Search found 86 matches
- Thu Nov 01, 2018 11:01 am
- Forum: NetPyNE
- Topic: VERSION RELEASES
- Replies: 28
- Views: 50703
Re: VERSION RELEASES
# Version 0.9.0 - Added support for reaction-diffusion (RxD) and usage examples - Improved performance (speed) of connectivity algorithms - Major code refactor to split functions across modules and subpackages - Switched to Python 3 as the default development environment - Optimized implementation o...
- Mon Jul 30, 2018 8:56 pm
- Forum: NetPyNE
- Topic: Importing HDF5 data to NetPyNE
- Replies: 1
- Views: 14408
Re: Importing HDF5 data to NetPyNE
Hi, It is possible to specify a custom list of connections -- see connList parameter in connectivity rules. So you can just load the data from the HDF5 file and pass the list of connections in a connectivity rule. The format is just the list of pre and postsynaptic gids. For preConds and postConds y...
- Tue Jul 10, 2018 11:45 am
- Forum: NetPyNE
- Topic: VERSION RELEASES
- Replies: 28
- Views: 50703
Re: VERSION RELEASES
# Version 0.7.9 https://github.com/Neurosim-lab/netpyne/releases/tag/v0.7.9 - Extended metadata structure to interact with NetPyNE-UI - Added preliminary data structures to support NEURON RxD - Added plot RxD concentration to analysis - Added netParams.correctBorder to compensate distance-dependent ...
- Wed Jul 04, 2018 4:36 pm
- Forum: NetPyNE
- Topic: Setpointer when defining a synapse
- Replies: 2
- Views: 16156
Re: Setpointer when defining a synapse
Hi Noemie, Currently, netpyne does not support synapses with pointers. I added a Github issue to add this feature in the future: https://github.com/Neurosim-lab/netpyne/issues/332 You could try creating the pointer "manually" after the network has been instantiated -- but it is not an eleg...
- Sat May 05, 2018 5:37 pm
- Forum: NetPyNE
- Topic: Import json format of morphology to NetPyNE
- Replies: 2
- Views: 15933
Re: Import json format of morphology to NetPyNE
Hi Javad, Thanks for your question. So the file format is .json but what is the data structure that the morphology is stored in? e.g is it a dictionary of sections with 3d pts, does it follow a similar structure to swc? Perhaps you can share the file to get a better idea. NetPyNE can import morpholo...
- Tue Apr 24, 2018 12:53 pm
- Forum: NetPyNE
- Topic: Slow speed to save sim results
- Replies: 2
- Views: 14411
Re: Slow speed to save sim results
Hi Stefano, Sorry to hear the saving is taking so long. The independence of num of cores is normal, since data is gathered on the master node and then saved. The similar speed with SSD drives might indicate that what's taking longer could be the internal conversion to Matlab format (prior to saving ...
- Sat Apr 21, 2018 5:59 pm
- Forum: NetPyNE
- Topic: VERSION RELEASES
- Replies: 28
- Views: 50703
Re: VERSION RELEASES
# Version 0.7.8 https://github.com/Neurosim-lab/netpyne/releases/tag/v0.7.8 - Added netParams.rotateCellsRandomly option to rotate cells randomly around y-axis - Added netParams.defineCellShapes option to convert stylized cell geometries to 3d points - Added 'histogram' option to plotSpikeStats - Im...
- Sat Mar 24, 2018 8:28 pm
- Forum: NetPyNE
- Topic: Field names are restricted to 31 characters
- Replies: 2
- Views: 15987
Re: Field names are restricted to 31 characters
Hi Stefano, I have never encountered this error but yes, it is related to the scipy savemat function, which has a limit of 31 chars per field: https://docs.scipy.org/doc/scipy/reference/generated/scipy.io.savemat.html There seems to be an option to increase it to 64: long_field_names = True hope thi...
Re: plotLFP
Hi Andrew, Sorry for the delay responding -- unfortunately the email alerts for this forum are not working. I have fixed a few minor bugs (including this one) since the release of this feature, so please try the github "development" version and let me know if it works; instructions to inst...
- Sat Feb 24, 2018 8:18 pm
- Forum: NetPyNE
- Topic: VERSION RELEASES
- Replies: 28
- Views: 50703
Re: VERSION RELEASES
# Version 0.7.7 https://github.com/Neurosim-lab/netpyne/releases/tag/v0.7.7 - Added LFP recording at arbitrary 3D locations - Added plotting of LFP time series, PSD, freq vs time and electrode locations - Updates to NeuroML conversion code. - ShapePlot now shows segment diameters as linewidths (Pyth...
- Thu Feb 15, 2018 11:30 am
- Forum: NetPyNE
- Topic: Mat file not saved properly in batch functions
- Replies: 1
- Views: 13736
Re: Mat file not saved properly in batch functions
Hi Vittorio,
Thanks for pointing this out, the issue was related to a bug in the "scipy" package — see https://github.com/scipy/scipy/issues/3487.
I found a workaround in netpyne and pushed to the GitHub ‘development' branch — it now works ok.
Thanks
Salva
Thanks for pointing this out, the issue was related to a bug in the "scipy" package — see https://github.com/scipy/scipy/issues/3487.
I found a workaround in netpyne and pushed to the GitHub ‘development' branch — it now works ok.
Thanks
Salva
- Thu Feb 08, 2018 12:41 pm
- Forum: NetPyNE
- Topic: Gap junction support - parallel simulation?
- Replies: 3
- Views: 34139
Re: Gap junction support - parallel simulation?
I fixed the bug that was preventing gap junctions to work with multiple cores. It will be released in the next version but you can try it now using the 'development' version of NetPyNE -- see instructions here: http://neurosimlab.org/netpyne/install.html#install-via-pip-development-version let me kn...
- Mon Feb 05, 2018 5:01 pm
- Forum: NetPyNE
- Topic: Gap junction support - parallel simulation?
- Replies: 3
- Views: 34139
Re: Gap junction support - parallel simulation?
Yes, it did originally, but I just tested it and seems some change introduced in a later version has broken mpi support -- I will post a message here once I fix it.
thanks for your message
thanks for your message
- Mon Jan 15, 2018 11:05 am
- Forum: NetPyNE
- Topic: VERSION RELEASES
- Replies: 28
- Views: 50703
Re: VERSION RELEASES
# Version 0.7.6 https://github.com/Neurosim-lab/netpyne/releases/tag/v0.7.6 - Added option to order raster spike trains by multipe tags (eg. ['pop', 'y']) - Enable providing a 2D list of spike times to VecStim populations - Added exception handling to analysis functions - Updated saveLoadV1 examples...
- Wed Dec 13, 2017 10:26 am
- Forum: NetPyNE
- Topic: Netpyne on clusters
- Replies: 4
- Views: 19010
Re: Netpyne on clusters
try adding this at the top of the main script you are calling:
Code: Select all
import matplotlib; matplotlib.use('Agg')