Search found 86 matches
- Wed Aug 30, 2017 8:18 pm
- Forum: NetPyNE
- Topic: VERSION RELEASES
- Replies: 28
- Views: 50766
Re: VERSION RELEASES
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...
- Tue Aug 15, 2017 11:18 pm
- Forum: NetPyNE
- Topic: Issue running model with 20 cores or more
- Replies: 7
- Views: 21461
Re: Issue running model with 20 cores or more
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...
- Mon Aug 14, 2017 11:29 am
- Forum: NetPyNE
- Topic: VERSION RELEASES
- Replies: 28
- Views: 50766
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...
- Mon Jul 24, 2017 7:28 pm
- Forum: NetPyNE
- Topic: NEURON: section stack overflow
- Replies: 5
- Views: 21288
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...
- Mon Jul 24, 2017 6:07 pm
- Forum: NetPyNE
- Topic: Trouble with sim.loadSimData()
- Replies: 1
- Views: 16224
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...
- Mon Jul 24, 2017 12:51 pm
- Forum: NetPyNE
- Topic: NEURON: section stack overflow
- Replies: 5
- Views: 21288
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.
I have pushed the changes to the github "development" branch and tested your code successfully. I will release fix in next version.
- Wed Jul 19, 2017 10:09 am
- Forum: NetPyNE
- Topic: NEURON: section stack overflow
- Replies: 5
- Views: 21288
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
- Wed Jul 19, 2017 9:22 am
- Forum: NetPyNE
- Topic: Adding uniform Synapses on 3D structure Cell
- Replies: 4
- Views: 17734
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...
- Tue Jul 11, 2017 9:30 pm
- Forum: Modeling networks
- Topic: possibility with constructing large-scale network
- Replies: 2
- Views: 12599
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
- Mon Jul 10, 2017 11:08 am
- Forum: NetPyNE
- Topic: Best Way to Modify Stimulation Source
- Replies: 5
- Views: 19347
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...
- Sat Jul 08, 2017 3:03 pm
- Forum: NetPyNE
- Topic: VERSION RELEASES
- Replies: 28
- Views: 50766
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...
- Fri Jul 07, 2017 11:16 pm
- Forum: NetPyNE
- Topic: Limit to network size?
- Replies: 1
- Views: 15708
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 ...
- Fri Jul 07, 2017 10:59 pm
- Forum: NetPyNE
- Topic: Best Way to Modify Stimulation Source
- Replies: 5
- Views: 19347
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...
- Fri Jul 07, 2017 10:49 pm
- Forum: NetPyNE
- Topic: AttributeError:'module' object has no attribute 'allSimData'
- Replies: 3
- Views: 16801
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...
- Tue Jun 20, 2017 3:24 pm
- Forum: NetPyNE
- Topic: AttributeError:'module' object has no attribute 'allSimData'
- Replies: 3
- Views: 16801
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...