Search found 70 matches

by salvadord
Mon Jul 30, 2018 8:56 pm
Forum: NetPyNE
Topic: Importing HDF5 data to NetPyNE
Replies: 1
Views: 240

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...
by salvadord
Tue Jul 10, 2018 11:45 am
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 13
Views: 7999

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 ...
by salvadord
Wed Jul 04, 2018 4:36 pm
Forum: NetPyNE
Topic: Setpointer when defining a synapse
Replies: 2
Views: 253

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 elegant soluti...
by salvadord
Sat May 05, 2018 5:37 pm
Forum: NetPyNE
Topic: Import json format of morphology to NetPyNE
Replies: 2
Views: 267

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...
by salvadord
Tue Apr 24, 2018 12:53 pm
Forum: NetPyNE
Topic: Slow speed to save sim results
Replies: 2
Views: 267

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 ...
by salvadord
Sat Apr 21, 2018 5:59 pm
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 13
Views: 7999

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...
by salvadord
Sat Mar 24, 2018 8:28 pm
Forum: NetPyNE
Topic: Field names are restricted to 31 characters
Replies: 2
Views: 236

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...
by salvadord
Wed Mar 21, 2018 6:20 pm
Forum: NetPyNE
Topic: plotLFP
Replies: 1
Views: 280

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 install here: ...
by salvadord
Sat Feb 24, 2018 8:18 pm
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 13
Views: 7999

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...
by salvadord
Thu Feb 15, 2018 11:30 am
Forum: NetPyNE
Topic: Mat file not saved properly in batch functions
Replies: 1
Views: 286

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
by salvadord
Thu Feb 08, 2018 12:41 pm
Forum: NetPyNE
Topic: Gap junction support - parallel simulation?
Replies: 3
Views: 312

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...
by salvadord
Mon Feb 05, 2018 5:01 pm
Forum: NetPyNE
Topic: Gap junction support - parallel simulation?
Replies: 3
Views: 312

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
by salvadord
Mon Jan 15, 2018 11:05 am
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 13
Views: 7999

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...
by salvadord
Wed Dec 13, 2017 10:26 am
Forum: NetPyNE
Topic: Netpyne on clusters
Replies: 4
Views: 1784

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')
by salvadord
Tue Dec 12, 2017 10:37 am
Forum: NetPyNE
Topic: Netpyne on clusters
Replies: 4
Views: 1784

Re: Netpyne on clusters

Seems like there is some issue with matplotlib -- can you import it by itself outside of netpyne?

You can use the command line option '-nogui' (this sets netpyne.__gui__ to False) to avoid importing graphic-related modules -- but you won't be able to use the most analysis functions.