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13/03/2012
An ontology to describe the field of Computational Neurosciences
Birgit Kriener
Computational Neuroscience Ontology
Erik De Schutter
Fahim T. Imam
INCF MultiScale Modeling Task Force
Lars Schwabe
Padraig Gleeson
Sean Hill
Stephen D. Larson
Subhasis Ray
This ontology is used to add the Definition class of annotation as in NIF.
The source of the definition can be defined with class from OBO-annotation
This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.
Yann Le Franc
version 0.5
name
numerical value
defined model type
This general class includes the most common types of models classified based on the level of description of the nervous system.
a generically_dependent_continuant that is a category of models regarded as sharing particular characteristics, qualities, and/or defined similarities.
defined type of model
definition based on the following NCI thesaurus entry: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Type_of_Event
model component
This class is based on the assumption that models can represented as particular assemblies of components that can be either specific to the different level of description (cellular, synaptic and network) or generic.
a generically dependent continuant that is a constituent part of a model
definition based on element from NCI Thesaurus: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Element_Part
model element
parameter
elementary model component role that defines an elementary model component as constant value determining the characteristics or behaviour of the model
reset potential
value of the membrane potential at which the model is maintained after the emission of a spike.
physical constant
SBO:0000565
http://en.wikipedia.org/wiki/Physical_constant
A physical constant that is required in the calculation of a system parameter
phenomenological plasticity model
http://www.scholarpedia.org/article/Models_of_synaptic_plasticity
http://www.scholarpedia.org/article/Models_of_synaptic_plasticity
long term plasticity model that is based on an input-output relationship between neuronal activity and synaptic plasticity. This type of model does not explicitly account for the biochemistry and physiology leading to synaptic plasticity.
cellular model
The distinction between the different subclasses is based on the different "spiking mechanisms".
a defined type of model that represent the biological activities of a cell.
synapse model
a defined type of model that represents the biological processes involved in synaptic transmission
network model
a defined type of model that represents biological neural networks.
plasticity model
a defined type of model that describes the mechanisms underlying the plasticity of the nervous system.
artificial neuron model
This class can be further subdivided into binary neuron, McCullogh neurons and all variants of the artificial neuron models.
a cellular model that represents the electrical activity of a nerve cell with simplified function
point process model
a cellular model that reproduce particular features of real neuron spiking patterns with statistical point process models.
spiking model
a cellular model that describes the mechanism of action potential emission in biological nerve cell.
balanced random network
PMID: 10809012
defined model that corresponds to a network of sparsely connected excitatory and inhibitory neurons which can switch between firing states depending on the balance between excitation and inhibition.
Hopfield network
defined model that is a form of recurrent artificial neural network invented by John Hopfield.
http://en.wikipedia.org/wiki/Hopfield_network
biophysical spiking model
a spiking model that describe the interactions between the ionic conductances that participates to the generation of an action potential
threshold-based spiking model
a spiking model that represents the spiking mechanism as the result of a threshold crossing.
reduced model
This class could become a superclass called dynamical models or dynamical system models in contrast with biophysical and threshold based models.
It should contain models like Fitzhugh-Nagumo, Morris-Lecar models.
biophysical model that is obtained by dimensionality reduction of a detailed model.
detailed model
biophysical model that describes in detail the conductance variations of the ionic currents responsible of the generation of an action potential
pulse-based model
This classe refers to detailed integrate-and-fire models as described in Destexhe A. (1997, PMID: 9097470) and Hill S. and Tononi G. (2005, PMID: 15537811)
a threshold based spiking neuron model that is an hybrid between Hodgkin and Huxley and integrate-and-fire models. The model describes the impact of fast sodium and delayed rectifier potassium conductances on the subthreshold membrane voltage dynamic and considers action potentials as pulses during which the sodium and potassium conductances are set to particular values representing their participation to the generation and repolarization of the action potential.
conductance-based model
one variable model
a threshold-based model that uses only one variable to describe the nerve cells behavior.
two variable model
a threshold-based model that uses two variables to describe the nerve cells behavior.
three variable model
a threshold-based model that uses three variables to describe the nerve cells behavior
spike response model
a threshold-based model that correspond to a generalization of the leaky integrate-and-fire model and give a simple description of action potential generation in neurons
current-based model
a model of chemical synapse that consider the impact of the chemical release as a current source in the post-synaptic model with the postsynaptic membrane voltage considered to be constant.
conductance-based model
a model of chemical synapse that consider the impact of the chemical release as a modification of conductance in the post-synaptic model with the post-synaptic potential varying over time.
rate model
network model composed of rate-based neuron models
artificial neural network model
corresponds to Kohonen maps, Multiple Layer perceptron, ...
network model composed of artificial neuron models.
spiking network model
network model that is composed of spiking neuron models.
chemical synapse model
a synapse model that describes the impact of chemical compounds released by the synapse
electrical synapse model
a synapse model that describe synapses transmitting directly ionic currents.
cellular plasticity model
This class would contains models that describes the link between potassium channels and NMDA activation as described in hippocampus for instance.
plasticity model that describes the variations of the cellular intrinsic excitability due to regulation of ionic conductances depending on the network activity.
synaptic plasticity model
model of plasticity that represents the mechanisms underlying changes in synaptic transmission, depending on the network or cellular activity.
synaptic plasticity rule
short term facilitation model
a model of short term synaptic plasticity that represents the increase of the synaptic efficacy for a short period of time.
cellular model component
aggregated model composed that is used to build cellular models
synapse model component
aggregated model component that is used to build synaptic models.
resting membrane potential
value of the neuronal membrane potential at rest
refractory mechanism
This is a general term that encompass the refractory period usually defined with a time constant and the resetting of the membrane potential during the refractory period.
a cellular model component that represents the mechanism by which the model is kept unresponsive to any stimulus after the emission of an action potential.
model quality
quality that represents a qualitative feature of the model that can be either independent of the model specification or a property resulting of the particular model specification
spiking mechanism
a cellular model component that represents the mechanisms generating action potential in a cellular model type.
morphology
a cellular model component that represents the morphology of the model
intracellular dynamic
a cellular model component that represents a chemical signaling occuring inside the nerve cell
stimulation current
current model that represents input currents provided to the model via an electrode (intracellular or extracellular).
generic model component
probabilistic component
a generic model component that represents the probabilistic variations of any model component.
ionic current model
a current model that describes the flow of ions through cellular membrane.
synaptic current
current model that represents the flow of ions triggered by the activation of a chemical or electrical synapse model.
abstract current model
a current model that is an abtraction of complex current interactions and which is used to reproduce a particular cellular behavior such as rebound or adaptation.
continuous
a spiking mechanism that considers the action potential initiation as a continuous process often based on the non linearity of the conductance changes supporting the initiation of an action potential. This mechanism is the opposite of a threshold-based mechanisms.
threshold-based
a spiking mechanism that considers the action potential initiation as a result of a thresholding operation.
point
a morphology that is used to represents the models without specified geometry.
single compartment
a morphology that consider the cellular morphology as a unique compartment
multiple compartment
a morphology that represents the modeled cell with multiple compartments. This morphology spans the models called the Ball-and-stick model and the models based on reconstructed morphologies.
reconstructed
morphological quality that represents model morphologies build upon the reconstruction of a real nerve cell morphology using imaging techniques such as camera lucida or two-photon imaging.
calcium dynamic
an intracellular dynamic model component that represents the variation of the intracellular calcium concentration over time.
biochemical dynamic
NOTE: Shouldn't be separated from calcium dynamic as calcium is also a molecular participant. One possible solution would be to change into: reduced calcium dynamic to represent the simplification of buffering and detailed biochemical reactions that details the calcium buffering!!!
an intracellular dynamic model component that represents the dynamic of the intracellular biochemical reactions and molecular participant concentrations over time.
network model component
a model component that is used to build network model types.
non linear spike generation current
abstract current model that represents an additional non-linear current ψ which leads to a divergence of the potential toward infinity in a finite time during the emission of an action potential.
defined model
a generically_dependent_continuant that represent the set of models commonly used to build other models.
integrate-and-fire
a defined model that represent the evolution of voltage as the derivative of the law of capacitance. The action potential is emitted when the value of the voltage reaches a threshold and is considered as Dirac function. After the emission the voltage is resetted to the resting potential value.
http://en.wikipedia.org/wiki/Biological_neuron_model#Integrate-and-fire
adaptive exponential integrate-and-fire
AdEx
a defined model that is a spiking neuron model with two variables. The first equation describes the dynamics of the membrane potential and includes an activation ter with an exponential voltage dependence. Voltage is coupled to a second equation which describes adaptation. Both variables are reset if an action potential has been triggered. This model has been introduced by Brette and Gerstner in 2005.
http://www.scholarpedia.org/article/Adaptive_exponential_integrate-and-fire_model
independent variable
http://en.wikipedia.org/wiki/Variable_(mathematics)
variable regarded as inputs to a system and may take on different values freely
dependent variable
http://en.wikipedia.org/wiki/Variable_(mathematics)
variable regarded as values that change as a consequence of changes in other values in the system.
exponential integrate-and-fire
EIF
a defined model that is an integrate-and-fire model in which the action potentials are generated by an exponential current instead of a fixed threshold. The exponential integrate-and-fire model is defined in Fourcaud-Trocme and al. 2003
w.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1001056
leaky integrate-and-fire
LIF, Lapicque's model
a defined model that is an integrate-and-fire model with a leak component added to the membrane potential, reflecting the diffusion of ions that occurs through the membrane when some equilibrium is not reached in the cell.
http://en.wikipedia.org/wiki/Biological_neuron_model#Leaky_integrate-and-fire
quadratic integrate-and-fire
QIF
a defined model that is an integrate-and-fire model in which the action potentials are generated by a quadratic current instead of a fixed threshold. The quadratic integrate-and-fire model is defined in Latham and al. 2000. This model is identical to the Theta neuron proposed by Ermentrout and Kopell (1986) with a variable change.
theta neuron model
a defined model that is well suited to describe the processes involving rapid changes in membrane potential, known as bursts. The theta model describes parabolic bursting and has been defined in Ermentrout and Kopell, SIAM journal of Applied Mathematics 1986.
http://en.wikipedia.org/wiki/Theta_model
adaptive integrate-and-fire
ALIF
a defined model that is a two-variable integrate-and-fire model. The second variable accounts for the currents involved in spike frequency adaptation. This variable increase transiently during action potentials and decay between action potential.
generalized integrate-and-fire
GIF
PMID: 12611957
a defined model that is a two variable integrate-and-fire model with a threshold for spike generation and a reset as in the leaky integrate-and-fire model. The two variables represent subthreshold resonance behavior and result from the linearization of the Hodgkin and Huxley equation around a subthreshold holding potential. This model is similar to the resonate-and-fire model proposed by Izhikevich (2001)
integrate-and-fire-or-burst
IFB
a defined model that is a two-variable integrate-and-fire model. The second variable is a slow variable that represents the inactivation of the low-threshold calcium current. This model reproduces the features of the bursting behavior of thalamo-cortical relay neurons and has been proposed by Smith and al., 2000
Izhikevich model
PMID: 18244602
a defined model that is a minimal two-variable integrate-and-fire model that reproduces different features depending on the value of 4 parameters. The second variable represents the adaptation. This model has been proposed in Izhikevich, 2003.
resonate-and-fire
PMID: 11665779
a defined model that is a two variable integrate-and-fire model proposed by Izhikevich in Izhikevich, 2001.
HindMarch and Rose model
PMID: 6144106
a defined model that is a three-variable model: the membrane potential written in dimensionless unit, the spiking variable that represent the fast transport of sodium and potassium ions and the bursting variable that represent the slow transport of other ions. This model aims to study the spiking-bursting behavior of the membrane potential observed in experiments.
http://en.wikipedia.org/wiki/Hindmarsh%E2%80%93Rose_model
Rotstein model
PMID: 16927211
a defined model that is three variable reduced model defined in Rotstein and al. 2006 in J. Comp. Neurosci.
Shinomoto model
PMID: 20478693
a defined model that is a multi-timescale adaptive threshold model of neuronal spiking incorporated into the stochastic framework of the linear-nonlinear Poisson model in the form of a generalized linear model.
spike response model
a defined model that is a generalization of the leaky integrate-and-fire model. As in the leaky integrate-and-fire model, action potentials are generated when the voltage passes a threshold. Leaky integrate-and-fire models are formulated using differential equations for the voltage, whereas the Spike Response Model is formulated using filters.
doi:10.1162/neco.1997.9.5.1015
http://icwww.epfl.ch/~gerstner/SPNM/node27.html
http://www.scholarpedia.org/article/Spike-response_model
spike response model SRM0
PMID: 16633938
a defined model that is a simplified version of the Spike Response Model and does not include a dependence of the response kernel κ upon the time since the last spike.
http://icwww.epfl.ch/~gerstner/SPNM/node27.html#SECTION02323000000000000000
http://www.scholarpedia.org/article/Spike-response_model#Spike_Response_Model_SRM.5C.28_0.5C.29
cumulative spike response model
PMID: 8888612
a defined model that is a spike response model where refractoriness and adaptation were modeled by the combined effects of the spike after potentials of several previous spikes, rather than only the most recent spike.
http://www.scholarpedia.org/article/Spike-response_model#Cumulative_Spike_Response_Model:_bursting_and_adaptation
spike response model with cumulative dynamic threshold
a defined model that is a spike response model in which the value of the threshold depends on all previous spikes not only the most recent one.
http://www.scholarpedia.org/article/Spike-response_model#Spike_Response_Model_with_a_cumulative_dynamic_threshold
dynamic threshold
a threshold-based spiking mechanism that represent the variation of the spiking threshold over time based on particular criterions.
fixed threshold
a threshold-based spiking mechanism that considers the threshold as constant over time.
spike shape kernel
a cellular model component that is used to build spike response model and which describes the form of the action potential and its spike after-potential. This kernel is a function of the time since the last action potential. It can describe a depolarizing, hyperpolarizing or resonating spike after-potential.
http://www.scholarpedia.org/article/Spike-response_model#Mathematical_formulation
responsiveness kernel
a cellular model component that is used to build spike response model and which describes the linear response to an incoming short pulse. The responsiveness kernel to an input pulse depends on the time since the last spike.
http://www.scholarpedia.org/article/Spike-response_model#Mathematical_formulation
linear filter of the membrane
adaptation current
an abstract current model that represents the mechanism of spiking frequency adaptation.
rebound current
abstract current model that represents the mechanisms of rebound.
spiking current
abstract current model that represents the mechanisms involved in the action potential and which is used to build HindMarch and Rose models
http://en.wikipedia.org/wiki/Hindmarsh%E2%80%93Rose_model
spiking variable, y
bursting current
abstract current model that represents the mechanisms of bursting and used to build HindMarch and Rose models.
bursting variable, z
http://en.wikipedia.org/wiki/Hindmarsh%E2%80%93Rose_model
membrane recovery variable
PMID: 18244602
abstract current model which accounts for the activation of potassium ionic currents and inactivation of sodium ionic currents and provides negative feedback to the membrane voltage
Connor-Stevens model
PMID: 5575343
a defined model that is an extended action potential generating model using gastropod somas. This model is similar to the Hodgkin and Huxley model and contains a sodium, potassium and leak current with faster dynamics for the sodium and potassium currents. In addition, a transient potassium current, called, A-current, has been included.
http://www.scholarpedia.org/article/Conductance-based_models#Examples_and_Variants
Wang-Buzsaki model
PMID: 8815919
a defined model that is a network model composed of single compartment models, derived from the original Hodgkin-Huxley model. This network model represents a network of hippocampal interneurons.
Fitzhugh-Nagumo model
Bonhoeffer-van der Pol model
PMID: 19431309
a defined model that is a two-dimensional simplification of the Hodgkin-Huxley model of spike generation in squid giant axons. The model consist of a voltage-like variable having cubic nonlinearity that allows regenerative self-excitation via positive feedback and a recovery variable having a linear dynamics that provides a slower negative feedback.
http://www.scholarpedia.org/article/FitzHugh-Nagumo_model
Morris-Lecar model
PMID: 7260316
a defined model that is a two-dimensional reduced excitation model applicable to systems having two non-inactivating voltage-sensitive conductances. The original form of the model employed an instantaneously responding voltage-sensitive calcium conductance for excitation and a delayed voltage-dependent potassium conductance for recovery.
http://www.scholarpedia.org/article/Morris-Lecar_model
synaptic action
a synapse model component that describes the impact of synaptic model on the post-synaptic model.
connection element
a synapse model component that describe how the synapse is connected between two neuron models
synaptic weight
a synapse model component that refers to the strength or amplitude of a connection between two nodes, corresponding in biology to the amount of influence the firing of one neuron has on another.
http://en.wikipedia.org/wiki/Synaptic_weight
plasticity mechanism
a synapse model component that relates to plasticity models.
synaptic conductance dynamic
a synaptic model component that describes the dynamic of the synaptic conductance in the post-synaptic model
synaptic delay
delay between the activation of the synapse and its impact on the post-synaptic model.
voltage dependent receptor activation
a synapse model component that describes the voltage dependent activation of receptor such as NMDA receptor that will participate in the total synaptic current.
release mechanism
a synapse model component that describes the neurotrasmitter release.
neurotransmittor diffusion
a synapse model component that describes the diffusion of neurotransmitter in the extracellular space.
post-synaptic element
a connection element which points to the model elements of the post-synaptic model that are used in the equations of the synapse model.
pre-synaptic element
a connection element which points to the model elements of the pre-synaptic model that are used in the equations of the synapse model.
voltage-dependent current model
an ionic current model that represents the current flowing through ionic channel triggered by the change in voltage.
voltage and ionic dependent current model
an ionic current model that represents the current flowing through ionic channel triggered by the change of voltage and the binding of a particular ion.
supervised learning
http://en.wikipedia.org/wiki/Supervised_learning
learning rule that produces an infered function to predict correct output value for any valid input object, based on an error function estimated through the training period with the presentation of input/output pairs.
ionic dependent current model
a biochemically activated current model that represents the current flowing through ionic channel triggered by the binding of a particular ion.
biochemically activated current
an ionic current model that represents the current flowing through ionic channels triggered by action of biochemical components.
unsupervised learning
learning rule that produces an infered function based on unlabeled data without any feedback to evaluate the potential solution.
excitatory action
a synaptic action that increases the post-synaptic model activity and/or voltage
inhibitory action
a synaptic action that decreases the post-synaptic activity and/or voltage
shunting action
a synaptic action that modifies the global conductance of the post-synaptic model
instantaneous rise and monexponential decay
a synaptic conductance dynamic which assumes an instanteanous rise of the conductance followed by an exponential decay with a time constant.
difference of two exponentials
a synaptic conductance dynamic that is described as the difference of two exponential functions which represent the rising and the decay phase with two distinct time constants.
alpha function
a synaptic conductance dynamic describing a conductance that has a rising phase with a certain rise time. As it has just a single time constant, the time course of the rise and decay are correlated.
cellular elements
a network model component that refers to the cellular model type used to build the network model
synaptic element
a network model component that refers to the synapse model type used to build the network model
connectivity pattern
a model component quality that represents a connectivity pattern obtained with specific connectivity rule
rate function
a cellular model component that describes the dynamic of the cellular model firing rate.
recurrent
a connectivity pattern in which connections between units form a directed cycle.
http://en.wikipedia.org/wiki/Recurrent_neural_network#Fully_recurrent_network
feedforward
a connectivity pattern in which connections between units do not form a directed cycle.
http://en.wikipedia.org/wiki/Feedforward_neural_networks
small world
a connectivity pattern in which most nodes are not neighbors of one another, but most node can be reached from every other by a small number of hops or steps.
http://en.wikipedia.org/wiki/Small-world_network
functional grouping
cellular grouping quality that represents cellular grouping defined by common functional criterons.
anatomical grouping
cellular grouping quality that represents cellular grouping based on anatomical information
current model
a cellular model component that represents the different types of modeled currents that can influence the trajectory of the membrane voltage
current localization
current model quality that represents the location of the current source on a neuronal model (somatic, primary dendrite, ...)
current distribution
current model quality that represents the spatial distribution of current sources (ionic channels, synaptic channels, stimulation electrode) on a compartment
connectivity rule
a network layout component that describe the rules used to establish connections between the cellular elements of the network model
voltage
http://www.ebi.ac.uk/sbo/main/SBO:0000259
capacitance
current
diameter
length
synaptic plasticity element
frequency
maximal conductance
random
cellular grouping quality that represents probabilistic grouping of cellular models within network models.
spike time
time constant
volume
indices
cellular grouping quality
a model component quality that represent the properties of cellular grouping in network models
rate-based neuron model
a cellular model that describe the firing activity of neuron using a rate function.
refractory period
a duration that represent the duration during which the model cannot emit a subsequent spike following an initial spike.
spiking threshold
voltage above which the model emits a spike
elementary model component role
role played by the model elements
cellular grouping
a network layout component that defines the common attribute or property used to create arbitrary groups of cellular model type.
spatial embedding
Models can be defined without any mention of space.
The model can be enriched with particular spatial embedding.
a generic model component that add spatial information to the model
two dimensional layout
relates to http://neurolex.org/wiki/Category:Two_dimensional_region
three dimensional layout
http://neurolex.org/wiki/Category:Three_dimensional_region
spatial coordinates
2D coordinates
3D coordinates
polar coordinates
pre-synaptic indice
This term should be transformed into a datatype.
a pre-synaptic element that specifies the indices of the pre-synaptic neuron model
user-defined
cellular distribution quality that represents the distribution of cellular models in network models arranged based on user-defined criterions that are not based on anatomical information.
is a quality
abstract morphology
a morphological quality that describe abstract representation of the morphology. Often cellular compartment are represented as iso-potential cylindrical compartments.
uniform
cellular distribution quality that represents a cellular distribution in network models where cellular models are uniformly distributed in the abstract space.
is a quality
pre-synaptic variable
elementary model component that specifies the variable of the neuronal model used into the equations of the synapse model.
developmental plasticity model
model of network plasticity based on developmental rules that will change the structure of the network.
Hodgkin and Huxley model
PMID: 12991237
defined model that describes how action potentials in neurons are initiated and propagated in squid giant axon.
http://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model
post-synaptic indice
a post-synaptic element that specifies the indices of the post-synaptic neuron model
anatomically defined
cellular distribution quality that represents the cellular distribution in the network model based on criterions derived from anatomical information
is a quality
morphological quality
Similar to sao1057800815
a model component quality that described the kind of morphology used in the neuron models.
functional quality
Example: oscillatory, bursting, synchronization, ...
a model quality that describes the intrinsic functional quality of the models
post-synaptic variable
elementary model component that specifies the variable of the neuronal model used into the equations of the synapse model.
uniform
a current distribution where current models are uniformly distributed.
learning rule
http://en.wikipedia.org/wiki/Learning_rule
network model component that is a method which improves the neural network's performance. It is done by updating the weights and bias level of a network after a network is stimulated in an environment.
random
a current distribution where current models are distributed according to a particular probability distribution.
non-linear
a current distribution where current models are distributed according to a non-linear function of space.
linear
a current distribution where current models are distributed according to a linear function of space.
concentration
current model quality
model component quality that represent specific properties attached to current models
model description
an information content entity that represents the differents types of formats which can exist for describing a model (scientific paper, database entry, XML format, ...)
mathematical concept
a thing that represents the differents mathematical concepts used to represent models.
link to SBO, Kisao, Teddy
network layout component
a network model component that describe the different level of organization of the network model
cellular distribution
a network layout component that represents the distribution of the cellular model type in euclidian or non euclidean space.
one dimensional layout
related to definition in NIF: http://neurolex.org/wiki/Category:One_dimensional_region
model
a generically_dependent_continuant that is a placeholder for any model
elementary model component
an elementary model component is the smallest model component on which aggregated component are built. These elements can have either the role of parameter or the role of variable.
http://www.thefreedictionary.com/elementary
short term plasticity model
model of synaptic plasticity that describes the short term changes in the synaptic activity.
short term plasticity rule
long term plasticity model
long term plasticity rule
model of synaptic plasticity that describes the long term changes in the synaptic activity.
rate-based plasticity model
a phenomenological model of long term synaptic plasticity that represent the variation of synaptic impact depending on the firing rate of the models.
spike timing dependent plasticity model
a phenomenological model of long term synaptic plasticity that represent the variation of synaptic efficacy depending on the relative spike timing of the pre- and post-synaptic models.
biophysical model
a model of long term synaptic plasticity that represents the biophysical mechanisms involved in the changes of synaptic efficacy.
homeostatic plasticity model
homeostatic plasticity rule
http://en.wikipedia.org/wiki/Homeostatic_plasticity
synaptic plasticity model that account for the capacity of neurons to regulate their own excitability relative to network activity.
Markram and Tsodyks model
PMID: 9012851
defined model that describes the impact of neurotransmitter release and synaptic depression.
Song and Abbott model
PMID: 10966623
defined model that is a phenomenological model of spike timing dependent plasticity
http://www.scholarpedia.org/article/Models_of_synaptic_plasticity#Spike_timing_based_models
zero dimensional layout
relates to http://neurolex.org/wiki/Category:Zero_dimensional_region
resistance
http://www.ebi.ac.uk/sbo/main/SBO:0000254
time
rate
developmental learning
learning rule based on the mechanisms taking place during the development of the nervous system.
reinforcement learning
a learning rule that allow to learn by interacting with an environment through a trial and error process during which the reward is maximized.
http://www.scholarpedia.org/article/Reinforcement_learning
reward-based learning
synaptic plasticity model component
a component of plasticity models that describes the rules governing the changes in synaptic efficacy.
pair-based rule
timing dependency that modifies the synaptic weight depending on the time difference between pairs of action potentials.
triplet-based rule
timing dependency that modifies the synaptic weight depending on the time difference between triplets of action potentials.
suppression model
reference the model from Froemke and Dan, 2002 described in Morrisson, 2008
timing dependency that accounts for the suppression of NMDA receptor during spike timing dependent long term depression
short term depression model
a model of short term synaptic plasticity that represent the decrease of the synaptic efficacy for a short period of time
model component quality
quality exhibited by model components
cellular distribution quality
model component quality that describes the distribution of cellular model in abstract space
ModelDB accession number
A CRID symbol that is sufficient to look up a model from ModelDB
mixed grouping
cellular grouping quality that represents the grouping of cellular model based on two criterions: anatomical and functional
delay
http://www.ebi.ac.uk/sbo/main/SBO:0000225
duration
http://www.ebi.ac.uk/sbo/main/SBO:0000347
obsolete
plasticity model component
a model component that is used to build a plasticity model type
timing dependency
a component of a synaptic plasticity rule that describes the dependency of synaptic changes on the relative spike timing in the pre- and post-synaptic models
weight update component
a component of a synaptic plasticity rule that describes the changes in synaptic weight.
voltage dependency
a component of a synaptic plasticity rule that describes the relation between the post-synaptic voltage and the change in synaptic efficacy.
weight independent
a weight update component that updates the weight with additive increment
additive
weight dependent
http://www.scholarpedia.org/article/Spike-timing_dependent_plasticity#Weight_dependence:_hard_bounds_and_soft_bounds
weight update component that updates the weight within bounded range by multiplying the changes by constants called soft bounds or multiplicative weight dependence.
learning rate
elementary model component that set the amount by which synaptic weight are updated
leakage current
abstract current model that approximates the passive properties of biological neurons.
http://www.scholarpedia.org/article/Conductance-based_models
aggregated model component
a model component that results from the aggregation of parameters and/or variable and/or mathematical operators
variable
elementary model component role that defines an elementary model component as a value that may change within the scope of a given problem or set of operations.
http://en.wikipedia.org/wiki/Variable_(mathematics)
membrane capacitance
Measure of the amount of electric charge stored (or separated) by the cellular membrane for a given electric potential. The unit of capacitance is the Farad.
membrane resistance
Measure of the degree to which the cellular membrane opposes the passage of an electric current. The SI unit of electrical resistance is the ohm.
membrane time constante