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NeuroMLlite_specification.yaml
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version: NeuroMLlite v0.6.1
specification:
Network:
definition: A Network containing multiple Population's, connected by Projection's
and receiving Input's
allowed_parameters:
notes:
type: str
description: ''
id:
type: str
description: Unique identifier for the Network
parameters:
type: Any
description: Dictionary of global parameters for the network
version:
type: str
description: Information on verson of NeuroMLlite
seed:
type: int
description: Seed for random number generator used when building network
temperature:
type: float
description: Temperature at which to run network (float in deg C)
network_reader:
type: NetworkReader
description: A class which can read in a network (e.g. from a structured
format)
allowed_children:
cells:
type: Cell
description: The Cells which can be present in Populations
synapses:
type: Synapse
description: The Synapse definitions which are used in Projections
input_sources:
type: InputSource
description: The InputSource definitions which define the types of
stimulus which can be applied in Inputs
regions:
type: RectangularRegion
description: The Regions in which Populations get placed.
populations:
type: Population
description: The Populations of Cells making up this network ...
projections:
type: Projection
description: The Projections between Populations
inputs:
type: Input
description: The inputs to apply to the elements of Populations
NetworkReader:
definition: A NetworkReader definition.
allowed_parameters:
notes:
type: str
description: ''
type:
type: str
description: The type of NetworkReader
parameters:
type: Any
description: Dictionary of parameters for the NetworkReader
Cell:
definition: A Cell definition.
allowed_parameters:
notes:
type: str
description: ''
id:
type: str
description: Unique identifier for this Cell
parameters:
type: Any
description: Dictionary of parameters for the cell
neuroml2_source_file:
type: str
description: File name of NeuroML2 file defining the cell
lems_source_file:
type: str
description: File name of LEMS file defining the cell
neuroml2_cell:
type: str
description: Name of standard NeuroML2 cell type
pynn_cell:
type: str
description: Name of standard PyNN cell type
arbor_cell:
type: str
description: Name of standard Arbor cell type
bindsnet_node:
type: str
description: Name of standard BindsNET node
Synapse:
definition: A Synapse definition.
allowed_parameters:
notes:
type: str
description: ''
id:
type: str
description: Unique identifier for this Synapse
parameters:
type: Any
description: Dictionary of parameters for the synapse
neuroml2_source_file:
type: str
description: File name of NeuroML2 file defining the synapse
lems_source_file:
type: str
description: File name of LEMS file defining the synapse
pynn_synapse_type:
type: str
description: 'The pynn synapse type. Valid values are: "curr_exp",
"curr_alpha", "cond_exp", "cond_alpha".'
pynn_receptor_type:
type: str
description: 'The pynn receptor type. Valid values are: "excitatory",
"inhibitory".'
InputSource:
definition: An InputSource definition.
allowed_parameters:
notes:
type: str
description: ''
id:
type: str
description: Unique identifier for this InputSource
parameters:
type: Any
description: Dictionary of parameters for the InputSource
neuroml2_source_file:
type: str
description: File name of NeuroML2 file defining the input source
neuroml2_input:
type: str
description: Name of standard NeuroML2 input
lems_source_file:
type: str
description: File name of LEMS file defining the input source
pynn_input:
type: str
description: Name of PyNN input
RectangularRegion:
definition: A RectangularRegion definition.
allowed_parameters:
notes:
type: str
description: ''
id:
type: str
description: Unique identifier for this rectangular region.
x:
type: float
description: x coordinate of corner of region
y:
type: float
description: y coordinate of corner of region
z:
type: float
description: z coordinate of corner of region
width:
type: float
description: width of the rectangular region
height:
type: float
description: height of the rectangular region
depth:
type: float
description: depth of the rectangular region
Population:
definition: A Population definition.
allowed_parameters:
notes:
type: str
description: ''
id:
type: str
description: Unique identifier for this Population
size:
type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
str]
description: The size of the population.
component:
type: str
description: The type of Cell to use in this population.
properties:
type: Any
description: A dictionary of properties (metadata) for this population.
random_layout:
type: RandomLayout
description: Layout in the random RectangularRegion.
relative_layout:
type: RelativeLayout
description: Position relative to RectangularRegion.
single_location:
type: SingleLocation
description: Explicit location of the one Cell in the population
RandomLayout:
definition: A RandomLayout definition.
allowed_parameters:
notes:
type: str
description: ''
region:
type: str
description: Region in which to place population
RelativeLayout:
definition: A RelativeLayout definition.
allowed_parameters:
notes:
type: str
description: ''
region:
type: str
description: The Region relative to which population should be positioned.
x:
type: float
description: x position relative to x coordinate of Region
y:
type: float
description: y position relative to y coordinate of Region
z:
type: float
description: z position relative to z coordinate of Region
SingleLocation:
definition: A SingleLocation definition.
allowed_parameters:
notes:
type: str
description: ''
location:
type: Location
description: Location of the single Cell.
Location:
definition: A Location definition.
allowed_parameters:
notes:
type: str
description: ''
x:
type: float
description: x coordinate of location
y:
type: float
description: y coordinate of location
z:
type: float
description: z coordinate of location
Projection:
definition: A Projection definition.
allowed_parameters:
notes:
type: str
description: ''
id:
type: str
description: Unique identifier for this Projection
presynaptic:
type: str
description: Presynaptic Population
postsynaptic:
type: str
description: Postsynaptic Population
synapse:
type: str
description: Which Synapse to use
pre_synapse:
type: str
description: 'For continuous connections, what presynaptic component
to use (default: silent analog synapse)'
type:
type: str
description: 'type of projection: projection (default; standard chemical,
event triggered), electricalProjection
(for gap junctions) or continuousProjection (for analogue/graded
synapses)'
delay:
type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
str]
description: 'Delay to use (default: 0)'
weight:
type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
str]
description: 'Weight to use (default: 1)'
random_connectivity:
type: RandomConnectivity
description: Use random connectivity
convergent_connectivity:
type: ConvergentConnectivity
description: Use convergent connectivity
one_to_one_connector:
type: OneToOneConnector
description: Connect cell index i in pre pop to cell index i in post
pop for all i
RandomConnectivity:
definition: A RandomConnectivity definition.
allowed_parameters:
notes:
type: str
description: ''
probability:
type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
str]
description: Random probability of connection.
ConvergentConnectivity:
definition: A ConvergentConnectivity definition.
allowed_parameters:
notes:
type: str
description: ''
num_per_post:
type: float
description: Number per post-synaptic neuron.
OneToOneConnector:
definition: A OneToOneConnector definition.
allowed_parameters:
notes:
type: str
description: ''
Input:
definition: An Input definition.
allowed_parameters:
notes:
type: str
description: ''
id:
type: str
description: Unique identifier for this Input
input_source:
type: str
description: Type of input to use in population
population:
type: str
description: Population to target
cell_ids:
type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
str]
description: Specific ids of _Cell_s to apply this input to (cannot
be used with percentage
percentage:
type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
str]
description: Percentage of Cells to apply input to
number_per_cell:
type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
str]
description: 'Number of individual inputs per selected Cell (default:
1)'
segment_ids:
type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
str]
description: 'Which segments to target (default: [0])'
weight:
type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
str]
description: 'Weight to use (default: 1)'