Steady state value of the transition between states in a GatingComplex
SynapseDirection	Java class for SynapseDirection.
SynapseInternalProperties	Variables specifying a single synapse or default values for a set of connections
SynapseProperties	Pre v1.7.1 format for global synapse properties.
SynapseType	Definition of a synaptic mechanism
SynapticLocation	Java class for SynapticLocation complex type.
TimeCourse	Time course of the transition between states in a GatingComplex
Transition	Transition between states in a GatingComplex
Units	Java class for Units.
UnnamedParameter	Definition of a value for a quantity and the associated groups of cables which have this value.
VariableNamedParameter	Definition of a value for a quantity which varies over a given group of cables
VariableParameter	Definition of a value for a quantity which varies over a given group of cables
VolumeUnits	Java class for VolumeUnits.
YesNo	Java class for YesNo.