Search found 80 matches

by salvadord
Tue Jul 23, 2019 6:13 pm
Forum: NetPyNE
Topic: Changing reversal potentials in NetPyNE
Replies: 2
Views: 266

Re: Changing reversal potentials in NetPyNE

Sorry for the delay responding. To change the reversal potential of ions, you can use eg. cellRule['secs']['soma']['ions']['na'] = {'e': 60} similarly for the internal and external concentrations of the ion you can use: cellRule['secs']['soma']['ions']['na'] = {'i': 15, 'o': 150 } Apologies, this is...
by salvadord
Sun Jul 21, 2019 5:25 pm
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 16
Views: 10685

Re: VERSION RELEASES

# Version 0.9.3 https://github.com/Neurosim-lab/netpyne/releases/tag/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() - Mo...
by salvadord
Sat Apr 27, 2019 2:36 pm
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 16
Views: 10685

Re: VERSION RELEASES

# Version 0.9.2 https://github.com/Neurosim-lab/netpyne/releases/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 'co...
by salvadord
Sun Jan 27, 2019 12:25 pm
Forum: NetPyNE
Topic: Reloading mechanisms library
Replies: 3
Views: 1452

Re: Reloading mechanisms library

Hey Cristoph, in case useful, you can also use this command to reload the mod files: `neuron.load_mechanisms(folder_with_mod)` and before that you could call the `nrnivmodl` command from python to recompile them. Never tried this but I think it should work.

salva
by salvadord
Mon Dec 03, 2018 10:38 am
Forum: NetPyNE
Topic: Multisplit Simulation
Replies: 1
Views: 769

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: 1209

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: 1209

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: 856

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: 1148

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: 16
Views: 10685

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: 1431

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: 16
Views: 10685

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: 1391

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: 1448

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: 1485

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 ...