Work towards creating a common JSON based format for compact network specification
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
examples
images
neuromllite Improved Oct 30, 2018
.gitignore Update for intfire Oct 25, 2018
.travis.yml
LICENSE.lesser
Manifest.in
README.md
regenerateAndTest.sh Regenerated Oct 10, 2018
setup.py Param sweep update Aug 20, 2018

README.md

NeuroMLlite: a common framework for reading/writing/generating network specifications

Work in progress. For the background to this see here: https://github.com/NeuroML/NetworkShorthand.

Architecture

Examples

The best way to see the currently proposed structure is to look at the examples

Ex. 1: Simple network, 2 populations & projection

Ex1

JSON | Python script

Can be exported to:

  • NeuroML 2 (XML or HDF5 format)
  • Graph (see above)

Ex. 2: Simple network, 2 populations, projection & inputs

Ex2

JSON | Python script | Generated NeuroML2

Can be exported to:

  • NeuroML 2 (XML or HDF5 format)
  • Graph (see above)

Ex. 3: As above, with simulation specification

JSON for network | JSON for simulation | Python script | Generated NeuroML2 | Generated LEMS

Can be exported to:

  • NeuroML 2 (XML or HDF5 format)
  • Graph (see Ex2)

Can be simulated using:

  • NetPyNE
  • jNeuroML
  • NEURON generated from jNeuroML
  • NetPyNE generated from jNeuroML

Ex. 4: A network with PyNN cells & inputs

Ex4

JSON | Python script | Generated NeuroML2

Can be exported to:

  • NeuroML 2 (XML or HDF5 format)
  • Graph (see above)

Can be simulated using:

  • NEST via PyNN
  • NEURON via PyNN
  • Brian via PyNN
  • jNeuroML
  • NEURON generated from jNeuroML
  • NetPyNE generated from jNeuroML

Ex. 5: A network with the Blue Brain Project connectivity data

Ex4

JSON | Python script

Can be exported to:

  • NeuroML 2 (XML or HDF5 format)
  • Graph (see above)

Can be simulated using:

  • NetPyNE

Ex. 6: A network based on Potjans and Diesmann 2014 (work in progress)

Ex6d Ex6f Ex6c

JSON | Python script | Generated NeuroML2

Can be exported to:

  • NeuroML 2 (XML or HDF5 format)
  • Graph (see above)

Ex. 7: A network based on Brunel 2000 (work in progress)

Ex7

JSON | Python script | Generated NeuroML2

Can be exported to:

  • NeuroML 2 (XML or HDF5 format)
  • Graph (see above)

Can be simulated using:

  • jNeuroML

Installation & usage

Installation of the basic framework should be fairly straightforward:

git clone https://github.com/NeuroML/NeuroMLlite.git
cd NeuroMLlite
sudo python setup.py install

Then simple examples can be run:

cd examples
python Example1.py  #  Generates the JSON representation of the network (console & save to file)

To generate the NeuroML 2 version of the network, first install pyNeuroML, then use the -nml flag:

sudo pip install pyNeuroML
python Example2.py -nml       # Saves the network structure to a *net.nml XML file

Other options (which will require Neuron, NetPyNE, PyNN, NEST, Brain etc. to be installed) include:

python Example4.py -jnml       # Generate NeuroML2 & LEMS simulation & run using jNeuroML
python Example4.py -jnmlnrn    # Generate NeuroML2 & LEMS simulation, use jNeuroML to generate Neuron code (py/hoc/mod), then run in Neuron
python Example4.py -jnmlnrn    # Generate NeuroML2 & LEMS simulation, use jNeuroML to generate NetPyNE code (py/hoc/mod), then run in NetPyNE
python Example4.py -netpyne    # Generate network in NetPyNE directly & run simulation
python Example4.py -pynnnrn    # Generate network in PyNN, run using simulator Neuron
python Example4.py -pynnnest   # Generate network in PyNN, run using simulator NEST
python Example4.py -pynnbrian  # Generate network in PyNN, run using simulator Brian

Graphs of the network structure can be generated at many levels of detail (1-6) and laid out using GraphViz engines (d - dot (default); c - circo; n - neato; f - fdp). See above images for generated examples.

python Example6.py -graph3d
python Example6.py -graph2f
python Example6.py -graph1n

Other examples

NeuroMLlite is being tested/used in the following repositories on OSB:

Build Status