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Compile .mod files with with (specify path after to compile specific mod files): nrnivmodl Check units with (nrnivmodl does not check unit consistency): modlunit file.mod Meaning of various NMODL keywords RANGE – varies with position (0-1) on a section. Read/set with section.var or section(0.5).var. If section.nseg > 1: section(0.5).var can have a different value than … Continue reading NEURON NMODL/MOD File Cheat Sheet

Often, I will quickly run a simulation test just using the NEURON GUI. However, once I’m ready to script the model and run from Python, it can be quite the hassle to figure the Python command(s) that are behind the actions I performed with the mouse. Luckily, there is a quick method do to that: … Continue reading How to find the command behind any NEURON GUI button

If you have unit tests or code coverage metrics enabled on your GitHub project that uses the NEURON simulator and you want Travis CI perform those automatically, then you’ll need a Travis CI YAML file that will install NEURON before running the tests. The script below is essentially a pure script version of the manual … Continue reading Tutorial: Using NEURON simulator with Python and Travis CI

I have recently found myself having to pour over 100’s of reconstructions of neurons from http://NeuroMorpho.org and make small changes before I can analyze them further. I needed a free tool that could: a) let me quickly preview the contents and b) make changes to the SWC files (e.g. move some branches around, set/change node … Continue reading Tools for editing SWC files (neuron morphology)