NOTE: the latest version of this documentation can be found on docs.neuroml.org!


For more information on NeuroML 2 and LEMS see here.
Note: these descriptions have been updated to the latest NeuroML v2.2 definitions, using the latest version of LEMS!

Networks

Network descriptions for NeuroML 2. Describes network elements containing populations (potentially of type populationList, and so specifying a list of cell locations), projections (i.e. lists of connections) and inputs.
Original LEMS ComponentType definitions: Networks.xml
Schema against which NeuroML based on these should be valid: NeuroML_v2.2.xsd

 
network

    extends baseStandalone

Network containing: populations (potentially of type populationList, and so specifying a list of cell locations); projections (with lists of connections) and/or explicitConnections; and inputLists (with lists of inputs) and/or explicitInputs. Note: often in NeuroML this will be of type networkWithTemperature if there are temperature dependent elements (e.g. ion channels).
Children elements regions region
populations basePopulation
projections projection
synapticConnections explicitConnection
electricalProjection electricalProjection
continuousProjection continuousProjection
explicitInputs explicitInput
inputs inputList
 
networkWithTemperature

    extends network

Same as network, but with an explicit temperature for temperature dependent elements (e.g. ion channels)
Parameters temperature temperature
 
basePopulation

    extends baseStandalone

A population of multiple instances of a specific component, which anything which extends baseCell.
Component References component baseCell
Child elements notes notes
annotation annotation
Children elements property property
 
population

    extends basePopulation

A population of components, with just one parameter for the size, i.e. number of components to create. Note: quite often this is used with type=populationList which means the size is determined by the number of instances (with locations) in the list. The size attribute is still set, and there will be a validation error if this does not match the number in the list.
Parameters size
    Number of instances of this Component to create when the population is instantiated
Dimensionless
 
populationList

    extends basePopulation

An explicit list of instances (with locations) of components in the population.
Text fields size
Children elements instances instance
 
instance
Specifies a single instance of a component in a population (placed at location).
Child elements location location
 
location
Specifies the (x,y,z) location of a single instance of a component in a population
Parameters x Dimensionless
y Dimensionless
z Dimensionless
 
region
Initial attempt to specify 3D region for placing cells. Work in progress...
Child elements rectangularExtent rectangularExtent
 
rectangularExtent
For defining a 3D rectangular box
Parameters xLength Dimensionless
xStart Dimensionless
yLength Dimensionless
yStart Dimensionless
zLength Dimensionless
zStart Dimensionless
 
projection
Projection from one population, presynapticPopulation to another, postsynapticPopulation, through synapse. Contains lists of connection or connectionWD elements.
Paths presynapticPopulation
postsynapticPopulation
Component References synapse baseSynapse
Children elements connections connection
connectionsWD connectionWD
 
explicitConnection
Explicit event connection between components
Text fields targetPort
Paths from
to
 
connection
Event connection directly between named components, which gets processed via a new instance of a synapse component which is created on the target component. Normally contained inside a projection element.
Text fields destination
preFractionAlong
postFractionAlong
preSegmentId
postSegmentId
Paths preCellId
postCellId
 
synapticConnection

    extends explicitConnection

Explicit event connection between named components, which gets processed via a new instance of a synapse component which is created on the target component
Text fields destination
Paths from
to
Component References synapse baseSynapse
 
synapticConnectionWD

    extends synapticConnection

Explicit event connection between named components, which gets processed via a new instance of a synapse component which is created on the target component, includes setting of weight and delay for the synaptic connection
Parameters delay time
weight Dimensionless
Paths from
to
 
connectionWD

    extends connection

Event connection between named components, which gets processed via a new instance of a synapse component which is created on the target component, includes setting of weight and delay for the synaptic connection
Parameters delay time
weight Dimensionless
Text fields destination
preFractionAlong
postFractionAlong
preSegmentId
postSegmentId
Paths preCellId
postCellId
 
electricalConnection
To enable connections between populations through gap junctions.
Component References synapse gapJunction
 
electricalConnectionInstance
To enable connections between populations through gap junctions. Populations need to be of type populationList and contain instance and location elements.
Text fields preFractionAlong
postFractionAlong
preSegment
postSegment
Paths preCell
postCell
Component References synapse gapJunction
 
electricalConnectionInstanceW

    extends electricalConnectionInstance

To enable connections between populations through gap junctions. Populations need to be of type populationList and contain instance and location elements. Includes setting of weight for the connection
Parameters weight Dimensionless
Text fields preFractionAlong
postFractionAlong
preSegment
postSegment
Paths preCell
postCell
 
electricalProjection
A projection between presynapticPopulation to another postsynapticPopulation through gap junctions.
Component References presynapticPopulation population
postsynapticPopulation population
Children elements connections electricalConnection
connectionInstances electricalConnectionInstance
 
continuousConnection
An instance of a connection in a continuousProjection between presynapticPopulation to another postsynapticPopulation through a preComponent at the start and postComponent at the end. Can be used for analog synapses.
Component References preComponent baseGradedSynapse
postComponent baseGradedSynapse
 
continuousConnectionInstance
An instance of a connection in a continuousProjection between presynapticPopulation to another postsynapticPopulation through a preComponent at the start and postComponent at the end. Populations need to be of type populationList and contain instance and location elements. Can be used for analog synapses.
Text fields preFractionAlong
postFractionAlong
preSegment
postSegment
Paths preCell
postCell
Component References preComponent baseGradedSynapse
postComponent baseGradedSynapse
 
continuousConnectionInstanceW

    extends continuousConnectionInstance

An instance of a connection in a continuousProjection between presynapticPopulation to another postsynapticPopulation through a preComponent at the start and postComponent at the end. Populations need to be of type populationList and contain instance and location elements. Can be used for analog synapses. Includes setting of weight for the connection
Parameters weight Dimensionless
Text fields preFractionAlong
postFractionAlong
preSegment
postSegment
Paths preCell
postCell
 
continuousProjection
A projection between presynapticPopulation and postsynapticPopulation through components preComponent at the start and postComponent at the end of a continuousConnection or continuousConnectionInstance. Can be used for analog synapses.
Component References presynapticPopulation population
postsynapticPopulation population
Children elements connections continuousConnection
connectionInstances continuousConnectionInstance
 
explicitInput
An explicit input (anything which extends basePointCurrent) to a target cell in a population
Text fields destination
sourcePort
targetPort
Paths target
Component References input basePointCurrent
 
inputList
An explicit list of inputs to a population.
Text fields population
Component References component basePointCurrent
Children elements inputs input
 
input
Specifies a single input to a target, optionally giving the segmentId (default 0) and fractionAlong the segment (default 0.5).
Text fields segmentId
fractionAlong
destination
Paths target
 
inputW

    extends input

Specifies input lists. Can set weight to scale individual inputs.
Parameters weight Dimensionless
Text fields destination
Paths target