Uses of Class
org.neuroml.model.Base

Packages that use Base
Package
Description
 
  • Uses of Base in org.neuroml.model

    Subclasses of Base in org.neuroml.model
    Modifier and Type
    Class
    Description
    class 
    Model based on Brette R and Gerstner W ( 2005 ) Adaptive Exponential Integrate-and-Fire Model as an Effective Description of Neuronal Activity.
    class 
    Alpha synapse: rise time and decay time are both tau_syn.
    class 
    Alpha current synapse: rise time and decay time are both **tau.** \n :param tau: Time course for rise and decay :type tau: time :param ibase: Baseline current increase after receiving a spike :type ibase: current
    class 
    Alpha synapse: rise time and decay time are both tau_syn.
    class 
    Ohmic synapse model where rise time and decay time are both **tau.** Max conductance reached during this time ( assuming zero conductance before ) is **gbase** * **weight.** \n :param tau: Time course of rise/decay :type tau: time :param gbase: Baseline conductance, generally the maximum conductance following a single spike :type gbase: conductance :param erev: Reversal potential of the synapse :type erev: voltage
    class 
    Base type of any cell ( e.
    class 
    Any cell with a membrane potential **v** with voltage units and a membrane capacitance **C.** Also defines exposed value **iSyn** for current due to external synapses and **iMemb** for total transmembrane current ( usually channel currents plus **iSyn** ) \n :param C: Total capacitance of the cell membrane :type C: capacitance
    class 
    Synapse model which exposes a conductance **g** in addition to producing a current.
    class 
    Synapse model suited for a sum of two expTwoSynapses which exposes a conductance **g** in addition to producing a current.
    class 
    Synapse model which produces a synaptic current.
    class 
    Base for projection (set of synaptic connections) between two populations
    class 
    Base type of any PyNN standard cell model.
    class 
    Base type of any PyNN standard integrate and fire model \n :param tau_refrac: :type tau_refrac: none :param v_thresh: :type v_thresh: none :param tau_m: :type tau_m: none :param v_rest: :type v_rest: none :param v_reset: :type v_reset: none :param cm: :type cm: none :param i_offset: :type i_offset: none :param tau_syn_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type tau_syn_E: none :param tau_syn_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type tau_syn_I: none :param v_init: :type v_init: none
    class 
    Base type of conductance based PyNN IaF cell models \n :param e_rev_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type e_rev_E: none :param e_rev_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type e_rev_I: none :param tau_refrac: :type tau_refrac: none :param v_thresh: :type v_thresh: none :param tau_m: :type tau_m: none :param v_rest: :type v_rest: none :param v_reset: :type v_reset: none :param cm: :type cm: none :param i_offset: :type i_offset: none :param tau_syn_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type tau_syn_E: none :param tau_syn_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type tau_syn_I: none :param v_init: :type v_init: none
    class 
    Base type for all PyNN synapses.
    class 
    Base type for all synapses, i.
    class 
    Base type for synapses with a dependence on membrane potential
    class 
    The biophysical properties of the **cell** , including the **membraneProperties** and the **intracellularProperties**
    class 
    The biophysical properties of the **cell** , including the **membraneProperties2CaPools** and the **intracellularProperties2CaPools** for a cell with two Ca pools
    class 
    Biexponential synapse that allows for optional block and plasticity mechanisms, which can be expressed as child elements.
    class 
    Cell with **segment** s specified in a **morphology** element along with details on its **biophysicalProperties** .
    class 
    Variant of cell with two independent Ca2+ pools.
    class 
    Java class for CellSet complex type.
    class 
    Specifies a time varying ohmic conductance density, **gDensity,** which is distributed on an area of the **cell** ( specified in **membraneProperties** ) with fixed reversal potential **erev** producing a current density **iDensity** \n :param erev: The reversal potential of the current produced :type erev: voltage :param condDensity: :type condDensity: conductanceDensity
    class 
    Specifies a time varying conductance density, **gDensity,** which is distributed on an area of the cell, producing a current density **iDensity** and whose reversal potential is calculated from the Goldman Hodgkin Katz equation.
    class 
    Time varying conductance density, **gDensity,** which is distributed on an area of the cell, producing a current density **iDensity.** Modified version of Jaffe et al.
    class 
    Specifies a time varying conductance density, **gDensity,** which is distributed on an area of the **cell,** producing a current density **iDensity** and whose reversal potential is calculated from the Nernst equation.
    class 
    This component is similar to the original component type **channelDensityNernst** but it is changed in order to have a reversal potential that depends on a second independent Ca++ pool ( ca2 ).
    class 
    Specifies a time varying ohmic conductance density, which is distributed on a region of the **cell.** The conductance density of the channel is not uniform, but is set using the **variableParameter** .
    class 
    Specifies a time varying conductance density, which is distributed on a region of the **cell,** and whose current is calculated from the Goldman-Hodgkin-Katz equation.
    class 
    Specifies a time varying conductance density, which is distributed on a region of the **cell,** and whose reversal potential is calculated from the Nernst equation.
    class 
    Same as **channelDensity** , but with a **vShift** parameter to change voltage activation of gates.
    class 
    Population of a **number** of ohmic ion channels.
    class 
    A **KSState** with **relativeConductance** of 0 \n :param relativeConductance: :type relativeConductance: none
    class 
    Generates a current which is the sum of all its child **basePointCurrent** element, e.
    class 
    Generates a current which is the sum of all its child **basePointCurrentDL** elements, e.
    class 
    Java class for ConcentrationModel_D complex type.
    class 
    A projection between **presynapticPopulation** and **postsynapticPopulation** through components **preComponent** at the start and **postComponent** at the end of a **continuousConnection** or **continuousConnectionInstance** .
    class 
    Model of an intracellular buffering mechanism for **ion** ( currently hard Coded to be calcium, due to requirement for **iCa** ) which has a baseline level **restingConc** and tends to this value with time course **decayConstant.** The ion is assumed to occupy a shell inside the membrane of thickness **shellThickness.** \n :param restingConc: :type restingConc: concentration :param decayConstant: :type decayConstant: time :param shellThickness: :type shellThickness: length
    class 
    Synapse consisting of two independent synaptic mechanisms ( e.
    class 
    Adaptive exponential integrate and fire neuron according to Brette R and Gerstner W ( 2005 ) with alpha-function-shaped post-synaptic conductance \n :param v_spike: :type v_spike: none :param delta_T: :type delta_T: none :param tau_w: :type tau_w: none :param a: :type a: none :param b: :type b: none :param e_rev_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type e_rev_E: none :param e_rev_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type e_rev_I: none :param tau_refrac: :type tau_refrac: none :param v_thresh: :type v_thresh: none :param tau_m: :type tau_m: none :param v_rest: :type v_rest: none :param v_reset: :type v_reset: none :param cm: :type cm: none :param i_offset: :type i_offset: none :param tau_syn_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type tau_syn_E: none :param tau_syn_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type tau_syn_I: none :param v_init: :type v_init: none
    class 
    Adaptive exponential integrate and fire neuron according to Brette R and Gerstner W ( 2005 ) with exponentially-decaying post-synaptic conductance \n :param v_spike: :type v_spike: none :param delta_T: :type delta_T: none :param tau_w: :type tau_w: none :param a: :type a: none :param b: :type b: none :param e_rev_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type e_rev_E: none :param e_rev_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type e_rev_I: none :param tau_refrac: :type tau_refrac: none :param v_thresh: :type v_thresh: none :param tau_m: :type tau_m: none :param v_rest: :type v_rest: none :param v_reset: :type v_reset: none :param cm: :type cm: none :param i_offset: :type i_offset: none :param tau_syn_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type tau_syn_E: none :param tau_syn_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type tau_syn_I: none :param v_init: :type v_init: none
    class 
    A projection between **presynapticPopulation** to another **postsynapticPopulation** through gap junctions.
    class 
    Conductance based synapse with instantaneous rise and single exponential decay ( with time constant tau_syn ) \n :param e_rev: :type e_rev: none :param tau_syn: :type tau_syn: none
    class 
    Current based synapse with instantaneous rise and single exponential decay ( with time constant tau_syn ) \n :param tau_syn: :type tau_syn: none
    class 
    Ohmic synapse model whose conductance rises instantaneously by ( **gbase** * **weight** ) on receiving an event, and which decays exponentially to zero with time course **tauDecay** \n :param tauDecay: Time course of decay :type tauDecay: time :param gbase: Baseline conductance, generally the maximum conductance following a single spike :type gbase: conductance :param erev: Reversal potential of the synapse :type erev: voltage
    class 
    Ohmic synapse similar to expTwoSynapse but consisting of two components that can differ in decay times and max conductances but share the same rise time.
    class 
    Ohmic synapse model whose conductance waveform on receiving an event has a rise time of **tauRise** and a decay time of **tauDecay.** Max conductance reached during this time ( assuming zero conductance before ) is **gbase** * **weight.** \n :param tauRise: :type tauRise: time :param tauDecay: :type tauDecay: time :param gbase: Baseline conductance, generally the maximum conductance following a single spike :type gbase: conductance :param erev: Reversal potential of the synapse :type erev: voltage
    class 
    Java class for ExtracellularProperties complex type.
    class 
    Java class for ExtracellularPropertiesLocal complex type.
    class 
    The Fitzhugh Nagumo model is a two-dimensional simplification of the Hodgkin-Huxley model of spike generation in squid giant axons.
    class 
    Simple dimensionless model of spiking cell from FitzHugh and Nagumo.
    class 
    Model of buffering of concentration of an ion ( currently hard coded to be calcium, due to requirement for **iCa** ) which has a baseline level **restingConc** and tends to this value with time course **decayConstant.** A fixed factor **rho** is used to scale the incoming current *independently of the size of the compartment* to produce a concentration change.
    class 
    A forward only **KSTransition** for a **gateKS** which specifies a **rate** ( type **baseHHRate** ) which follows one of the standard Hodgkin Huxley forms ( e.
    class 
    Gap junction/single electrical connection \n :param conductance: :type conductance: conductance
    class 
    Gate composed of subgates contributing with fractional conductance \n :param instances: :type instances: none
    class 
    Java class for GateFractionalSubgate complex type.
    class 
    Gate which follows the general Hodgkin Huxley formalism but is instantaneous, so tau = 0 and gate follows exactly inf value \n :param instances: :type instances: none
    class 
    Gate which follows the general Hodgkin Huxley formalism \n :param instances: :type instances: none
    class 
    Gate which follows the general Hodgkin Huxley formalism \n :param instances: :type instances: none
    class 
    Gate which follows the general Hodgkin Huxley formalism \n :param instances: :type instances: none
    class 
    Gate which follows the general Hodgkin Huxley formalism \n :param instances: :type instances: none
    class 
    Gate which follows the general Hodgkin Huxley formalism \n :param instances: :type instances: none
    class 
    Note all sub elements for gateHHrates, gateHHratesTau, gateFractional etc.
    class 
    A gate which consists of multiple **KSState** s and **KSTransition** s giving the rates of transition between them \n :param instances: :type instances: none
    class 
    Graded/analog synapse.
    class 
    Single-compartment Hodgkin-Huxley-type neuron with transient sodium and delayed-rectifier potassium currents using the ion channel models from Traub.
    class 
    The Hindmarsh Rose model is a simplified point cell model which captures complex firing patterns of single neurons, such as periodic and chaotic bursting.
    class 
    Integrate and fire cell with capacitance **C,** **leakConductance** and **leakReversal** \n :param leakConductance: :type leakConductance: conductance :param leakReversal: :type leakReversal: voltage :param thresh: :type thresh: voltage :param reset: :type reset: voltage :param C: Total capacitance of the cell membrane :type C: capacitance
    class 
    Integrate and fire cell with capacitance **C,** **leakConductance,** **leakReversal** and refractory period **refract** \n :param refract: :type refract: time :param leakConductance: :type leakConductance: conductance :param leakReversal: :type leakReversal: voltage :param thresh: :type thresh: voltage :param reset: :type reset: voltage :param C: Total capacitance of the cell membrane :type C: capacitance
    class 
    Integrate and fire cell which returns to its leak reversal potential of **leakReversal** with a time constant **tau** \n :param leakReversal: :type leakReversal: voltage :param tau: :type tau: time :param thresh: The membrane potential at which to emit a spiking event and reset voltage :type thresh: voltage :param reset: The value the membrane potential is reset to on spiking :type reset: voltage
    class 
    Integrate and fire cell which returns to its leak reversal potential of **leakReversal** with a time course **tau.** It has a refractory period of **refract** after spiking \n :param refract: :type refract: time :param leakReversal: :type leakReversal: voltage :param tau: :type tau: time :param thresh: The membrane potential at which to emit a spiking event and reset voltage :type thresh: voltage :param reset: The value the membrane potential is reset to on spiking :type reset: voltage
    class 
    Leaky integrate and fire model with fixed threshold and alpha-function-shaped post-synaptic conductance \n :param e_rev_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type e_rev_E: none :param e_rev_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type e_rev_I: none :param tau_refrac: :type tau_refrac: none :param v_thresh: :type v_thresh: none :param tau_m: :type tau_m: none :param v_rest: :type v_rest: none :param v_reset: :type v_reset: none :param cm: :type cm: none :param i_offset: :type i_offset: none :param tau_syn_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type tau_syn_E: none :param tau_syn_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type tau_syn_I: none :param v_init: :type v_init: none
    class 
    Leaky integrate and fire model with fixed threshold and exponentially-decaying post-synaptic conductance \n :param e_rev_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type e_rev_E: none :param e_rev_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type e_rev_I: none :param tau_refrac: :type tau_refrac: none :param v_thresh: :type v_thresh: none :param tau_m: :type tau_m: none :param v_rest: :type v_rest: none :param v_reset: :type v_reset: none :param cm: :type cm: none :param i_offset: :type i_offset: none :param tau_syn_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type tau_syn_E: none :param tau_syn_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type tau_syn_I: none :param v_init: :type v_init: none
    class 
    Leaky integrate and fire model with fixed threshold and alpha-function-shaped post-synaptic current \n :param tau_refrac: :type tau_refrac: none :param v_thresh: :type v_thresh: none :param tau_m: :type tau_m: none :param v_rest: :type v_rest: none :param v_reset: :type v_reset: none :param cm: :type cm: none :param i_offset: :type i_offset: none :param tau_syn_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type tau_syn_E: none :param tau_syn_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type tau_syn_I: none :param v_init: :type v_init: none
    class 
    Leaky integrate and fire model with fixed threshold and decaying-exponential post-synaptic current \n :param tau_refrac: :type tau_refrac: none :param v_thresh: :type v_thresh: none :param tau_m: :type tau_m: none :param v_rest: :type v_rest: none :param v_reset: :type v_reset: none :param cm: :type cm: none :param i_offset: :type i_offset: none :param tau_syn_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type tau_syn_E: none :param tau_syn_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell :type tau_syn_I: none :param v_init: :type v_init: none
    class 
    An inhomogeneous parameter specified across the **segmentGroup** ( see **variableParameter** for usage ).
    class 
    An explicit list of **input** s to a **population.**
    class 
    Note **ionChannel** and **ionChannelHH** are currently functionally identical.
    class 
    Note **ionChannel** and **ionChannelHH** are currently functionally identical.
    class 
    A kinetic scheme based ion channel with multiple **gateKS** s, each of which consists of multiple **KSState** s and **KSTransition** s giving the rates of transition between them \n :param conductance: :type conductance: conductance
    class 
    Java class for IonChannelScalable complex type.
    class 
    Same as **ionChannel** , but with a **vShift** parameter to change voltage activation of gates.
    class 
    Cell based on the modified Izhikevich model in Izhikevich 2007, Dynamical systems in neuroscience, MIT Press \n :param v0: Initial membrane potential :type v0: voltage :param k: :type k: conductance_per_voltage :param vr: Resting membrane potential :type vr: voltage :param vt: Spike threshold :type vt: voltage :param vpeak: Peak action potential value :type vpeak: voltage :param a: Time scale of recovery variable u :type a: per_time :param b: Sensitivity of recovery variable u to subthreshold fluctuations of membrane potential v :type b: conductance :param c: After-spike reset value of v :type c: voltage :param d: After-spike increase to u :type d: current :param C: Total capacitance of the cell membrane :type C: capacitance
    class 
    Cell based on the 2003 model of Izhikevich, see http://izhikevich.org/publications/spikes.htm \n :param v0: Initial membrane potential :type v0: voltage :param a: Time scale of the recovery variable U :type a: none :param b: Sensitivity of U to the subthreshold fluctuations of the membrane potential V :type b: none :param c: After-spike reset value of V :type c: none :param d: After-spike increase to U :type d: none :param thresh: Spike threshold :type thresh: voltage
    class 
    Behaves just like a one way gap junction.
    class 
    The collection of **segment** s which specify the 3D structure of the cell, along with a number of **segmentGroup** s
    class 
    Network containing: **population** s ( potentially of type **populationList** , and so specifying a list of cell **location** s ); **projection** s ( with lists of **connection** s ) and/or **explicitConnection** s; and **inputList** s ( with lists of **input** s ) and/or **explicitInput** s.
    class 
    Java class for NeuroMLDocument complex type.
    class 
    A **KSState** with **relativeConductance** of 1 \n :param relativeConductance: :type relativeConductance: none
    class 
    Reduced CA3 cell model from Pinsky, P.
    class 
    Poisson spike generator firing at **averageRate,** which is connected to single **synapse** that is triggered every time a spike is generated, producing an input current.
    class 
    A population of components, with just one parameter for the **size,** i.
    class 
    Projection from one population, **presynapticPopulation** to another, **postsynapticPopulation,** through **synapse.** Contains lists of **connection** or **connectionWD** elements.
    class 
    Generates a constant current pulse of a certain **amplitude** for a specified **duration** after a **delay.** Scaled by **weight,** if set \n :param delay: Delay before change in current.
    class 
    Dimensionless equivalent of **pulseGenerator** .
    class 
    Generates a ramping current after a time **delay,** for a fixed **duration.** During this time the current steadily changes from **startAmplitude** to **finishAmplitude.** Scaled by **weight,** if set \n :param delay: Delay before change in current.
    class 
    Dimensionless equivalent of **rampGenerator** .
    class 
    Java class for ReactionScheme complex type.
    class 
    Initial attempt to specify 3D region for placing cells.
    class 
    A reverse only **KSTransition** for a **gateKS** which specifies a **rate** ( type **baseHHRate** ) which follows one of the standard Hodgkin Huxley forms ( e.
    class 
    A method to describe a group of **segment** s in a **morphology** , e.
    class 
    Dummy synapse which emits no current.
    class 
    Generates a sinusoidally varying current after a time **delay,** for a fixed **duration.** The **period** and maximum **amplitude** of the current can be set as well as the **phase** at which to start.
    class 
    Dimensionless equivalent of **sineGenerator** .
    class 
    Java class for Space complex type.
    class 
    Description of a chemical species identified by **ion,** which has internal, **concentration,** and external, **extConcentration** values for its concentration \n :param initialConcentration: :type initialConcentration: concentration :param initialExtConcentration: :type initialExtConcentration: concentration
    class 
    Set of spike ComponentTypes, each emitting one spike at a certain time.
    class 
    Simple generator of spikes at a regular interval set by **period** \n :param period: Time between spikes.
    class 
    Generator of spikes whose ISI is distributed according to an exponential PDF with scale: 1 / **averageRate** \n :param averageRate: The average rate at which spikes are emitted :type averageRate: per_time
    class 
    Generator of spikes with a random interspike interval of at least **minISI** and at most **maxISI** \n :param maxISI: Maximum interspike interval :type maxISI: time :param minISI: Minimum interspike interval :type minISI: time
    class 
    Generator of spikes whose ISI distribution is the maximum entropy distribution over [ **minimumISI,** +infinity ) with mean: 1 / **averageRate** \n :param minimumISI: The minimum interspike interval :type minimumISI: time :param averageRate: The average rate at which spikes are emitted :type averageRate: per_time
    class 
    Spike source, generating spikes according to a Poisson process.
    class 
    Elements which can stand alone and be referenced by id, e.g.
    class 
    KS Transition specified in terms of time constant **tau** and steady state **inf**
    class 
    Spike array connected to a single **synapse,** producing a current triggered by each **spike** in the array.
    class 
    Poisson spike generator firing at **averageRate** after a **delay** and for a **duration,** connected to single **synapse** that is triggered every time a spike is generated, providing an input current.
    class 
    Voltage clamp.
    class 
    Voltage clamp with 3 clamp levels.
    Fields in org.neuroml.model with type parameters of type Base
    Modifier and Type
    Field
    Description
    protected List<Base>
     
    Methods in org.neuroml.model that return Base
    Modifier and Type
    Method
    Description
    ObjectFactory.createBase()
    Create an instance of Base
    Methods in org.neuroml.model that return types with arguments of type Base
    Modifier and Type
    Method
    Description
    Gets the value of the forwardTransitionAndReverseTransitionOrTauInfTransition property.