www.neuron.yale.edu

Hi Alexandra, I just tested the model and I was able to instantiate the izh2003 cell. I'm on Mac OS and what I did is just compile the mod files and then run the simple.py script. I noticed you are using hoc code, so just curious to know if you tried the python version (simple.py) and if that one wo...

Hi Ziemowit, Thanks for your email and interest in the tool! Yes, everything you mention is possible in netpyne and we actually have a closely related example, where we control a simple virtual arm using RL and STDP: https://github.com/Neurosim-lab/netpyne/tree/development/examples/RL_arm Please hav...

Arpit, The NetPyNE-based version of the HNN network model is available here and ready to use: https://github.com/jonescompneurolab/hnn/tree/netpyne/netpyne The NetPyNE-UI is available online here: www.netpyne.org/gui and here: http://netpyne.opensourcebrain.org/ . A new version of the online NetPyNE...

# Version 0.9.5 https://github.com/Neurosim-lab/netpyne/releases/tag/v0.9.5 - Print start and end date/time - Avoid removing batch folder so can rerun and complete batch simulations - Added loadBalance option to print individual node computer times - Initialize hoc events recursivley to reduce event...

Hi, sorry for the delay. We plan to add support so you can add stims to point processes. In the meantime, you are quite right that those are the main possible approaches: 1) This is the one we've used in the past; you can see an example here: https://github.com/ceciliaromaro/PD_in_NetPyNE/blob/maste...

# Version 0.9.4 https://github.com/Neurosim-lab/netpyne/releases/tag/v0.9.4 - Added option to avoid creating connections with weight=0 - Made recording of dipoles optional with attribute cfg.recordDipoles - Rotated conn matrix x-axis labels so can fit large matrices - Added 'removeWeightNorm' argume...

Sorry for the delay responding. To change the reversal potential of ions, you can use eg. cellRule['secs']['soma']['ions']['na'] = {'e': 60} similarly for the internal and external concentrations of the ion you can use: cellRule['secs']['soma']['ions']['na'] = {'i': 15, 'o': 150 } Apologies, this is...

# Version 0.9.3 https://github.com/Neurosim-lab/netpyne/releases/tag/v.0.9.3 - Improved conversion from SONATA format, including 300 biophys cell example - Added saveCellConns, pt3dRelativeToCellLocation and invertedYCoord cfg options - Added lineWidth as argument of plotRatePSD() and plotLFP() - Mo...

# Version 0.9.2 https://github.com/Neurosim-lab/netpyne/releases/tag/v0.9.2 - Support for saving simulation at intervals - Improved Python cell template import so can read section names from a Python list or dict of sections - Fixed replicability issue across different number of cores when using 'co...

Hey Cristoph, in case useful, you can also use this command to reload the mod files: `neuron.load_mechanisms(folder_with_mod)` and before that you could call the `nrnivmodl` command from python to recompile them. Never tried this but I think it should work.

salva

Sorry, multisplit is not currently supported in NetPyNE, but I have added it to the list of features to add: https://github.com/Neurosim-lab/netpyne/issues/399 You could try to create the network in NetPyNE, then set up the multisplit, and run the sim via NetPyNE, but I haven't tried this, and it co...

Thanks Krishna. I need the GrCTemp.py to actually test the model. You can paste it here or email to salvadordura@gmail.com

Hi Krishna,

Could you please share your code so we can look at the details? If it's not too long you can post it here. Alternatively you can share the link to a repo (eg. in Github) or send it to me by email (salvadordura@gmail.com).

Thanks

Hi Krishna, Sorry that you are having issues with the GUI. We are about to release a new version within the next couple of weeks that should be easier to install and use. If you sign up to the mailing list ( www.netpyne.org/mailing ) you will get an email when it is released. If you still have issue...

Hi, The tut8_analysis.py was just provided as an example of how to analyze output data. It may not work with all models. The reason that df.popRates might be missing is that you need to set cfg.printPopAvgRates = True -- this records the avg population rates and stores them in simData. If you want t...