PyNN and NineML

NineML is a declarative XML-based language for describing neuronal network models. One of its key features is the separation into an “abstraction layer”, which provides the mathematical details of the model components (neurons, synapses, etc.), and a “user layer”, which describes how the components are put together to form a network model.

PyNN can work with NineML in two ways:

• at the user layer level - exporting an entire PyNN model as XML or importing a NineML XML file into PyNN and running simulations with the resulting model;
• at the abstraction layer level - constructing PyNN CellType classes from NineML neuron/synapse components (and, in the future, PyNN dynamic synapse classes from NineML synaptic plasticity components).

Note

most of what is described below does not work yet, or is not properly tested - this document is currently a statement of intent, which will gradually turn into proper documentation as things get implemented/tested]

Exporting a PyNN model as XML

Using pyNN.nineml as the simulator backend will cause the model to be written to XML rather than simulated. This requires specifying an output file name in the setup() call:

import pyNN.nineml as sim

sim.setup(filename="my_model.xml")

...

sim.end()

Writing to file takes place when sim.end() is called. Note that any PyNN calls related to recording or saving data are ignored. It is possible that in future this information could be saved in a simulation experiment description format such as SEDML

Using a NineML abstraction layer model in a NEST or NEURON simulation

This requires code-generation support for the backend simulator. For NEST, this will be built-in to some future release; for NEURON, the nineml2nmodl package is required [currently available in the NineML svn, will be released on PyPI at some point]. Brian support is also envisaged.

import pyNN.neuron as sim

celltype_cls = sim.nineml_celltype(
                    name="my_neuron_type",
                    neuron_model="iaf.xml",
                    synapse_models={
                        "AMPA": "coba_syn.xml",
                        "NMDA": "nmda_syn.xml",
                        "GABAA": "coba_syn.xml"
                    })

parameters = {
    'iaf.cm': 1.0, 'iaf.gl': 50.0, 'iaf.taurefrac': 5.0,
    'iaf.vrest': -65.0, 'iaf.vreset': -65.0, 'iaf.vthresh': -50.0,
    'AMPA.tau': 2.0, 'GABAA.tau': 5.0, 'AMPA.vrev': 0.0, 'GABAA.vrev': -70.0,
    'NMDA.taur': 3.0, 'NMDA.taud': 40.0, 'NMDA.gmax': 1.2, 'NMDA.E': 0.0,
    'NMDA.gamma': 0.062, 'NMDA.mgconc': 1.2, 'NMDA.beta': 3.57
    }

cells = sim.Population(100, celltype_cls, parameters)

cells.record(("iaf.v", "AMPA.g", "NMDA.g", "GABAA.v"))

Simulating an entire NineML model with NEST or NEURON

Again, this requires code-generation support for the backend simulator, or for PyNN to be able to recognize the components as equivalent to existing PyNN standard models.

Todo

For example, the PyNN Git repository could contain

NineML representations of the standard models; these representations would then each have a URL including version information, and if these URLs are used in the user layer description, PyNN can safely use a standard model rather than doing code generation.

import pyNN.neuron as sim

network = sim.NineMLNetwork("my_network_model.xml") # user layer description

network.populations["excitatory cells"].record("spikes")

sim.run(1000.0)

network.populations["excitatory_cells"].write("spikes")

sim.end()