Search found 80 matches

by salvadord
Wed Jul 19, 2017 10:09 am
Forum: NetPyNE
Topic: NEURON: section stack overflow
Replies: 5
Views: 10025

Re: NEURON: section stack overflow

There were some bug fixes in the import code in v0.7.1 so it might have messed something. Could you please share the FRcellTemplate.hoc so I can try it out myself? thanks
by salvadord
Wed Jul 19, 2017 9:22 am
Forum: NetPyNE
Topic: Adding uniform Synapses on 3D structure Cell
Replies: 4
Views: 9004

Re: Adding uniform Synapses on 3D structure Cell

Hi Mohamed, thanks for your message. By default, when synsPerConn > 1, netpyne distributes synapses uniformly based on dendritic length in um (sums up all dend lengths and places syns at equally spaced intervals). However, it does not take into account section area. However, if you want to place 1 s...
by salvadord
Tue Jul 11, 2017 9:30 pm
Forum: Modeling networks
Topic: possibility with constructing large-scale network
Replies: 2
Views: 5648

Re: possibility with constructing large-scale network

Another option that you could consider is using NetPyNE (a tool for NEURON), which allows you to define connectivity rules using a high-level declarative format -- see this post for more information: viewtopic.php?f=45&t=3670
by salvadord
Mon Jul 10, 2017 11:08 am
Forum: NetPyNE
Topic: Best Way to Modify Stimulation Source
Replies: 5
Views: 10344

Re: Best Way to Modify Stimulation Source

The error you are getting seems to be happening during the creation of one of the Netstim/Vecstim populations, in particular something related to the 'rate' parameter. Note that after calling the modifyStims() func if you want to rerun the sim, you need to call sim.simulate() and not sim.createSimul...
by salvadord
Sat Jul 08, 2017 3:03 pm
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 16
Views: 11375

Version 0.7.1

# Version 0.7.1 https://github.com/Neurosim-lab/netpyne/releases/tag/v0.7.1 - Updates and bug fixes of NeuroML importer/exporter - Added missing error checks and made error messages clearer - Added warning when point process mechanism (eg. VecStim) required for pop is not found - Added 'ylim' option...
by salvadord
Fri Jul 07, 2017 11:16 pm
Forum: NetPyNE
Topic: Limit to network size?
Replies: 1
Views: 8626

Re: Limit to network size?

Hi Ben, Thanks for encouragement, great to hear NetPyNE is useful. I am currently running simulations of a model with ~10k cells, where ~2k have 700+ compartments, and the rest ~2-6 compartments. 1 sec of simulation runs in ~1h using 48 cores. There is no limitation per se in the network size using ...
by salvadord
Fri Jul 07, 2017 10:59 pm
Forum: NetPyNE
Topic: Best Way to Modify Stimulation Source
Replies: 5
Views: 10344

Re: Best Way to Modify Stimulation Source

Sorry for the delayed response, for some reason I wasn't getting email notifications for the forum posts. modifyStims should work for what you want to do, but please share your code and explain exactly what you want to modify and I'll check. Also note that modify funcs only make sense if the network...
by salvadord
Fri Jul 07, 2017 10:49 pm
Forum: NetPyNE
Topic: AttributeError:'module' object has no attribute 'allSimData'
Replies: 3
Views: 9098

Re: AttributeError:'module' object has no attribute 'allSimD

Sorry for the delayed response, for some reason I wasn't getting email notifications for the forum posts. The variable sim.allSimData only exists on node 0, so to solve your issue you just need to put your last lines of code within an if condition that makes sure only node 0 executes them : if sim.r...
by salvadord
Tue Jun 20, 2017 3:24 pm
Forum: NetPyNE
Topic: AttributeError:'module' object has no attribute 'allSimData'
Replies: 3
Views: 9098

Re: AttributeError:'module' object has no attribute 'allSimD

I tried it on the prev code you sent me and it worked ok: Cells: 103 Connections: 3231 (31.37 per cell) Spikes: 0 (0.00 Hz) Simulated time: 0.5 s; 2 workers Run time: 0.58 s Done; saving time = 0.00 s. Plotting raster... No spikes available to plot raster Plotting recorded cell traces ... Plotting 2...
by salvadord
Mon Jun 19, 2017 11:19 pm
Forum: NetPyNE
Topic: Unable to save data as a MATLAB file
Replies: 2
Views: 8862

Re: Unable to save data as a MATLAB file

Thanks for your message. Unfortunately I hadn't tested saving to .mat after the latest changes and there was a small bug -- I fixed it and pushed to the development branch in github: https://github.com/Neurosim-lab/netpyne/tree/development . It will be included in the next version release, but if yo...
by salvadord
Thu Jun 15, 2017 11:12 pm
Forum: NetPyNE
Topic: Issue stimulating cells that I imported
Replies: 2
Views: 9069

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: 16
Views: 11375

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: 9
Views: 10617

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: 9
Views: 10617

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: 16
Views: 11375

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...