Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update mapping NeuroML2 to & from PyNN #73

pgleeson opened this issue Feb 10, 2016 · 0 comments

Update mapping NeuroML2 to & from PyNN #73

pgleeson opened this issue Feb 10, 2016 · 0 comments


Copy link

@pgleeson pgleeson commented Feb 10, 2016

Examples of integration between PyNN and NeuroML2 are being added to:

Scenario: Model in PyNN; convert it equivalent in NeuroML2

In progress here: (recent version has been merged into PyNN master: NeuralEnsemble/PyNN#509). There is example of a PyNN file converted to NeuroML2 on (latest export is here)

Longer term:

  • Export network connectivity to binary format (e.g. HDF5) from PyNN & have that supported also by NeuroML pipeline (see #93)

Scenario: Network model in NeuroML 2; need to convert it to equivalent in PyNN using jNeuroML

Started here:

Initially only worked for models only using NML2 equivalents of PyNN cells, e.g. Now using tips here and here to make sure this jNeuroML generated code is compatible with PyNN.

  • test for export of abstract cells, e.g. IaF, Izhikevich; add to .travis.yml
  • support plotting/saving of non v variables
  • test for export of connections; add to .travis.yml
  • test for export of connectionWDs; add to .travis.yml
  • test for single cond based cell; add to .travis.yml
  • test for multicomp cells; add to .travis.yml
  • test/document running generated examples on parallel Neuron

Scenario: Cell model in NeuroML 2/LEMS; need to use it in PyNN script as a cell for Population

Similar to above, but use statement like:

cell_type, cell_instance = import_neuroml2_cell(file="MyNeuroML.nml",cell_id = "mycell") 

inside existing PyNN script. Note something similar to this is possible in NetPyNE already, see here.

pgleeson added a commit to NeuroML/org.neuroml.export that referenced this issue Feb 17, 2016
Work towards NeuroML/NeuroML2#73
@pgleeson pgleeson self-assigned this Jan 18, 2017
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Linked pull requests

Successfully merging a pull request may close this issue.

None yet
1 participant
You can’t perform that action at this time.