Networks |
| Network descriptions in NeuroML 2. Describes network elements containing populations |
| Original LEMS ComponentType definitions: Networks.xml Schema against which NeuroML based on these should be valid: NeuroML_v2beta.xsd |
| network | ||
| Network containing populations, projections and lists of explicitConnections (either directly between components of the populations or via synapses) | ||
| Children elements | extracellularProperties | extracellularProperties | regions | region | populations | basePopulation | projections | projection | synapticConnections | explicitConnection | explicitInputs | explicitInput | inputs | inputList |
| Exposures | temperature Temperature will be taken from extracellularProperties child. NOTE: temperature will be absolute zero if absent!! |
temperature |
| Dynamics |
Derived Variables temperature = extracellularProperties[*]/temperature (exposed as temperature) |
|
| extracellularProperties | ||
| A ComponentType holding information about the environment outside specific cells, e.g. the ambient temperature | ||
| Parameters | temperature | temperature |
| Exposures | temperature | temperature |
| Dynamics |
Derived Variables temperature = temperature (exposed as temperature) |
|
| basePopulation | ||
| A population of cells (anything which extends baseCell) | ||
| Component References | component | baseCell |
| Requirements | temperature Normally comes from the extracellularProperties in the network |
temperature |
|
population
extends basePopulation |
||
| A population of components, with just one parameter for the size | ||
| Parameters | size Number of instances of this Component to create when the population is instantiated |
Dimensionless |
| Component References | component | ??? |
| Requirements | temperature (from basePopulation) | temperature |
|
populationList
extends basePopulation |
||
| An explicit list of the cells in the population. Work in progress... | ||
| Component References | component | baseCell |
| Children elements | instances | instance |
| Requirements | temperature (from basePopulation) | temperature |
| instance | ||
| Initial attempt to specify instances in populations. Work in progress... | ||
| Child elements | location | location |
| location | ||
| Initial attempt to specify instances in populations. Work in progress... | ||
| 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 to another. Currently it's better to define an explicit list of connections, using explicitConnection. Work in progress... | ||
| Paths | presynapticPopulation | postsynapticPopulation |
| Component References | synapse | baseSynapse |
| Child elements | synapseComponent | synapseComponent |
| Children elements | connections | connection |
| synapseComponent | ||
| Work in progress... | ||
| Component References | component | baseSynapse |
| connection | ||
| Explicit event connection directly between named components | ||
| Paths | preCellId | postCellId |
| explicitConnection | ||
| Explicit event connection between components | ||
| Text fields | targetPort | |
| Paths | from | to |
|
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 |
| 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. Not yet stable... | ||
| Text fields | population | |
| Component References | component | basePointCurrent |
| Children elements | inputs | input |
| input | ||
| Initial attempt to specify input lists. Work in progress... | ||
| Text fields | destination | |
| Paths | target | |