www.neuron.yale.edu

.bash_profile (and sometimes .bashrc) is often used as a place to add things to the PATH on login. Read those to find out where and how NEURON and InterViews were being added to the PATH under bash. Read the documentation of zsh to figure out what you have to do now.

Is it better to use Python If you're already familiar with Python, use Python. If you're already familiar with hoc and don't know much about Python, this would be a good time to switch to Python, especially if you will be doing much programming. If you don't know much (or any) Python or hoc, this i...

What was the fix?

In NetCon can we pass array elements (time of spike) as a source variable No, but you would have discovered this fact by reading the Programmer's Reference documentation of the NetCon class. Presumably you have some precalculated spike times that you would like to use. Download and expand the gzipp...

My own two bits: Regarding your first question, don't worry about it. The comment is a comment, not a warning. Adaptive integration is generally not useful in either serial or parallel simulations of networks, so you won't be using the CVODE integrator. And NEURON won't use IDA unless (1) its analys...

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The error message SubsetDomainIterator is not a template in /tmp/nrnLyc69M near line 12111 primary_apical_list_x = new SubsetDomainIterator(primary_apical_list, 0, 0, 0) suggested that the code that defines the SubsetDomainIterator class was not being executed. The SubsetDomainIterator class is a he...

Thanks for posting an excellent question.

ODEs can be implemented in mod files. A POINT_PROCESS can be used to add a bag of equations to NEURON. State variables are automatically RANGE variables, visible to hoc and Python. ASSIGNED variables need to be specified as RANGE or GLOBAL to be visible to hoc and Python; RANGE is the more flexible ...

Zip up the files needed to reproduce the error and email them to ted dot carnevale at yale dot edu and I'll let you know what I find out. What version of NEURON are you running (what is the first line that the interpreter prints out when NEURON starts), and what version of Mac OS (or whatever the co...

Session files contain code that recreates GUI objects, such as graphs and panels. Loading a session file will recreate the GUI objects that were saved to it. Loading a session file will not launch a simulation. To launch a simulation you must execute a command such as run() or continuerun() (h.run()...

What happens if you launch a simulation?

Try it.

Indeed there is. It's the paper cited under the heading Parallel communication in NEURON in the 4th "ball and stick" tutorial-- Hines M.L. and Carnevale N.T. Translating network models to parallel hardware in NEURON, Journal of Neuroscience Methods 169 (2008) 425–455 The citation in the tutorial has...

"How do I collect data . . . " Use the Vector class's record() method. Documented in the Programmer's Reference. As I will be running NEURON on a supercomputer . . . Make friends with your local tech support people. Work through the "Scripting NEURON with Python" tutorial (see link on the Documenta...