Search found 84 matches

by salvadord
Mon Aug 14, 2017 11:29 am
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 19
Views: 12953

Re: VERSION RELEASES

Version 0.7.2 https://github.com/Neurosim-lab/netpyne/releases/tag/v0.7.2 - Improved NeuroML importing/exporting - Added error checking for simConfig - Added popColors option to plotSpikeHist and plotRatePSD - Added support to load params, cfg, net and simData from .mat files - Made root section (wi...
by salvadord
Mon Jul 24, 2017 7:28 pm
Forum: NetPyNE
Topic: NEURON: section stack overflow
Replies: 5
Views: 10906

Re: NEURON: section stack overflow

You can use the github development version (many of our lab members do it this way so they always have access to the latest features): 1) uninstall the pip version: pip remove netpyne 2) clone the github version: git clone https://github.com/Neurosim-lab/netpyne.git 3) make sure you are in the devel...
by salvadord
Mon Jul 24, 2017 6:07 pm
Forum: NetPyNE
Topic: Trouble with sim.loadSimData()
Replies: 1
Views: 9408

Re: Trouble with sim.loadSimData()

Hi, indeed loading from .mat wasn't yet implemented -- only load from .pkl and .json was available. However, I have just added this feature and pushed to the github development branch. If you want to resimulate or reanalyze results etc. you will also need the net , so probably best to use sim.loadAl...
by salvadord
Mon Jul 24, 2017 12:51 pm
Forum: NetPyNE
Topic: NEURON: section stack overflow
Replies: 5
Views: 10906

Re: NEURON: section stack overflow

For some reason when deleting sections after importing the cell they were accumulating on the stack, so had to use h.pop_section() to avoid error.

I have pushed the changes to the github "development" branch and tested your code successfully. I will release fix in next version.
by salvadord
Wed Jul 19, 2017 10:09 am
Forum: NetPyNE
Topic: NEURON: section stack overflow
Replies: 5
Views: 10906

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: 9885

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: 6032

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: 11326

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: 19
Views: 12953

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: 9164

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: 11326

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: 9853

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: 9853

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: 9503

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: 9617

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...