NeuroML / pyNeuroML

A single package in Python unifying scripts and modules for reading, writing, simulating and analysing NeuroML2/LEMS models.

https://docs.neuroml.org/Userdocs/Software/pyNeuroML.html

NeuroML/pyNeuroML Issues

Add functionality to overlay data on to 3D visualisations
Updated a month ago
Cached functions: cast arguments to hashable types before invocation
Closed a month ago
Implement vispy based viewing of SWC files
Closed a month ago3
Tracking: multiple 3D vispy based visualisations do not work in a single jupyter notebook
Updated a month ago
vispy-viewer: make it run in jupyter notebooks using jupyter_rfb
Closed a month ago1
Morphology plotting: handle cells where morphology is a standalone element that is referenced in cell
Closed a month ago3
Allow visualization of morphology only NML files
Closed a month ago
Add function to export SWC graph to a new SWC file
Closed a month ago1
Add SWC exporter
Closed a month ago2
Add option to save vispy generated meshdata
Closed 2 months ago5
Check if users are passing the correct file type for various pynml commands
Closed 2 months ago5
Error: pyneuroml/povray/OverlaySimulation.py:279:31: F821 Undefined name `volts`
Closed 2 months ago
[simulation] Add method to run multiple sims in parallel using pp
Closed 2 months ago
Chore: run `no_implicit_optional` on code base
Closed 2 months ago
Installation issues: Vispy and Conda?
Closed 2 months ago2
Include generation of animated matplotlib plots
Closed 3 months ago13
Refactor: de-duplicate PlotSpikes code
Closed 3 months ago2
[vispy viewer] align cells along its first principal component
Closed 3 months ago3
Add utility function to translate cell to that soma is at origin
Closed 3 months ago
Add a SWC loader
Closed 3 months ago3
Enable coverage info on the repo
Closed 3 months ago1
Speed up unit tests
Closed 4 months ago1
Tests on master failing
Closed 4 months ago
Make getting model file list SBML aware
Updated 4 months ago
Implement exporting to Neuroglancer formats
Updated 5 months ago1
[Bug] pynml-plotmorph: vispy: no mouse events
Updated 5 months ago3
Add analysis of KineticState channels to `pynml-channelanalysis`
Updated 5 months ago
Extend `pynml` to include a `-biosimulations` flag to submit simulations
Updated 6 months ago
[Bug] ExportSWC: exceptions are wrong
Updated 6 months ago2
Implement functions to send generated OMEX file to Biomodels using API
Updated 6 months ago
Implement metadata generation for OMEX file generation
Updated 6 months ago
Ascertain and set `NEURON_HOME` if the environment variable is not set
Updated 6 months ago5
Add option to generate SEDML file from LEMS and use this as master in exported OMEX archive
Updated 6 months ago
archiving/nsg: include HDF5 exports
Updated 6 months ago2
Add option to validate SED-ML files
Closed 6 months ago2
Add tests running simple neuron + netpyne sims on nsg
Updated 6 months ago1
Add utility function to create SpikeArray from file
Updated 6 months ago
[vispy viewer] investigate if we can record a video of the rotating image
Updated 6 months ago2
Add function to generate LFP plots
Updated 7 months ago2
Add warnings about missing files of model during visualisation
Updated 7 months ago1
[cell analysis] Implement morphological statistics for NeuroML cell models
Updated 7 months ago
reloading data uses quantity path string instead of column id
Closed 8 months ago
Issue compiling .mod files on Apple Silicon [Bug]
Closed 9 months ago5
Add option to validate SBML
Closed a year ago3
As a user, I would like to add headers to the output files I generate so I can easily see what was recorded in each item at a later date
Closed a year ago3
Add functionality to generate ion channel distribution metrics in models
Closed a year ago
Print `python -version`, neuron path etc. info in `pyneuroml -version`
Closed a year ago
Implement archiving to combine archive format
Closed a year ago2
Suggested updates to 2D plots etc
Closed a year ago1
As a user, I want to be able to run my simulations using different backends without modifying my Python NeuroML simulation code
Updated 2 years ago