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suny-downstate-medical-center / netpyne

A Python package to facilitate the development, parallel simulation, optimization and analysis of multiscale biological neuronal networks in NEURON.
http://www.netpyne.org
MIT License
146 stars 137 forks source link

NetPyNE to NeuroML 2 conversion #12

Open pgleeson opened 8 years ago

pgleeson commented 8 years ago

Work on this is happening in this branch: https://github.com/Neurosim-lab/netpyne/tree/neuroml_export

NetPyNE -> NeuroML 2

See sim.py

See NetPyNEWriter.java, run.vm

salvadord commented 8 years ago

@pgleeson - as mentioned I just released a version that make some changes to the netParams and simConfig structures: they are now objects of class NetParams and SimConfig, so can use the object methods to add stuff easily. Also, all the inner structures (popParams, cellParams etc) are now orderedDicts (for consistency). All the tuts, examples and most of documentation is already updated. Sorry about the format changes, we are hoping this will be the last major change for a while. I'm happy to update the neuroml export/import funcs.

pgleeson commented 8 years ago

Ok, I'll look at the changes and make the updates in the nml import/export. I have a simple example of import working here: https://github.com/Neurosim-lab/netpyne/blob/c9794646cf7af138581b48d288bda3015c2d9f1c/examples/NeuroMLImport/SimpleNet_import.py

salvadord commented 8 years ago

@pgleeson - I was trying to test the neuroml export examples in the neuroml_export branch, but I don't get any new files, and last line says: pyNeuroML >>> Unable to find file: /u/salvadord/Documents/ISB/Models/netpyne_repo/examples/HHTut/HH.cell.nml!

anything I'm missing or doing wrong?

Update: Actually I did get a new file: HHTut.net.nml, so guess just missing HH.cell.nml?

pgleeson commented 8 years ago

Working on generating the required NML <cell>/<izhikevich2007Cell> elements now... Previously I had manually placed a HH.cell.nml etc. there for testing.

pgleeson commented 8 years ago

@salvadord your issue above is solved in the latest version

salvadord commented 8 years ago

That's great, thanks!