www.neuron.yale.edu

@ted, is there some documentation or an example of how to implement multithreaded simulation without the NEURON GUI?

I have a single cell model with 2500 or so compartments that I would like to speed up. It is implemented using BMTK's bionet, which runs NEURON on the back end. I was reading some older posts and understand it's possible to parallelize a single cell, but that development time is substantial. Is that...

Hey all, I have been contributing to BMTK (https://github.com/alleninstitute/bmtk), which uses NEURON to model biophysical neural networks. I talked briefly with Ted at SfN about this issue I've been having implementing gap junctions so thought I would formalize that here to see if anyone can help. ...

Well I tried your installation commands and it worked! I'm not sure if installing in /oasis/scratch/ instead of $HOME was the cure or something else. Thanks so much!

I don't think the Anaconda installation is available to others, it is just in my home directory. It is the install available here (I just accepted all the defaults): wget https://repo.anaconda.com/archive/Anaconda2-2018.12-Linux-x86_64.sh bash Anaconda2-2018.12-Linux-x86_64.sh Here's this: $ ldd /ho...

The .so file in /home/latimerb/utils/nrn/lib/python/neuron/ is hoc.so. Yes, which python is anaconda and yes pwd was /home/latimerb/utils/nrn $ which python ~/anaconda2/bin/python In config.status, it says: S["NRNPYTHON_LIBS"]="-lnrnpython -L/home/latimerb/anaconda2/lib -lpython2.7 -l...

The file in <prefix>lib/python/neuron is called hoc.so. Sorry, I pasted the wrong error using a different configuration. This is the error when I do the config like this: $ ./configure --prefix=`pwd` --without-iv --with-nrnpython=`which python` --with-paranrn $ make $ make install $ export PYTHONPAT...

As I progressed I realized it would be easier to just download Anaconda 2.7 to my home directory and use this as my python distribution since it automatically installs other packages I need. So I deleted everything and installed Anaconda 2.7 (https://repo.anaconda.com/archive/Anaconda2-2018.12-Linux...

Using Python 2.7 (module load python) seems to have fixed the issue. Now I don't need to use any extra configuration parameters. Here are the installation commands for (mostly my own) future reference: module load python mkdir utils cd utils wget https://neuron.yale.edu/ftp/neuron/versions/v7.6/7.6....

Thanks Michael. I tried your suggestions but still face the same issue. Here are the commands I used for installation: wget https://neuron.yale.edu/ftp/neuron/versions/v7.6/7.6.5/nrn-7.6.5.tar.gz tar xzf nrn-7.6.5.tar.gz rm nrn-7.6.5.tar.gz mv nrn-7.6 nrn cd nrn ./configure --prefix=`pwd` --without-...

Hi all, I have installed NEURON + Python on many different systems but for some reason am hitting a wall while trying to do "import neuron" on the Comet supercomputer (CentOS 6.10). I followed the instructions at https://neuron.yale.edu/neuron/download/compile_linux and am downloading NEUR...

Hi Ted, I believe you may be right.. I had assumed they were using the GUI because they have multiple .ses files here: https://github.com/AllenInstitute/biophys_optimize/tree/master/biophys_optimize/passive But upon closer inspection, it looks like they do create some reference to h.MulRunFitter() h...

Hi all, I'm trying to adopt the Allen Institute's single-cell model creation workflow: https://www.nature.com/articles/s41467-017-02718-3 However, during the "passive fitting" stage of the process (i.e. determining the optimal capacitance and leak conductance for the model), they use NEURO...

This is awesome, thanks for the reply!

Awesome, thank you!