www.neuron.yale.edu

Version 0.7.3 https://github.com/Neurosim-lab/netpyne/releases/tag/v0.7.3 - Option to create section lists based on y displacement from soma (addCellParamsSecList) - Converted popParams, cellParams etc to object of their own class and added method to set param - Added 'disynapticBias' option to incr...

Yes, please share your code; also any info on the machine/software you are running this on would be useful -- e.g. OS, number of cores, NEURON version, netpyne version, etc. We have tested netpyne simulations on up to 512 cores on supercomputers, but I will check running your code on 20+ cores and l...

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...

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...

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...

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.

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

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...

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

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...

# 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...

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 ...

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...

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...

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...