Search found 76 matches

by salvadord
Mon Dec 03, 2018 10:38 am
Forum: NetPyNE
Topic: Multisplit Simulation
Replies: 1
Views: 41

Re: Multisplit Simulation

Sorry, multisplit is not currently supported in NetPyNE, but I have added it to the list of features to add: https://github.com/Neurosim-lab/netpyne/issues/399 You could try to create the network in NetPyNE, then set up the multisplit, and run the sim via NetPyNE, but I haven't tried this, and it co...
by salvadord
Thu Nov 29, 2018 11:26 am
Forum: NetPyNE
Topic: Point process not located in a section
Replies: 4
Views: 230

Re: Point process not located in a section

Thanks Krishna. I need the GrCTemp.py to actually test the model. You can paste it here or email to salvadordura@gmail.com
by salvadord
Thu Nov 22, 2018 1:41 pm
Forum: NetPyNE
Topic: Point process not located in a section
Replies: 4
Views: 230

Re: Point process not located in a section

Hi Krishna,

Could you please share your code so we can look at the details? If it's not too long you can post it here. Alternatively you can share the link to a repo (eg. in Github) or send it to me by email (salvadordura@gmail.com).

Thanks
by salvadord
Thu Nov 22, 2018 1:39 pm
Forum: NetPyNE
Topic: NetPyNE UI
Replies: 1
Views: 221

Re: NetPyNE UI

Hi Krishna, Sorry that you are having issues with the GUI. We are about to release a new version within the next couple of weeks that should be easier to install and use. If you sign up to the mailing list ( www.netpyne.org/mailing ) you will get an email when it is released. If you still have issue...
by salvadord
Thu Nov 22, 2018 1:35 pm
Forum: NetPyNE
Topic: Analysing the output data (supercomputers)
Replies: 1
Views: 427

Re: Analysing the output data (supercomputers)

Hi, The tut8_analysis.py was just provided as an example of how to analyze output data. It may not work with all models. The reason that df.popRates might be missing is that you need to set cfg.printPopAvgRates = True -- this records the avg population rates and stores them in simData. If you want t...
by salvadord
Thu Nov 01, 2018 11:01 am
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 14
Views: 8508

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...
by salvadord
Mon Jul 30, 2018 8:56 pm
Forum: NetPyNE
Topic: Importing HDF5 data to NetPyNE
Replies: 1
Views: 577

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: 14
Views: 8508

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: 556

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: 596

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: 595

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: 14
Views: 8508

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: 608

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: 537

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: 14
Views: 8508

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...