Search found 80 matches

by salvadord
Sun Dec 03, 2017 9:13 pm
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 17
Views: 9809

Re: Spike source and target sections

Perhaps the cell is not being imported correctly and those sections don't exist?

Can you share your full code? Either as a link to a repo (eg. github) or zip file to salvadordura@gmail.com

Thanks
by salvadord
Sun Dec 03, 2017 3:17 pm
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 16
Views: 11375

Re: VERSION RELEASES

# Version 0.7.5 https://github.com/Neurosim-lab/netpyne/releases/tag/v0.7.5 - Improved NeuroML conversion support - Make cfg.checkErrors = True by default, but set to False if using multiple cores or batch - Added methods to rename netParams dict keys in a nested format (needed for GUI) - Added anal...
by salvadord
Tue Nov 28, 2017 10:13 am
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 17
Views: 9809

Re: Spike source and target sections

Stefano, The sections must exist in the cell rule in order to be able to connect to them. But if you are importing an existing cell I assume these section will already exist. To target these sections in the connParams rule, you can just use a list of strings e.g. netParams.connParams['A_pop->B_pop']...
by salvadord
Tue Nov 28, 2017 10:01 am
Forum: NetPyNE
Topic: Error: sec had previously been connected to parent sec
Replies: 1
Views: 4161

Re: Error: sec had previously been connected to parent sec

Hi Sergio, Just remove the line: netParams.cellParams['goc'] = goc_cellRule When you use the importCellParams() it already stores the imported rule in netParams, in this case in netParams[‘Golgi_2007’] (since label=‘Golgi_2007’). Therefore you were duplicating the cell rule by storing it in cellPara...
by salvadord
Tue Nov 28, 2017 10:00 am
Forum: NetPyNE
Topic: Error: sec had previously been connected to parent sec
Replies: 1
Views: 4161

Error: sec had previously been connected to parent sec

Received by email: "Hello Salvador, I get this message when I use importCellParams: Notice: <netpyne.cell.CompartCell object at 0x7f74a36621d0>.dend_2(0) had previously been connected to parent <netpyne.cell.CompartCell object at 0x7f74a36621d0>.soma(1) Here's the code: goc_cellRule = netParams.impo...
by salvadord
Mon Nov 27, 2017 12:20 pm
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 17
Views: 9809

Re: Spike source and target sections

Hi Stefano, Thanks for for your question, and for trying out NetPyNE. Yes, it is possible to do what you are asking: 1) you can set the source of the action potential by simply adding the 'spikeGenLoc' ("spike generation location") to that section in the cell rule; e.g. say you want it at a section ...
by salvadord
Mon Nov 27, 2017 12:03 pm
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 17
Views: 9809

Spike source and target sections

Question received by email: "Hi Salvador. I have just started using your Netpyne framework, to test the possibility to build a network with "particular characteristics". I was able to import two of my Python/neuron HH models and to define the code to see their basic behaviour, with or without a curr...
by salvadord
Sun Nov 26, 2017 7:38 pm
Forum: NetPyNE
Topic: How to set initial voltage of simulation
Replies: 6
Views: 11459

Re: How to set initial voltage of simulation

NetPyNE is intended as a declarative language where all specifications can potentially be stored in json format, that's why it uses a different syntax from the procedural NEURON language. In many cases, especially for complex network models, the amount of code required will be less in NetPyNE. For e...
by salvadord
Sun Nov 19, 2017 8:26 pm
Forum: NetPyNE
Topic: Save/load state
Replies: 1
Views: 6621

Re: Save/load state

Hi Andrew, Unfortunately, the save/load state feature in netpyne is still in the TO DO list, see here: https://github.com/Neurosim-lab/netpyne/issues/172 -- if you have a nice code example from your model you can add it as a comment to the github issue and that might help with the implementation. Th...
by salvadord
Sun Nov 19, 2017 10:53 am
Forum: NetPyNE
Topic: Save/load state
Replies: 1
Views: 6621

Save/load state

Question received by email from Andrew Knox: "One other question. Ideally I’d like to be able to run the model for ~10 seconds to let it come to steady state, then save that state and run a number of simulations with different parameters from that point in time. What’s the best way to do this? I had...
by salvadord
Fri Nov 17, 2017 6:45 pm
Forum: NetPyNE
Topic: C++ memory? error, using NetPyNE
Replies: 10
Views: 14475

Re: C++ memory? error, using NetPyNE

what's the script to generate the mod files from those channels?

I'll email you anyway, thanks.
by salvadord
Fri Nov 17, 2017 6:08 pm
Forum: NetPyNE
Topic: C++ memory? error, using NetPyNE
Replies: 10
Views: 14475

Re: C++ memory? error, using NetPyNE

thanks. Now I'm getting a bunch of these messages: "Id not found in <neuroml> element. All ids: ['CavL', 'CavN', ... ]" and then error: "ValueError: argument not a density mechanism name." I tried nrnivmodl on the mod files in root folder and then symlinking x86_64 folder in /NeuroML2/network but th...
by salvadord
Thu Nov 16, 2017 9:31 pm
Forum: NetPyNE
Topic: C++ memory? error, using NetPyNE
Replies: 10
Views: 14475

Re: C++ memory? error, using NetPyNE

Getting this error: IOError: ``HippocampalNet_scale500_oc.net.nml.h5`` does not exist

maybe need to add that file to the repo?

thanks
by salvadord
Tue Nov 14, 2017 6:26 pm
Forum: NetPyNE
Topic: C++ memory? error, using NetPyNE
Replies: 10
Views: 14475

Re: C++ memory? error, using NetPyNE

Hmm the spike times don't really use up that much space so can probably them from all cells. Cell traces however do require more memory, so the 40 traces might be causing the problem. Can you point me again to the repo with code you are running and I'll try myself to see if can find any issues? than...
by salvadord
Wed Oct 25, 2017 11:17 am
Forum: NetPyNE
Topic: C++ memory? error, using NetPyNE
Replies: 10
Views: 14475

Re: C++ memory? error, using NetPyNE

Hi András, Thanks for your question. We had a similar post recently: https://www.neuron.yale.edu/phpBB/viewtopic.php?f=45&t=3727&sid=30e51a901a2f8d0a62f85ee9ab8424ad The conclusion from that post was that if the amount of data to be gathered and the number of cores used is above a threshold, the mpi...