Neurosim-lab/netpyne: v0.9.9
Authors/Creators
- Salvador Dura-Bernal
- Joe Graham1
- Padraig Gleeson2
- ericaygriffith
- Adrian Quintana3
- jjcarre
- Cliff Kerr4
- William Lytton5
- David Kedziora
- barefoothiker
- kelley92
- Ariel Alejandro Brassesco
- Matteo Cantarelli6
- jchen6727
- Afonso Pinto7
- Sam Neymotin8
- campbell-mclauchlan
- Facu
- Gil Lee
- adamjhn
- Blake Caldwell
- Eric Thomson9
- IPSIA
- FernandoSBorges
- Lucas10
- Tom Morse11
- 1. @Neurosim-lab
- 2. University College London
- 3. @EyeSeeTea
- 4. Institute for Disease Modeling
- 5. SUNY Downstate
- 6. @MetaCell @openworm
- 7. @MetaCell
- 8. Nathan Kline Institute
- 9. NIH Bioinformatics Scientist
- 10. Freelance
- 11. Yale
Description
New features
Plot current source density (CSD) from local field potential (LFP) simulated data
Additional customization of 3D shape plot: show voltage as color, change proportions, include axis labels
Enable modifyConns based on properties of presynaptic neurons
Replaced -np with -n so compatible for all commands: mpiexec/mpirun/srun
Updated netrxd.py and network.py to include RxD's Parameter class, naming of States and Regions, and specification of Region geometries that do not require arguments like 'membrane' and 'inside'
Improved recordTraces such that the cond 'gid' can accept a list of numbers as well as a single number
Added a new tutorial going through use of NetPyNE with virtual environments and Jupyter notebooks
Added cfg.use_fast_imem to enable recording membrane voltage via seg.imembrane
Added swc import ability to importCell (and thus importCellParams)
Batch now polls processes, prints their output and terminates them once completed
Updated web documentation to explain importing SWC files and add Recording Configuration section
Added link to Jupyter notebook tutorial and video to website front page
Bug fixes
Made rate_b be positional instead of keyword argument in rxd multiCompartmentReaction
Check if _morphSegCoords exists in population before using
Fixed bug to avoid recursive creating of synMechs when loading with cfg.oneSynPerNetcon=True
Fixed an issue with running rxd code twice
Wait until all subprocesses have ended before completing mpi_bulletin batches
Fixed repeated rxd simulation issue for rates and reactions
Fixed pointNeuron spikePattern 'sync' option
Files
Neurosim-lab/netpyne-v0.9.9.zip
Files
(26.5 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/Neurosim-lab/netpyne/tree/v0.9.9 (URL)