NeuroML core classes

nml Module

Note: This module is included in the top level of the neuroml package, so you can use these classes by importing neuroml:

from neuroml import AdExIaFCell

class neuroml.nml.nml.AdExIaFCell(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, C=None, g_l=None, EL=None, reset=None, VT=None, thresh=None, del_t=None, tauw=None, refract=None, a=None, b=None)

Bases: neuroml.nml.nml.BaseCellMembPotCap

superclass

alias of BaseCellMembPotCap

class neuroml.nml.nml.AlphaCondSynapse(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, tau_syn=None, e_rev=None)

Bases: neuroml.nml.nml.BasePynnSynapse

superclass

alias of BasePynnSynapse

class neuroml.nml.nml.AlphaCurrSynapse(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, tau_syn=None)

Bases: neuroml.nml.nml.BasePynnSynapse

superclass

alias of BasePynnSynapse

class neuroml.nml.nml.AlphaCurrentSynapse(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, tau=None, ibase=None)

Bases: neuroml.nml.nml.BaseCurrentBasedSynapse

superclass

alias of BaseCurrentBasedSynapse

class neuroml.nml.nml.AlphaSynapse(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, gbase=None, erev=None, tau=None)

Bases: neuroml.nml.nml.BaseConductanceBasedSynapse

superclass

alias of BaseConductanceBasedSynapse

class neuroml.nml.nml.Annotation(anytypeobjs_=None)

Bases: neuroml.nml.nml.GeneratedsSuper

Placeholder for MIRIAM related metadata, among others.

class neuroml.nml.nml.Base(neuro_lex_id=None, id=None, extensiontype_=None)

Bases: neuroml.nml.nml.BaseWithoutId

Anything which can have a unique (within its parent) id of the form NmlId (spaceless combination of letters, numbers and underscore).

superclass

alias of BaseWithoutId

class neuroml.nml.nml.BaseCell(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, extensiontype_=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.BaseCellMembPotCap(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, C=None, extensiontype_=None)

Bases: neuroml.nml.nml.BaseCell

This is to prevent it conflicting with attribute c (lowercase) e.g. in izhikevichCell2007

superclass

alias of BaseCell

class neuroml.nml.nml.BaseConductanceBasedSynapse(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, gbase=None, erev=None, extensiontype_=None)

Bases: neuroml.nml.nml.BaseVoltageDepSynapse

superclass

alias of BaseVoltageDepSynapse

class neuroml.nml.nml.BaseConductanceBasedSynapseTwo(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, gbase1=None, gbase2=None, erev=None, extensiontype_=None)

Bases: neuroml.nml.nml.BaseVoltageDepSynapse

superclass

alias of BaseVoltageDepSynapse

class neuroml.nml.nml.BaseConnection(neuro_lex_id=None, id=None, extensiontype_=None)

Bases: neuroml.nml.nml.BaseNonNegativeIntegerId

Base of all synaptic connections (chemical/electrical/analog, etc.) inside projections

superclass

alias of BaseNonNegativeIntegerId

class neuroml.nml.nml.BaseConnectionNewFormat(neuro_lex_id=None, id=None, pre_cell=None, pre_segment='0', pre_fraction_along='0.5', post_cell=None, post_segment='0', post_fraction_along='0.5', extensiontype_=None)

Bases: neuroml.nml.nml.BaseConnection

Base of all synaptic connections with preCell, postSegment, etc. See BaseConnectionOldFormat

superclass

alias of BaseConnection

class neuroml.nml.nml.BaseConnectionOldFormat(neuro_lex_id=None, id=None, pre_cell_id=None, pre_segment_id='0', pre_fraction_along='0.5', post_cell_id=None, post_segment_id='0', post_fraction_along='0.5', extensiontype_=None)

Bases: neuroml.nml.nml.BaseConnection

Base of all synaptic connections with preCellId, postSegmentId, etc. Note: this is not the best name for these attributes, since Id is superfluous, hence BaseConnectionNewFormat

superclass

alias of BaseConnection

class neuroml.nml.nml.BaseCurrentBasedSynapse(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, extensiontype_=None)

Bases: neuroml.nml.nml.BaseSynapse

superclass

alias of BaseSynapse

class neuroml.nml.nml.BaseNonNegativeIntegerId(neuro_lex_id=None, id=None, extensiontype_=None)

Bases: neuroml.nml.nml.BaseWithoutId

Anything which can have a unique (within its parent) id, which must be an integer zero or greater.

superclass

alias of BaseWithoutId

class neuroml.nml.nml.BaseProjection(neuro_lex_id=None, id=None, presynaptic_population=None, postsynaptic_population=None, extensiontype_=None)

Bases: neuroml.nml.nml.Base

Base for projection (set of synaptic connections) between two populations

superclass

alias of Base

class neuroml.nml.nml.BasePynnSynapse(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, tau_syn=None, extensiontype_=None)

Bases: neuroml.nml.nml.BaseSynapse

superclass

alias of BaseSynapse

class neuroml.nml.nml.BaseSynapse(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, extensiontype_=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.BaseVoltageDepSynapse(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, extensiontype_=None)

Bases: neuroml.nml.nml.BaseSynapse

superclass

alias of BaseSynapse

class neuroml.nml.nml.BaseWithoutId(neuro_lex_id=None, extensiontype_=None)

Bases: neuroml.nml.nml.GeneratedsSuper

Base element without ID specified yet, e.g. for an element with a particular requirement on its id which does not comply with NmlId (e.g. Segment needs nonNegativeInteger).

class neuroml.nml.nml.BiophysicalProperties(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, membrane_properties=None, intracellular_properties=None, extracellular_properties=None)

Bases: neuroml.nml.nml.Standalone

Standalone element which is usually inside a single cell, but could be outside and referenced by id.

superclass

alias of Standalone

class neuroml.nml.nml.BiophysicalProperties2CaPools(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, membrane_properties2_ca_pools=None, intracellular_properties2_ca_pools=None, extracellular_properties=None)

Bases: neuroml.nml.nml.Standalone

Standalone element which is usually inside a single cell, but could be outside and referenced by id.

superclass

alias of Standalone

class neuroml.nml.nml.BlockingPlasticSynapse(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, gbase=None, erev=None, tau_decay=None, tau_rise=None, plasticity_mechanism=None, block_mechanism=None)

Bases: neuroml.nml.nml.ExpTwoSynapse

superclass

alias of ExpTwoSynapse

class neuroml.nml.nml.Cell(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, morphology_attr=None, biophysical_properties_attr=None, morphology=None, biophysical_properties=None, extensiontype_=None)

Bases: neuroml.nml.nml.BaseCell

Should only be used if morphology element is outside the cell. This points to the id of the morphology Should only be used if biophysicalProperties element is outside the cell. This points to the id of the biophysicalProperties

superclass

alias of BaseCell

class neuroml.nml.nml.Cell2CaPools(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, morphology_attr=None, biophysical_properties_attr=None, morphology=None, biophysical_properties=None, biophysical_properties2_ca_pools=None)

Bases: neuroml.nml.nml.Cell

superclass

alias of Cell

class neuroml.nml.nml.CellSet(neuro_lex_id=None, id=None, select=None, anytypeobjs_=None)

Bases: neuroml.nml.nml.Base

superclass

alias of Base

class neuroml.nml.nml.ChannelDensity(neuro_lex_id=None, id=None, ion_channel=None, cond_density=None, erev=None, segment_groups='all', segments=None, ion=None, variable_parameters=None, extensiontype_=None)

Bases: neuroml.nml.nml.Base

Specifying the ion here again is redundant, this will be set in ionChannel definition. It is added here TEMPORARILY since selecting all ca or na conducting channel populations/densities in a cell would be difficult otherwise. Also, it will make it easier to set the correct native simulator value for erev (e.g. ek for ion = k in NEURON). Currently a required attribute. It should be removed in the longer term, due to possible inconsistencies in this value and that in the ionChannel element. TODO: remove.

superclass

alias of Base

class neuroml.nml.nml.ChannelDensityGHK(neuro_lex_id=None, id=None, ion_channel=None, permeability=None, segment_groups='all', segments=None, ion=None)

Bases: neuroml.nml.nml.Base

Specifying the ion here again is redundant, this will be set in ionChannel definition. It is added here TEMPORARILY since selecting all ca or na conducting channel populations/densities in a cell would be difficult otherwise. Also, it will make it easier to set the correct native simulator value for erev (e.g. ek for ion = k in NEURON). Currently a required attribute. It should be removed in the longer term, due to possible inconsistencies in this value and that in the ionChannel element. TODO: remove.

superclass

alias of Base

class neuroml.nml.nml.ChannelDensityGHK2(neuro_lex_id=None, id=None, ion_channel=None, cond_density=None, segment_groups='all', segments=None, ion=None)

Bases: neuroml.nml.nml.Base

Specifying the ion here again is redundant, this will be set in ionChannel definition. It is added here TEMPORARILY since selecting all ca or na conducting channel populations/densities in a cell would be difficult otherwise. Also, it will make it easier to set the correct native simulator value for erev (e.g. ek for ion = k in NEURON). Currently a required attribute. It should be removed in the longer term, due to possible inconsistencies in this value and that in the ionChannel element. TODO: remove.

superclass

alias of Base

class neuroml.nml.nml.ChannelDensityNernst(neuro_lex_id=None, id=None, ion_channel=None, cond_density=None, segment_groups='all', segments=None, ion=None, variable_parameters=None, extensiontype_=None)

Bases: neuroml.nml.nml.Base

Specifying the ion here again is redundant, this will be set in ionChannel definition. It is added here TEMPORARILY since selecting all ca or na conducting channel populations/densities in a cell would be difficult otherwise. Also, it will make it easier to set the correct native simulator value for erev (e.g. ek for ion = k in NEURON). Currently a required attribute. It should be removed in the longer term, due to possible inconsistencies in this value and that in the ionChannel element. TODO: remove.

superclass

alias of Base

class neuroml.nml.nml.ChannelDensityNernstCa2(neuro_lex_id=None, id=None, ion_channel=None, cond_density=None, segment_groups='all', segments=None, ion=None, variable_parameters=None)

Bases: neuroml.nml.nml.ChannelDensityNernst

superclass

alias of ChannelDensityNernst

class neuroml.nml.nml.ChannelDensityNonUniform(neuro_lex_id=None, id=None, ion_channel=None, erev=None, ion=None, variable_parameters=None)

Bases: neuroml.nml.nml.Base

Specifying the ion here again is redundant, this will be set in ionChannel definition. It is added here TEMPORARILY since selecting all ca or na conducting channel populations/densities in a cell would be difficult otherwise. Also, it will make it easier to set the correct native simulator value for erev (e.g. ek for ion = k in NEURON). Currently a required attribute. It should be removed in the longer term, due to possible inconsistencies in this value and that in the ionChannel element. TODO: remove.

superclass

alias of Base

class neuroml.nml.nml.ChannelDensityNonUniformGHK(neuro_lex_id=None, id=None, ion_channel=None, ion=None, variable_parameters=None)

Bases: neuroml.nml.nml.Base

Specifying the ion here again is redundant, this will be set in ionChannel definition. It is added here TEMPORARILY since selecting all ca or na conducting channel populations/densities in a cell would be difficult otherwise. Also, it will make it easier to set the correct native simulator value for erev (e.g. ek for ion = k in NEURON). Currently a required attribute. It should be removed in the longer term, due to possible inconsistencies in this value and that in the ionChannel element. TODO: remove.

superclass

alias of Base

class neuroml.nml.nml.ChannelDensityNonUniformNernst(neuro_lex_id=None, id=None, ion_channel=None, ion=None, variable_parameters=None)

Bases: neuroml.nml.nml.Base

Specifying the ion here again is redundant, this will be set in ionChannel definition. It is added here TEMPORARILY since selecting all ca or na conducting channel populations/densities in a cell would be difficult otherwise. Also, it will make it easier to set the correct native simulator value for erev (e.g. ek for ion = k in NEURON). Currently a required attribute. It should be removed in the longer term, due to possible inconsistencies in this value and that in the ionChannel element. TODO: remove.

superclass

alias of Base

class neuroml.nml.nml.ChannelDensityVShift(neuro_lex_id=None, id=None, ion_channel=None, cond_density=None, erev=None, segment_groups='all', segments=None, ion=None, variable_parameters=None, v_shift=None)

Bases: neuroml.nml.nml.ChannelDensity

superclass

alias of ChannelDensity

class neuroml.nml.nml.ChannelPopulation(neuro_lex_id=None, id=None, ion_channel=None, number=None, erev=None, segment_groups='all', segments=None, ion=None, variable_parameters=None)

Bases: neuroml.nml.nml.Base

Specifying the ion here again is redundant, this will be set in ionChannel definition. It is added here TEMPORARILY since selecting all ca or na conducting channel populations/densities in a cell would be difficult otherwise. Also, it will make it easier to set the correct native simulator value for erev (e.g. ek for ion = k in NEURON). Currently a required attribute. It should be removed in the longer term, due to possible inconsistencies in this value and that in the ionChannel element. TODO: remove.

superclass

alias of Base

class neuroml.nml.nml.ClosedState(neuro_lex_id=None, id=None)

Bases: neuroml.nml.nml.Base

superclass

alias of Base

class neuroml.nml.nml.ComponentType(name=None, extends=None, description=None, Property=None, Parameter=None, Constant=None, Exposure=None, Requirement=None, InstanceRequirement=None, Dynamics=None)

Bases: neuroml.nml.nml.GeneratedsSuper

Contains an extension to NeuroML by creating custom LEMS ComponentType.

class neuroml.nml.nml.CompoundInput(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, pulse_generators=None, sine_generators=None, ramp_generators=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.CompoundInputDL(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, pulse_generator_dls=None, sine_generator_dls=None, ramp_generator_dls=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.ConcentrationModel_D(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, ion=None, resting_conc=None, decay_constant=None, shell_thickness=None, type='decayingPoolConcentrationModel')

Bases: neuroml.nml.nml.DecayingPoolConcentrationModel

superclass

alias of DecayingPoolConcentrationModel

class neuroml.nml.nml.ConditionalDerivedVariable(name=None, dimension=None, description=None, exposure=None, Case=None)

Bases: neuroml.nml.nml.NamedDimensionalVariable

LEMS ComponentType for ConditionalDerivedVariable

class neuroml.nml.nml.Connection(neuro_lex_id=None, id=None, pre_cell_id=None, pre_segment_id='0', pre_fraction_along='0.5', post_cell_id=None, post_segment_id='0', post_fraction_along='0.5')

Bases: neuroml.nml.nml.BaseConnectionOldFormat

Individual chemical (event based) synaptic connection, weight==1 and no delay

superclass

alias of BaseConnectionOldFormat

class neuroml.nml.nml.ConnectionWD(neuro_lex_id=None, id=None, pre_cell_id=None, pre_segment_id='0', pre_fraction_along='0.5', post_cell_id=None, post_segment_id='0', post_fraction_along='0.5', weight=None, delay=None)

Bases: neuroml.nml.nml.BaseConnectionOldFormat

Individual synaptic connection with weight and delay

superclass

alias of BaseConnectionOldFormat

class neuroml.nml.nml.Constant(name=None, dimension=None, value=None, description=None)

Bases: neuroml.nml.nml.GeneratedsSuper

LEMS ComponentType for Constant.

class neuroml.nml.nml.ContinuousConnection(neuro_lex_id=None, id=None, pre_cell=None, pre_segment='0', pre_fraction_along='0.5', post_cell=None, post_segment='0', post_fraction_along='0.5', pre_component=None, post_component=None, extensiontype_=None)

Bases: neuroml.nml.nml.BaseConnectionNewFormat

Individual continuous/analog synaptic connection

superclass

alias of BaseConnectionNewFormat

class neuroml.nml.nml.ContinuousConnectionInstance(neuro_lex_id=None, id=None, pre_cell=None, pre_segment='0', pre_fraction_along='0.5', post_cell=None, post_segment='0', post_fraction_along='0.5', pre_component=None, post_component=None, extensiontype_=None)

Bases: neuroml.nml.nml.ContinuousConnection

Individual continuous/analog synaptic connection - instance based

superclass

alias of ContinuousConnection

class neuroml.nml.nml.ContinuousConnectionInstanceW(neuro_lex_id=None, id=None, pre_cell=None, pre_segment='0', pre_fraction_along='0.5', post_cell=None, post_segment='0', post_fraction_along='0.5', pre_component=None, post_component=None, weight=None)

Bases: neuroml.nml.nml.ContinuousConnectionInstance

Individual continuous/analog synaptic connection - instance based. Includes setting of _weight for the connection

superclass

alias of ContinuousConnectionInstance

class neuroml.nml.nml.ContinuousProjection(neuro_lex_id=None, id=None, presynaptic_population=None, postsynaptic_population=None, continuous_connections=None, continuous_connection_instances=None, continuous_connection_instance_ws=None)

Bases: neuroml.nml.nml.BaseProjection

Projection between two populations consisting of analog connections (e.g. graded synapses)

superclass

alias of BaseProjection

class neuroml.nml.nml.DecayingPoolConcentrationModel(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, ion=None, resting_conc=None, decay_constant=None, shell_thickness=None, extensiontype_=None)

Bases: neuroml.nml.nml.Standalone

Should not be required, as it’s present on the species element!

superclass

alias of Standalone

class neuroml.nml.nml.DerivedVariable(name=None, dimension=None, description=None, exposure=None, value=None, select=None)

Bases: neuroml.nml.nml.NamedDimensionalVariable

LEMS ComponentType for DerivedVariable

class neuroml.nml.nml.DoubleSynapse(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, synapse1=None, synapse2=None, synapse1_path=None, synapse2_path=None)

Bases: neuroml.nml.nml.BaseVoltageDepSynapse

superclass

alias of BaseVoltageDepSynapse

class neuroml.nml.nml.Dynamics(StateVariable=None, DerivedVariable=None, ConditionalDerivedVariable=None, TimeDerivative=None)

Bases: neuroml.nml.nml.GeneratedsSuper

LEMS ComponentType for Dynamics

class neuroml.nml.nml.EIF_cond_alpha_isfa_ista(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, cm=None, i_offset=None, tau_syn_E=None, tau_syn_I=None, v_init=None, tau_m=None, tau_refrac=None, v_reset=None, v_rest=None, v_thresh=None, e_rev_E=None, e_rev_I=None, a=None, b=None, delta_T=None, tau_w=None, v_spike=None)

Bases: neuroml.nml.nml.EIF_cond_exp_isfa_ista

superclass

alias of EIF_cond_exp_isfa_ista

class neuroml.nml.nml.EIF_cond_exp_isfa_ista(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, cm=None, i_offset=None, tau_syn_E=None, tau_syn_I=None, v_init=None, tau_m=None, tau_refrac=None, v_reset=None, v_rest=None, v_thresh=None, e_rev_E=None, e_rev_I=None, a=None, b=None, delta_T=None, tau_w=None, v_spike=None, extensiontype_=None)

Bases: neuroml.nml.nml.basePyNNIaFCondCell

superclass

alias of basePyNNIaFCondCell

class neuroml.nml.nml.ElectricalConnection(neuro_lex_id=None, id=None, pre_cell=None, pre_segment='0', pre_fraction_along='0.5', post_cell=None, post_segment='0', post_fraction_along='0.5', synapse=None, extensiontype_=None)

Bases: neuroml.nml.nml.BaseConnectionNewFormat

Individual electrical synaptic connection

superclass

alias of BaseConnectionNewFormat

class neuroml.nml.nml.ElectricalConnectionInstance(neuro_lex_id=None, id=None, pre_cell=None, pre_segment='0', pre_fraction_along='0.5', post_cell=None, post_segment='0', post_fraction_along='0.5', synapse=None, extensiontype_=None)

Bases: neuroml.nml.nml.ElectricalConnection

Projection between two populations consisting of analog connections (e.g. graded synapses)

superclass

alias of ElectricalConnection

class neuroml.nml.nml.ElectricalConnectionInstanceW(neuro_lex_id=None, id=None, pre_cell=None, pre_segment='0', pre_fraction_along='0.5', post_cell=None, post_segment='0', post_fraction_along='0.5', synapse=None, weight=None)

Bases: neuroml.nml.nml.ElectricalConnectionInstance

Projection between two populations consisting of analog connections (e.g. graded synapses). Includes setting of weight for the connection

superclass

alias of ElectricalConnectionInstance

class neuroml.nml.nml.ElectricalProjection(neuro_lex_id=None, id=None, presynaptic_population=None, postsynaptic_population=None, electrical_connections=None, electrical_connection_instances=None, electrical_connection_instance_ws=None)

Bases: neuroml.nml.nml.BaseProjection

Projection between two populations consisting of electrical connections (gap junctions)

superclass

alias of BaseProjection

class neuroml.nml.nml.ExpCondSynapse(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, tau_syn=None, e_rev=None)

Bases: neuroml.nml.nml.BasePynnSynapse

superclass

alias of BasePynnSynapse

class neuroml.nml.nml.ExpCurrSynapse(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, tau_syn=None)

Bases: neuroml.nml.nml.BasePynnSynapse

superclass

alias of BasePynnSynapse

class neuroml.nml.nml.ExpOneSynapse(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, gbase=None, erev=None, tau_decay=None)

Bases: neuroml.nml.nml.BaseConductanceBasedSynapse

superclass

alias of BaseConductanceBasedSynapse

class neuroml.nml.nml.ExpThreeSynapse(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, gbase1=None, gbase2=None, erev=None, tau_decay1=None, tau_decay2=None, tau_rise=None)

Bases: neuroml.nml.nml.BaseConductanceBasedSynapseTwo

superclass

alias of BaseConductanceBasedSynapseTwo

class neuroml.nml.nml.ExpTwoSynapse(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, gbase=None, erev=None, tau_decay=None, tau_rise=None, extensiontype_=None)

Bases: neuroml.nml.nml.BaseConductanceBasedSynapse

superclass

alias of BaseConductanceBasedSynapse

class neuroml.nml.nml.ExplicitInput(target=None, input=None, destination=None)

Bases: neuroml.nml.nml.GeneratedsSuper

Single explicit input. Introduced to test inputs in LEMS. Will probably be removed in favour of inputs wrapped in inputList element

class neuroml.nml.nml.Exposure(name=None, dimension=None, description=None)

Bases: neuroml.nml.nml.GeneratedsSuper

LEMS Exposure (ComponentType property)

class neuroml.nml.nml.ExtracellularProperties(neuro_lex_id=None, id=None, species=None)

Bases: neuroml.nml.nml.Base

superclass

alias of Base

class neuroml.nml.nml.FitzHughNagumo1969Cell(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, a=None, b=None, I=None, phi=None, V0=None, W0=None)

Bases: neuroml.nml.nml.BaseCell

superclass

alias of BaseCell

class neuroml.nml.nml.FitzHughNagumoCell(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, I=None)

Bases: neuroml.nml.nml.BaseCell

superclass

alias of BaseCell

class neuroml.nml.nml.FixedFactorConcentrationModel(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, ion=None, resting_conc=None, decay_constant=None, rho=None)

Bases: neuroml.nml.nml.Standalone

Should not be required, as it’s present on the species element!

superclass

alias of Standalone

class neuroml.nml.nml.ForwardTransition(neuro_lex_id=None, id=None, from_=None, to=None, anytypeobjs_=None)

Bases: neuroml.nml.nml.Base

superclass

alias of Base

class neuroml.nml.nml.GapJunction(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, conductance=None)

Bases: neuroml.nml.nml.BaseSynapse

Gap junction/single electrical connection

superclass

alias of BaseSynapse

class neuroml.nml.nml.GateFractional(neuro_lex_id=None, id=None, instances=None, notes=None, q10_settings=None, sub_gates=None)

Bases: neuroml.nml.nml.Base

superclass

alias of Base

class neuroml.nml.nml.GateFractionalSubgate(neuro_lex_id=None, id=None, fractional_conductance=None, notes=None, q10_settings=None, steady_state=None, time_course=None)

Bases: neuroml.nml.nml.Base

superclass

alias of Base

class neuroml.nml.nml.GateHHInstantaneous(neuro_lex_id=None, id=None, instances=None, notes=None, steady_state=None)

Bases: neuroml.nml.nml.Base

superclass

alias of Base

class neuroml.nml.nml.GateHHRates(neuro_lex_id=None, id=None, instances=None, notes=None, q10_settings=None, forward_rate=None, reverse_rate=None)

Bases: neuroml.nml.nml.Base

superclass

alias of Base

class neuroml.nml.nml.GateHHRatesInf(neuro_lex_id=None, id=None, instances=None, notes=None, q10_settings=None, forward_rate=None, reverse_rate=None, steady_state=None)

Bases: neuroml.nml.nml.Base

superclass

alias of Base

class neuroml.nml.nml.GateHHRatesTau(neuro_lex_id=None, id=None, instances=None, notes=None, q10_settings=None, forward_rate=None, reverse_rate=None, time_course=None)

Bases: neuroml.nml.nml.Base

superclass

alias of Base

class neuroml.nml.nml.GateHHRatesTauInf(neuro_lex_id=None, id=None, instances=None, notes=None, q10_settings=None, forward_rate=None, reverse_rate=None, time_course=None, steady_state=None)

Bases: neuroml.nml.nml.Base

superclass

alias of Base

class neuroml.nml.nml.GateHHTauInf(neuro_lex_id=None, id=None, instances=None, notes=None, q10_settings=None, time_course=None, steady_state=None)

Bases: neuroml.nml.nml.Base

superclass

alias of Base

class neuroml.nml.nml.GateHHUndetermined(neuro_lex_id=None, id=None, instances=None, type=None, notes=None, q10_settings=None, forward_rate=None, reverse_rate=None, time_course=None, steady_state=None, sub_gates=None)

Bases: neuroml.nml.nml.Base

Note all sub elements for gateHHrates, gateHHratesTau, gateFractional etc. allowed here. Which are valid should be constrained by what type is set

superclass

alias of Base

class neuroml.nml.nml.GateKS(neuro_lex_id=None, id=None, instances=None, notes=None, q10_settings=None, closed_states=None, open_states=None, forward_transition=None, reverse_transition=None, tau_inf_transition=None)

Bases: neuroml.nml.nml.Base

superclass

alias of Base

class neuroml.nml.nml.GradedSynapse(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, conductance=None, delta=None, Vth=None, k=None, erev=None)

Bases: neuroml.nml.nml.BaseSynapse

Based on synapse in Methods of http://www.nature.com/neuro/journal/v7/n12/abs/nn1352.html.

superclass

alias of BaseSynapse

class neuroml.nml.nml.HH_cond_exp(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, cm=None, i_offset=None, tau_syn_E=None, tau_syn_I=None, v_init=None, v_offset=None, e_rev_E=None, e_rev_I=None, e_rev_K=None, e_rev_Na=None, e_rev_leak=None, g_leak=None, gbar_K=None, gbar_Na=None)

Bases: neuroml.nml.nml.basePyNNCell

superclass

alias of basePyNNCell

class neuroml.nml.nml.IF_cond_alpha(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, cm=None, i_offset=None, tau_syn_E=None, tau_syn_I=None, v_init=None, tau_m=None, tau_refrac=None, v_reset=None, v_rest=None, v_thresh=None, e_rev_E=None, e_rev_I=None)

Bases: neuroml.nml.nml.basePyNNIaFCondCell

superclass

alias of basePyNNIaFCondCell

class neuroml.nml.nml.IF_cond_exp(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, cm=None, i_offset=None, tau_syn_E=None, tau_syn_I=None, v_init=None, tau_m=None, tau_refrac=None, v_reset=None, v_rest=None, v_thresh=None, e_rev_E=None, e_rev_I=None)

Bases: neuroml.nml.nml.basePyNNIaFCondCell

superclass

alias of basePyNNIaFCondCell

class neuroml.nml.nml.IF_curr_alpha(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, cm=None, i_offset=None, tau_syn_E=None, tau_syn_I=None, v_init=None, tau_m=None, tau_refrac=None, v_reset=None, v_rest=None, v_thresh=None)

Bases: neuroml.nml.nml.basePyNNIaFCell

superclass

alias of basePyNNIaFCell

class neuroml.nml.nml.IF_curr_exp(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, cm=None, i_offset=None, tau_syn_E=None, tau_syn_I=None, v_init=None, tau_m=None, tau_refrac=None, v_reset=None, v_rest=None, v_thresh=None)

Bases: neuroml.nml.nml.basePyNNIaFCell

superclass

alias of basePyNNIaFCell

class neuroml.nml.nml.IafCell(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, leak_reversal=None, thresh=None, reset=None, C=None, leak_conductance=None, extensiontype_=None)

Bases: neuroml.nml.nml.BaseCell

superclass

alias of BaseCell

class neuroml.nml.nml.IafRefCell(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, leak_reversal=None, thresh=None, reset=None, C=None, leak_conductance=None, refract=None)

Bases: neuroml.nml.nml.IafCell

superclass

alias of IafCell

class neuroml.nml.nml.IafTauCell(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, leak_reversal=None, thresh=None, reset=None, tau=None, extensiontype_=None)

Bases: neuroml.nml.nml.BaseCell

superclass

alias of BaseCell

class neuroml.nml.nml.IafTauRefCell(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, leak_reversal=None, thresh=None, reset=None, tau=None, refract=None)

Bases: neuroml.nml.nml.IafTauCell

superclass

alias of IafTauCell

class neuroml.nml.nml.InhomogeneousParameter(neuro_lex_id=None, id=None, variable=None, metric=None, proximal=None, distal=None)

Bases: neuroml.nml.nml.Base

superclass

alias of Base

class neuroml.nml.nml.InitMembPotential(value=None, segment_groups='all', segments=None)

Bases: neuroml.nml.nml.ValueAcrossSegOrSegGroup

Using a thin extension of ValueAcrossSegOrSegGroup to facilitate library generation (e.g. libNeuroML)

class neuroml.nml.nml.Input(id=None, target=None, destination=None, segment_id=None, fraction_along=None, extensiontype_=None)

Bases: neuroml.nml.nml.GeneratedsSuper

Individual input to the cell specified by target

class neuroml.nml.nml.InputList(neuro_lex_id=None, id=None, populations=None, component=None, input=None, input_ws=None)

Bases: neuroml.nml.nml.Base

List of inputs to a population. Currents will be provided by the specified component.

superclass

alias of Base

class neuroml.nml.nml.InputW(id=None, target=None, destination=None, segment_id=None, fraction_along=None, weight=None)

Bases: neuroml.nml.nml.Input

Individual input to the cell specified by target. Includes setting of _weight for the connection

superclass

alias of Input

class neuroml.nml.nml.IonChannel(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, q10_conductance_scalings=None, species=None, type=None, conductance=None, gates=None, gate_hh_rates=None, gate_h_hrates_taus=None, gate_hh_tau_infs=None, gate_h_hrates_infs=None, gate_h_hrates_tau_infs=None, gate_hh_instantaneouses=None, gate_fractionals=None, extensiontype_=None)

Bases: neuroml.nml.nml.IonChannelScalable

Note ionChannel and ionChannelHH are currently functionally identical. This is needed since many existing examples use ionChannel, some use ionChannelHH. NeuroML v2beta4 should remove one of these, probably ionChannelHH.

superclass

alias of IonChannelScalable

class neuroml.nml.nml.IonChannelHH(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, q10_conductance_scalings=None, species=None, type=None, conductance=None, gates=None, gate_hh_rates=None, gate_h_hrates_taus=None, gate_hh_tau_infs=None, gate_h_hrates_infs=None, gate_h_hrates_tau_infs=None, gate_hh_instantaneouses=None, gate_fractionals=None)

Bases: neuroml.nml.nml.IonChannel

Note ionChannel and ionChannelHH are currently functionally identical. This is needed since many existing examples use ionChannel, some use ionChannelHH. NeuroML v2beta4 should remove one of these, probably ionChannelHH.

superclass

alias of IonChannel

class neuroml.nml.nml.IonChannelKS(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, species=None, conductance=None, gate_kses=None)

Bases: neuroml.nml.nml.Standalone

Kinetic scheme based ion channel.

superclass

alias of Standalone

class neuroml.nml.nml.IonChannelScalable(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, q10_conductance_scalings=None, extensiontype_=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.IonChannelVShift(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, q10_conductance_scalings=None, species=None, type=None, conductance=None, gates=None, gate_hh_rates=None, gate_h_hrates_taus=None, gate_hh_tau_infs=None, gate_h_hrates_infs=None, gate_h_hrates_tau_infs=None, gate_hh_instantaneouses=None, gate_fractionals=None, v_shift=None)

Bases: neuroml.nml.nml.IonChannel

Same as ionChannel, but with a vShift parameter to change voltage activation of gates. The exact usage of vShift in expressions for rates is determined by the individual gates.

superclass

alias of IonChannel

class neuroml.nml.nml.Izhikevich2007Cell(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, C=None, v0=None, k=None, vr=None, vt=None, vpeak=None, a=None, b=None, c=None, d=None)

Bases: neuroml.nml.nml.BaseCellMembPotCap

superclass

alias of BaseCellMembPotCap

class neuroml.nml.nml.IzhikevichCell(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, v0=None, thresh=None, a=None, b=None, c=None, d=None)

Bases: neuroml.nml.nml.BaseCell

superclass

alias of BaseCell

class neuroml.nml.nml.LinearGradedSynapse(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, conductance=None)

Bases: neuroml.nml.nml.BaseSynapse

Behaves just like a one way gap junction.

superclass

alias of BaseSynapse

class neuroml.nml.nml.Morphology(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, segments=None, segment_groups=None)

Bases: neuroml.nml.nml.Standalone

Standalone element which is usually inside a single cell, but could be outside and referenced by id.

superclass

alias of Standalone

class neuroml.nml.nml.Network(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, type=None, temperature=None, spaces=None, regions=None, extracellular_properties=None, populations=None, cell_sets=None, synaptic_connections=None, projections=None, electrical_projections=None, continuous_projections=None, explicit_inputs=None, input_lists=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.NeuroMLDocument(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, includes=None, extracellular_properties=None, intracellular_properties=None, morphology=None, ion_channel=None, ion_channel_hhs=None, ion_channel_v_shifts=None, ion_channel_kses=None, decaying_pool_concentration_models=None, fixed_factor_concentration_models=None, alpha_current_synapses=None, alpha_synapses=None, exp_one_synapses=None, exp_two_synapses=None, exp_three_synapses=None, blocking_plastic_synapses=None, double_synapses=None, gap_junctions=None, silent_synapses=None, linear_graded_synapses=None, graded_synapses=None, biophysical_properties=None, cells=None, cell2_ca_poolses=None, base_cells=None, iaf_tau_cells=None, iaf_tau_ref_cells=None, iaf_cells=None, iaf_ref_cells=None, izhikevich_cells=None, izhikevich2007_cells=None, ad_ex_ia_f_cells=None, fitz_hugh_nagumo_cells=None, fitz_hugh_nagumo1969_cells=None, pinsky_rinzel_ca3_cells=None, pulse_generators=None, pulse_generator_dls=None, sine_generators=None, sine_generator_dls=None, ramp_generators=None, ramp_generator_dls=None, compound_inputs=None, compound_input_dls=None, voltage_clamps=None, voltage_clamp_triples=None, spike_arrays=None, timed_synaptic_inputs=None, spike_generators=None, spike_generator_randoms=None, spike_generator_poissons=None, spike_generator_ref_poissons=None, poisson_firing_synapses=None, transient_poisson_firing_synapses=None, IF_curr_alpha=None, IF_curr_exp=None, IF_cond_alpha=None, IF_cond_exp=None, EIF_cond_exp_isfa_ista=None, EIF_cond_alpha_isfa_ista=None, HH_cond_exp=None, exp_cond_synapses=None, alpha_cond_synapses=None, exp_curr_synapses=None, alpha_curr_synapses=None, SpikeSourcePoisson=None, networks=None, ComponentType=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.OpenState(neuro_lex_id=None, id=None)

Bases: neuroml.nml.nml.Base

superclass

alias of Base

class neuroml.nml.nml.PinskyRinzelCA3Cell(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, i_soma=None, i_dend=None, gc=None, g_ls=None, g_ld=None, g_na=None, g_kdr=None, g_ca=None, g_kahp=None, g_kc=None, g_nmda=None, g_ampa=None, e_na=None, e_ca=None, e_k=None, e_l=None, qd0=None, pp=None, alphac=None, betac=None, cm=None)

Bases: neuroml.nml.nml.BaseCell

superclass

alias of BaseCell

class neuroml.nml.nml.Point3DWithDiam(x=None, y=None, z=None, diameter=None)

Bases: neuroml.nml.nml.GeneratedsSuper

A 3D point with diameter.

class neuroml.nml.nml.PoissonFiringSynapse(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, average_rate=None, synapse=None, spike_target=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.Population(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, component=None, size=None, type=None, extracellular_properties=None, layout=None, instances=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.Projection(neuro_lex_id=None, id=None, presynaptic_population=None, postsynaptic_population=None, synapse=None, connections=None, connection_wds=None)

Bases: neuroml.nml.nml.BaseProjection

Projection (set of synaptic connections) between two populations. Chemical/event based synaptic transmission

superclass

alias of BaseProjection

class neuroml.nml.nml.Property(tag=None, value=None)

Bases: neuroml.nml.nml.GeneratedsSuper

Generic property with a tag and value

class neuroml.nml.nml.PulseGenerator(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, delay=None, duration=None, amplitude=None)

Bases: neuroml.nml.nml.Standalone

Generates a constant current pulse of a certain amplitude (with dimensions for current) for a specified duration after a delay.

superclass

alias of Standalone

class neuroml.nml.nml.PulseGeneratorDL(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, delay=None, duration=None, amplitude=None)

Bases: neuroml.nml.nml.Standalone

Generates a constant current pulse of a certain amplitude (non dimensional) for a specified duration after a delay.

superclass

alias of Standalone

class neuroml.nml.nml.RampGenerator(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, delay=None, duration=None, start_amplitude=None, finish_amplitude=None, baseline_amplitude=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.RampGeneratorDL(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, delay=None, duration=None, start_amplitude=None, finish_amplitude=None, baseline_amplitude=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.ReactionScheme(neuro_lex_id=None, id=None, source=None, type=None, anytypeobjs_=None)

Bases: neuroml.nml.nml.Base

superclass

alias of Base

class neuroml.nml.nml.Region(neuro_lex_id=None, id=None, spaces=None, anytypeobjs_=None)

Bases: neuroml.nml.nml.Base

superclass

alias of Base

class neuroml.nml.nml.Resistivity(value=None, segment_groups='all', segments=None)

Bases: neuroml.nml.nml.ValueAcrossSegOrSegGroup

Using a thin extension of ValueAcrossSegOrSegGroup to facilitate library generation (e.g. libNeuroML)

class neuroml.nml.nml.ReverseTransition(neuro_lex_id=None, id=None, from_=None, to=None, anytypeobjs_=None)

Bases: neuroml.nml.nml.Base

superclass

alias of Base

class neuroml.nml.nml.Segment(neuro_lex_id=None, id=None, name=None, parent=None, proximal=None, distal=None)

Bases: neuroml.nml.nml.BaseNonNegativeIntegerId

superclass

alias of BaseNonNegativeIntegerId

class neuroml.nml.nml.SegmentGroup(neuro_lex_id=None, id=None, notes=None, properties=None, annotation=None, members=None, includes=None, paths=None, sub_trees=None, inhomogeneous_parameters=None)

Bases: neuroml.nml.nml.Base

superclass

alias of Base

class neuroml.nml.nml.SilentSynapse(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None)

Bases: neuroml.nml.nml.BaseSynapse

Dummy synapse which emits no current. Used as presynaptic endpoint for analog synaptic connection (continuousConnection).

superclass

alias of BaseSynapse

class neuroml.nml.nml.SineGenerator(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, delay=None, phase=None, duration=None, amplitude=None, period=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.SineGeneratorDL(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, delay=None, phase=None, duration=None, amplitude=None, period=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.Space(neuro_lex_id=None, id=None, based_on=None, structure=None)

Bases: neuroml.nml.nml.Base

superclass

alias of Base

class neuroml.nml.nml.Species(value=None, segment_groups='all', segments=None, id=None, concentration_model=None, ion=None, initial_concentration=None, initial_ext_concentration=None)

Bases: neuroml.nml.nml.ValueAcrossSegOrSegGroup

Specifying the ion here again is redundant, the ion name should be the same as id. Kept for now until LEMS implementation can select by id. TODO: remove.

class neuroml.nml.nml.SpecificCapacitance(value=None, segment_groups='all', segments=None)

Bases: neuroml.nml.nml.ValueAcrossSegOrSegGroup

Using a thin extension of ValueAcrossSegOrSegGroup to facilitate library generation (e.g. libNeuroML)

class neuroml.nml.nml.Spike(neuro_lex_id=None, id=None, time=None)

Bases: neuroml.nml.nml.BaseNonNegativeIntegerId

superclass

alias of BaseNonNegativeIntegerId

class neuroml.nml.nml.SpikeArray(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, spikes=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.SpikeGenerator(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, period=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.SpikeGeneratorPoisson(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, average_rate=None, extensiontype_=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.SpikeGeneratorRandom(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, max_isi=None, min_isi=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.SpikeGeneratorRefPoisson(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, average_rate=None, minimum_isi=None)

Bases: neuroml.nml.nml.SpikeGeneratorPoisson

superclass

alias of SpikeGeneratorPoisson

class neuroml.nml.nml.SpikeSourcePoisson(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, start=None, duration=None, rate=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.SpikeThresh(value=None, segment_groups='all', segments=None)

Bases: neuroml.nml.nml.ValueAcrossSegOrSegGroup

Using a thin extension of ValueAcrossSegOrSegGroup to facilitate library generation (e.g. libNeuroML)

class neuroml.nml.nml.Standalone(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, extensiontype_=None)

Bases: neuroml.nml.nml.Base

Elements which can stand alone and be referenced by id, e.g. cell, morphology.

superclass

alias of Base

class neuroml.nml.nml.SynapticConnection(from_=None, to=None, synapse=None, destination=None)

Bases: neuroml.nml.nml.GeneratedsSuper

Single explicit connection. Introduced to test connections in LEMS. Will probably be removed in favour of connections wrapped in projection element

class neuroml.nml.nml.TauInfTransition(neuro_lex_id=None, id=None, from_=None, to=None, steady_state=None, time_course=None)

Bases: neuroml.nml.nml.Base

superclass

alias of Base

class neuroml.nml.nml.TimedSynapticInput(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, synapse=None, spike_target=None, spikes=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.TransientPoissonFiringSynapse(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, average_rate=None, delay=None, duration=None, synapse=None, spike_target=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.VoltageClamp(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, delay=None, duration=None, target_voltage=None, simple_series_resistance=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.VoltageClampTriple(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, active=None, delay=None, duration=None, conditioning_voltage=None, testing_voltage=None, return_voltage=None, simple_series_resistance=None)

Bases: neuroml.nml.nml.Standalone

superclass

alias of Standalone

class neuroml.nml.nml.basePyNNCell(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, cm=None, i_offset=None, tau_syn_E=None, tau_syn_I=None, v_init=None, extensiontype_=None)

Bases: neuroml.nml.nml.BaseCell

superclass

alias of BaseCell

class neuroml.nml.nml.basePyNNIaFCell(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, cm=None, i_offset=None, tau_syn_E=None, tau_syn_I=None, v_init=None, tau_m=None, tau_refrac=None, v_reset=None, v_rest=None, v_thresh=None, extensiontype_=None)

Bases: neuroml.nml.nml.basePyNNCell

superclass

alias of basePyNNCell

class neuroml.nml.nml.basePyNNIaFCondCell(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, cm=None, i_offset=None, tau_syn_E=None, tau_syn_I=None, v_init=None, tau_m=None, tau_refrac=None, v_reset=None, v_rest=None, v_thresh=None, e_rev_E=None, e_rev_I=None, extensiontype_=None)

Bases: neuroml.nml.nml.basePyNNIaFCell

superclass

alias of basePyNNIaFCell