Search found 85 matches

by salvadord
Thu Jun 15, 2017 11:12 pm
Forum: NetPyNE
Topic: Issue stimulating cells that I imported
Replies: 2
Views: 9766

Re: Issue stimulating cells that I imported

Thanks for your message, Brenyn. Your code looks very good. I'm happy to say that in this case the error was due to a minor typo: for pops 'PN_B', 'PN_C' and 'INT' you used 'cellModel ' (with a space) instead of 'cellModel' -- this change fixes your issues. This is the type of error that will be hig...
by salvadord
Wed Jun 14, 2017 11:08 am
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 20
Views: 13673

Re: VERSION RELEASES

This applies only to version 0.7.0. We understand this is a big issue and we will avoid it in the future; however, we are still at a relatively early stage of development and this change was necessary to ensure proper randomization of multiple features. Please also note that all previous versions we...
by salvadord
Mon Jun 12, 2017 2:03 pm
Forum: NetPyNE
Topic: Stimulating network using spike trains
Replies: 11
Views: 13747

Re: Stimulating network using spike trains

Aah I know what it can be! You need to have the vecevent.mod file which contains the VecStim mechanism compiled in the folder where you are running the sim. Sorry, in the next version I will modify netpyne so it gives a warning if the mod mechanism is not available.
by salvadord
Mon Jun 12, 2017 11:39 am
Forum: NetPyNE
Topic: Stimulating network using spike trains
Replies: 11
Views: 13747

Re: Stimulating network using spike trains

Works for me using your code, so please check that you are not accidentally using an older version (happens often). You can check the version via sys.version() and can check where the files are located using import netpyne; print netpyne.__file__ In theory, to upgrade you should just need to do pip ...
by salvadord
Fri Jun 09, 2017 10:41 pm
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 20
Views: 13673

Version 0.7.0

Version 0.7.0 IMPORTANT NOTE: NO BACKWARD REPRODUCIBILITY -- due to improvements in the random number generators it won't be possible to reproduce results of previous versions that required random values, e.g. random spike streams, connections or cell locations. Also, the 'gauss()' method used in st...
by salvadord
Fri Jun 09, 2017 10:41 pm
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 20
Views: 13673

VERSION RELEASES

NetPyNE releases will be published in this topic
by salvadord
Fri Jun 09, 2017 9:58 pm
Forum: NetPyNE
Topic: Stimulating network using spike trains
Replies: 11
Views: 13747

Re: Stimulating network using spike trains

Sorry Ben, didn't realize that feature was in the development branch. I will release a new netpyne version (0.7.0) today, so you just have to upgrade to that one and it should work.
by salvadord
Thu Jun 08, 2017 1:11 pm
Forum: NetPyNE
Topic: Stimulating network using spike trains
Replies: 11
Views: 13747

Re: Stimulating network using spike trains

Hi Ben, Thanks for your kind comments and feedback. To provide a list of predefined spike times as stimuli to the network you can create a population of VecStim and provide the list of spk times directly, e.g.: netParams.popParams['bkg'] = {'cellModel': 'VecStim', 'numCells': 1, 'spkTimes': [1,10,20...
by salvadord
Tue Jun 06, 2017 2:34 pm
Forum: NetPyNE
Topic: Programming and Debugging a declarative language
Replies: 1
Views: 9273

Re: Programming and Debugging a declarative language

Here are some steps to help debug NetPyNE code (which, as mentioned in previous post, is a declarative language): 1) Run first the file containing the NetParams object (e.g. python netParams.py ). From version 0.7.0 onwards, NetPyNE provides error checking (set cfg.checkErrors=True ), indicating any...
by salvadord
Tue May 16, 2017 10:50 pm
Forum: NetPyNE
Topic: Welcome to the NetPyNE Forum!
Replies: 0
Views: 9598

Welcome to the NetPyNE Forum!

Welcome to the NetPyNE Forum! NetPyNE (Network development Python package for NEURON) is a python package to facilitate the development, parallel simulation and analysis of biological neuronal networks using the NEURON simulator. This forum area is your place to receive support about the NetPyNE too...