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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? ...

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

I'll email you anyway, thanks.

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 /Neu...

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

maybe need to add that file to the repo?

thanks

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...

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,...

I added a short tutorial on running batch simulations: http://www.neurosimlab.org/netpyne/tuto ... tutorial-8

Hope it helps... and please let me know if you have any more questions.

Hi Sergio, thanks for using the tool and asking this useful question! If you just want to explore parameters manually, you can modify them in simConfig and netParams and then just change 'simLabel' (in simConfig) so the output is saved to different output files. However, NetPyNE has a built-in Batch...

FYI, I tested your full model using 24 cores and also got an mpi error during gathering for 276sec and 50sec sims; but it ran ok for 10sec sims. So seems to be related to a memory issue when gathering too much output data (long sims) from many cores. If you definitely need those long simulation time...

I'm looking at this issue now, sorry for the delay. Tried running your code but its missing LA_Template.py -- can you please send the missing file (or a full updated version of your model) ? I also noticed that you are trying to run the simulation for 276 seconds, which is a relatively long time -- ...

# Version 0.7.4 https://github.com/Neurosim-lab/netpyne/releases/tag/v0.7.4 - Added polarity param to analysis.plotEPSPAmp() - Added sim.gitChangeset() function and store netpyne_changeset in every output file - Added function ijsonLoad() to load faster and save tags conns to json - Fixed bug in con...

Ah ok! Problem is you are calling the plotShape() function before even creating the network. It should go after sim.createSimulateAnalyze() Note netpyne is a declarative language so nothing gets executed/created until you call sim.createSimulateAnalyze(). Alternatively, you can include plotShape in ...

So I assume you followed all the steps in prev post? Can you please run python and include here the output of import netpyne; print netpyne.__file__ ? Then go to whatever folder shows up and include here the output of git branch and git log -1 ? We need to make sure the development version of netpyn...

1) Remove any current version via pip uninstall netpyne 2) cd parent_folder_where_you_want_netpyne_repo 3) git clone https://github.com/Neurosim-lab/netpyne.git 4) cd netpyne 5) git checkout developmnet 6) pip install -e . pip will add a symlink in the default python packages folder to the cloned ne...

Hi Vittorio, I've updated the plotShape documentation and added some examples: http://www.neurosimlab.org/netpyne/reference.html#analysis-related-functions At the moment its not possible to create a movie via netpyne (will add to github list of requests), but you can of course generate multiple snap...