# Version 0.9.2
https://github.com/Neurosim-lab/netpyne ... tag/v0.9.2
- Support for saving simulation at intervals
- Improved Python cell template import so can read section names from a Python list or dict of sections
- Fixed replicability issue across different number of cores when using 'connList' connectivity rules
- Improved speed performance of 'connList' connectivity rules
- Updated RxD calcium buffering example
- Added netClamp example to re-simulate activity of single cell from network data
- Added support for recording and plotting variable time step
- Replaced spectrogram FFT method with Morlet wavelet method
- Updated installation instructions
- Added 'fontSize' argument to several plots
- Fixed issue completing batches in Python 3
- Fixed bug saving evolutionary optimization batch output file
- Fixed bug in plotShape()
- Fixed bug in plotSpikeStats()
- Fixed bug loading files with colons
- Fixed issue sorting raster by population and y coord
VERSION RELEASES
Moderator: tom_morse
Re: VERSION RELEASES
# Version 0.9.3
https://github.com/Neurosim-lab/netpyne ... ag/v.0.9.3
- Improved conversion from SONATA format, including 300 biophys cell example
- Added saveCellConns, pt3dRelativeToCellLocation and invertedYCoord cfg options
- Added lineWidth as argument of plotRatePSD() and plotLFP()
- Modified plotLFP and plotRatePSD to use Morlet wavelet for PSD calculation
- Added lineWidth argument to some raster and LFP plots
- Added shuffling test to granger causality functions
- Fixed bug plotting traces with one fig per trace
- Fixed bug in granger functions - required conversion to int
- Fixed bug in plotShape when cells sections not available
- Return meaningful cell info via 'repr' and 'str' for pointCell, compartCell
- Fixed spelling typos in documentation
https://github.com/Neurosim-lab/netpyne ... ag/v.0.9.3
- Improved conversion from SONATA format, including 300 biophys cell example
- Added saveCellConns, pt3dRelativeToCellLocation and invertedYCoord cfg options
- Added lineWidth as argument of plotRatePSD() and plotLFP()
- Modified plotLFP and plotRatePSD to use Morlet wavelet for PSD calculation
- Added lineWidth argument to some raster and LFP plots
- Added shuffling test to granger causality functions
- Fixed bug plotting traces with one fig per trace
- Fixed bug in granger functions - required conversion to int
- Fixed bug in plotShape when cells sections not available
- Return meaningful cell info via 'repr' and 'str' for pointCell, compartCell
- Fixed spelling typos in documentation
Re: VERSION RELEASES
# Version 0.9.4
https://github.com/Neurosim-lab/netpyne ... tag/v0.9.4
- Added option to avoid creating connections with weight=0
- Made recording of dipoles optional with attribute cfg.recordDipoles
- Rotated conn matrix x-axis labels so can fit large matrices
- Added 'removeWeightNorm' argument to plotConn() function
- Added cfg option 'oneSynPerNetcon' to conn rules to create one synapse object per Netcon
- Added first version of Contributors Guide
- Fixed file write permissions for evol optim batches
- Fixed bug calculating normally distributed rhythmic inputs - was using variance instead of std
- Fixed bug in iplotDipole when smoothing window size = 0
- Fixed bug in plotSpikeStats pop order
- Fixed bug is plots with scalebars
- Fixed bug in grid lines of plotConn
- Fixed bug in subConnParams by sorting conns to ensure reproducibility on different number of cores
- Fixed bug so uses 'Agg' backend if no display env variable e.g. in clusters
https://github.com/Neurosim-lab/netpyne ... tag/v0.9.4
- Added option to avoid creating connections with weight=0
- Made recording of dipoles optional with attribute cfg.recordDipoles
- Rotated conn matrix x-axis labels so can fit large matrices
- Added 'removeWeightNorm' argument to plotConn() function
- Added cfg option 'oneSynPerNetcon' to conn rules to create one synapse object per Netcon
- Added first version of Contributors Guide
- Fixed file write permissions for evol optim batches
- Fixed bug calculating normally distributed rhythmic inputs - was using variance instead of std
- Fixed bug in iplotDipole when smoothing window size = 0
- Fixed bug in plotSpikeStats pop order
- Fixed bug is plots with scalebars
- Fixed bug in grid lines of plotConn
- Fixed bug in subConnParams by sorting conns to ensure reproducibility on different number of cores
- Fixed bug so uses 'Agg' backend if no display env variable e.g. in clusters
Re: VERSION RELEASES
# Version 0.9.5
https://github.com/Neurosim-lab/netpyne ... tag/v0.9.5
- Print start and end date/time
- Avoid removing batch folder so can rerun and complete batch simulations
- Added loadBalance option to print individual node computer times
- Initialize hoc events recursivley to reduce event queue overhead
- Added plotRateSpectrogram analysis function
- Added option to save at intervals
- Fixed bug: wrong indentation for initializing fixedInterval in batch.py
- Fixed bug in _distributeSynsUniformly function
- Fixed bug in subConnParams grouped synapses
- Fixed bug in analysis.granger figure save name
- Fixed bug in printRunTime function
https://github.com/Neurosim-lab/netpyne ... tag/v0.9.5
- Print start and end date/time
- Avoid removing batch folder so can rerun and complete batch simulations
- Added loadBalance option to print individual node computer times
- Initialize hoc events recursivley to reduce event queue overhead
- Added plotRateSpectrogram analysis function
- Added option to save at intervals
- Fixed bug: wrong indentation for initializing fixedInterval in batch.py
- Fixed bug in _distributeSynsUniformly function
- Fixed bug in subConnParams grouped synapses
- Fixed bug in analysis.granger figure save name
- Fixed bug in printRunTime function
-
- Posts: 3
- Joined: Wed Aug 22, 2007 8:37 pm
- Location: Tempe, AZ
Re: VERSION RELEASES
# Version 0.9.6
https://github.com/Neurosim-lab/netpyne ... ag/v0.9.6
- Added useful hover information to iplots
- Improvements to iplotTraces
- Added interactive plot for connectivity (iplotConn)
- Added 'dynamicRates' option for NetStim populations
- Added option to have a uniform distribution of rates for Vecstim pulses
- Added function for distributed saving at intervals
- Added issue templates for GitHub
- Overhaul of contribution guide (CONTRIBUTING.md)
- Improved documentation
- Fixed bugs and improved exception handling in plotConn
- Fixed loadSave V1 example model
- Fixed bug calculating popRates when no spikes
- Fixed bug in _distributeSynsUniformly()
- Fixed bug in saveCellParamsRule()
- Fixed bug in batch.py: initCfg params were not being updated for evol optim
- Fixed bug in subconn.py: missing initialization of newWeightNorm
- Fixed bug in run.py: print run time with 2 significant figures
- Fixed output stat filenames of evolutionary optim: .cvs to .csv
- Fixed bug in interval saving
- Fixed bug in spikes.py in plotSpikeStats
https://github.com/Neurosim-lab/netpyne ... ag/v0.9.6
- Added useful hover information to iplots
- Improvements to iplotTraces
- Added interactive plot for connectivity (iplotConn)
- Added 'dynamicRates' option for NetStim populations
- Added option to have a uniform distribution of rates for Vecstim pulses
- Added function for distributed saving at intervals
- Added issue templates for GitHub
- Overhaul of contribution guide (CONTRIBUTING.md)
- Improved documentation
- Fixed bugs and improved exception handling in plotConn
- Fixed loadSave V1 example model
- Fixed bug calculating popRates when no spikes
- Fixed bug in _distributeSynsUniformly()
- Fixed bug in saveCellParamsRule()
- Fixed bug in batch.py: initCfg params were not being updated for evol optim
- Fixed bug in subconn.py: missing initialization of newWeightNorm
- Fixed bug in run.py: print run time with 2 significant figures
- Fixed output stat filenames of evolutionary optim: .cvs to .csv
- Fixed bug in interval saving
- Fixed bug in spikes.py in plotSpikeStats
-
- Posts: 3
- Joined: Wed Aug 22, 2007 8:37 pm
- Location: Tempe, AZ
Re: VERSION RELEASES
We have released NetPyNE version 0.9.7, which includes some major improvements:
- All analyses functions can now generate interactive HTML plots (via Bokeh package)
- Online documentation and tutorials have been updated and expanded (see http://www.netpyne.org/)
- Simplified cell type specification to facilitate model building
- New parameter optimization methods: Adaptive Stochastic Descent and Optuna (see examples)
See github.com/Neurosim-lab/netpyne/blob/v0.9.7/CHANGES.md for a complete list of improvements.
See netpyne.org/install.html for instructions on installation or updating.
Additionally, we have released our new NetPyNE GUI (see fig below) with a more intuitive interface, better performance and new features. Try out the new NetPyNE GUI without installing any software at: netpyne.org/gui
To learn more please check out our Tutorial and Workshop at CNS'2020 (register for free at http://cnsorg.org/cns-2020):
Tutorial: "Building mechanistic multiscale models, from molecules to networks, using NEURON and NetPyNE", July 18; website: https://sites.google.com/neurosim.downs ... 0-tutorial
Workshop: "Tools and resources for developing and sharing models in computational neuroscience", July 21-22; website: https://neuralensemble.github.io/Networks_SIG/CNS2020
- All analyses functions can now generate interactive HTML plots (via Bokeh package)
- Online documentation and tutorials have been updated and expanded (see http://www.netpyne.org/)
- Simplified cell type specification to facilitate model building
- New parameter optimization methods: Adaptive Stochastic Descent and Optuna (see examples)
See github.com/Neurosim-lab/netpyne/blob/v0.9.7/CHANGES.md for a complete list of improvements.
See netpyne.org/install.html for instructions on installation or updating.
Additionally, we have released our new NetPyNE GUI (see fig below) with a more intuitive interface, better performance and new features. Try out the new NetPyNE GUI without installing any software at: netpyne.org/gui
To learn more please check out our Tutorial and Workshop at CNS'2020 (register for free at http://cnsorg.org/cns-2020):
Tutorial: "Building mechanistic multiscale models, from molecules to networks, using NEURON and NetPyNE", July 18; website: https://sites.google.com/neurosim.downs ... 0-tutorial
Workshop: "Tools and resources for developing and sharing models in computational neuroscience", July 21-22; website: https://neuralensemble.github.io/Networks_SIG/CNS2020
-
- Posts: 3
- Joined: Wed Aug 22, 2007 8:37 pm
- Location: Tempe, AZ
Re: VERSION RELEASES
NetPyNE v0.9.8 is now available.
For a complete list of changes and bug fixes see: https://github.com/Neurosim-lab/netpyne ... tag/v0.9.8
See here for instructions to install or update to the latest version: http://www.netpyne.org/install.html
NetPyNE Version 0.9.8
New features
- analysis.plotLFP can now be applied to external data
- Evolutionary and Optuna optimization can now read results from .pkl files
- Enabled recording of stimulus variables (e.g. SEClamp i)
- Added options in load func to avoid instantiating cells, conns, stims and/or rxd
- Analysis and plotting of rate vs current (f-I) curve for single cell tuning
- Recording and plotting of current dipoles in arbitrary subset of populations
- Added option to plot LFP spectrogram with log y-axis
- Added option to plot the log of connectivity in plotConn
- Enabled random distribution of multiple synapses with synsPerConn>1 and connRandomSecFromList=True
- Added lineWidth option to plot2Dnet (thanks Eric!)
- Updated Travis Continuous Integration to use NEURON 7.8.1 (from 7.6.2)
- Removed trailing white space from all Python files in the repository
Bug fixes
- Fixed bug when using index with recordTraces
- Fixed axes values in plotRxDConcentration and iplotRxDConcentration
- Added links to necessary mod files in the importing cell models tutorial
- Added aux_fun.inc to doc/source/code/mod as it's needed for some examples
- Blocked terminal output from Git when no repository is found (i.e. with pip install netpyne)
- Avoid adding section-based weightNorm values to point neurons (was affecting tut_import.py)
- Prevent error when loading pointCell params from json by converting Dict to dict
- Fixed bug in plotShape (thanks Eric!)
- Updated setup.py so PyPI website renders the README as markdown
- Fixed expected numSpikes in test of M1detailed example
- Merged GUI branch into development branch
- Fixed bug in iplotConn
- Fixed bug and coloring in iplotSpikeStats with different themes
For a complete list of changes and bug fixes see: https://github.com/Neurosim-lab/netpyne ... tag/v0.9.8
See here for instructions to install or update to the latest version: http://www.netpyne.org/install.html
NetPyNE Version 0.9.8
New features
- analysis.plotLFP can now be applied to external data
- Evolutionary and Optuna optimization can now read results from .pkl files
- Enabled recording of stimulus variables (e.g. SEClamp i)
- Added options in load func to avoid instantiating cells, conns, stims and/or rxd
- Analysis and plotting of rate vs current (f-I) curve for single cell tuning
- Recording and plotting of current dipoles in arbitrary subset of populations
- Added option to plot LFP spectrogram with log y-axis
- Added option to plot the log of connectivity in plotConn
- Enabled random distribution of multiple synapses with synsPerConn>1 and connRandomSecFromList=True
- Added lineWidth option to plot2Dnet (thanks Eric!)
- Updated Travis Continuous Integration to use NEURON 7.8.1 (from 7.6.2)
- Removed trailing white space from all Python files in the repository
Bug fixes
- Fixed bug when using index with recordTraces
- Fixed axes values in plotRxDConcentration and iplotRxDConcentration
- Added links to necessary mod files in the importing cell models tutorial
- Added aux_fun.inc to doc/source/code/mod as it's needed for some examples
- Blocked terminal output from Git when no repository is found (i.e. with pip install netpyne)
- Avoid adding section-based weightNorm values to point neurons (was affecting tut_import.py)
- Prevent error when loading pointCell params from json by converting Dict to dict
- Fixed bug in plotShape (thanks Eric!)
- Updated setup.py so PyPI website renders the README as markdown
- Fixed expected numSpikes in test of M1detailed example
- Merged GUI branch into development branch
- Fixed bug in iplotConn
- Fixed bug and coloring in iplotSpikeStats with different themes