Component layer

The SpineML component layer syntax describes the functional entities, i.e. neurons and synapses, that are used as building blocks from a model. The syntax is derived from the NineML abstraction layer and LEMS common object model specification with some very minor changes requiring the specification of an initial regime and some minor syntax changes to the specification of ports.

A technical description of the NineML Abstraction layer is available here.

Differences from NineML Abstraction Layer

We now describe the differences between the NineML Abstraction layer and the SpineML Component layer explicitly.

Ports

In SpineML we use W3C shemas for validation. This means that the port tags require seperation into several types.

AnalogSendPort

Contains	Description
@name::String	state variable or alias for output
@is_per_connection::bool	for weightupdates sends an output for each connection, instead of each destination neuron

AnalogReceivePort

Contains	Description
@name::String	port identifying name
@dimension::String	port dimensionality
@post::bool [optional]	for weightupdates remaps the input into connections as though it were a postsynaptic input

AnalogReducePort

Contains	Description
@name::String	port identifting name
@dimension::String	port dimensionality
@reduce_op::String	operation used to combine multiple inputs
@post::bool [optional]	for weightupdates remaps the input into connections as though it were a postsynaptic input

EventSendPort

Contains	Description
@name::String	port identifying name
@is_per_connection::bool [optional]	for weightupdates sends an output for each connection, instead of each destination neuron

EventReceivePort

Contains	Description
@name::String	port identifying name
@dimension::String	port dimensionality
@post::bool [optional]	for weightupdates remaps the input into connections as though it were a postsynaptic input

Impulses

We have added a new communication port type: Impulse. Impulses transfer an event with a value. The tags associated with these ports align with the event port tags, with the following form.

ImpulseSendPort

Contains	Description
@name::String	statevariable, parameter or alias for output
@is_per_connection::bool [optional]	for weightupdates sends an output for each connection, instead of each destination neuron

ImpulseReceivePort

Contains	Description
@name::String	port identifying name
@dimension::Stirng	port dimensionality
@post::bool [optional]	for weightupdates remaps the input into connections as though it were a postsynaptic input

ImpulseOut

As EventOut

OnImpulse

As OnEvent, however the ImpulseRecievePort name can be used in the contained MathinLine tags as a variable.

Small differences

ComponentClass contains an attribute type, which can take the values neuron_body,postsynapse or weight_update.

Dynamics contains an attribute initial_regime which denotes the starting Regime.

NineML is replaced as the root tag by SpineML.

Dimensionality

The units and dimensions of components parameters and analog/impulse input ports are specified within a component description. A single @dimension attribute is used for this purpose and consists of a value derived from, a Si unit described by using a prefix and unit from the following tables. E.g. millivolts (mV) is prefix=m, unit=V.

Prefix	Description
G	giga (109)
M	mega (106)
k	kilo (103)
c	centi (10-2)
m	milli (10-3)
u	micro (10-6)
n	nano (10-9)
p	pico (10-12)
f	femto (10-15)

Unit	Description
V	volt (voltage)
Ohm	Ohm (resistance)
g	gram (weight)
m	meter (distance)
S	siemens (conductance)
A	ampere (current)
cd	candela (luminosity)
mol	mole (substance)
degC	degree Celsius (temperature)
s	seconds (time)
F	farad (capacitance)
Hz	hertz (frequency)