Guides
These guides cover the core concepts you need to build and simulate models with NEURON. Start with What is NEURON? for an overview, or jump to How to get started with NEURON if you are ready to dive in.
What is NEURON?
An overview of NEURON’s capabilities, design philosophy, and advantages for computational neuroscience.
How to Get Started
Installation, first steps, key resources, and pointers to tutorials and the discussion board.
Units in NEURON
Default units for time, voltage, current, length, and
conductance — plus how to use neuron.units.
FAQ
Answers to frequently asked questions about running, troubleshooting, and configuring NEURON.
Getting Started
- What is NEURON?
- How to get started with NEURON
- Biology Modeling FAQ
- How do I work with neuron morphologies?
- How do I simulate a current clamp pulse experiment?
- How do I simulate a current clamp with non-pulse behavior?
- How do I make cytosolic concentrations change in response to ion channel activity?
- How do I make cytosolic concentrations diffuse and respond to ion channel activity?
- Units used in NEURON
- Frequently asked questions (FAQ)
- Now that I’ve installed NEURON, how do I run it?
- What’s the best way to learn how to use NEURON?
- How do I create a NEURON model?
- Help! I’m having a hard time implementing models!
- Why can’t NEURON read the text file (or
hocfile) that I created? - How do I print a hard copy of a NEURON window?
- How do I plot something other than membrane potential?
- How do I save and edit figures?
- I’ve used the NEURON Main Menu to construct and manage models. How can I save what I have done?
- What is a ses (session) file? Can I edit it?
- How do I use NEURON’s tools for electrotonic analysis?
- Why should I use an odd value for nseg?
- What’s a good stretegy for specifying nseg?
- How do I change the background color used in NEURON’s shape plots and other graphs?
- How do I change the color scale used in shape plots?
- I see an error message that says … procedure too big in ./foo.hoc …
- Where can I find examples of mod files?
- How do I compile mod files?
- I can’t get mod files to compile.
- I installed a new version of NEURON, and now I see error messages like this: ‘mecanisms fooba needs to be re-translated. its version 5.2 “c” code is incompatible with this neuron version’.
- Is there a list of functions that are built into NMODL?
- Is there a list of functions that are built into hoc?
- What units does NEURON use for current, concentration, etc.?
- When I type a new value into a numeric field, it doesn’t seem to have any effect.
- What is the difference between SEClamp and VClamp, and which should I use?
- SEClamp and IClamp just deliver rectangular step waveforms. How can I make them produce an arbitrary waveform, e.g. something that I calculated or recorded from a real cell?
- I just want a current clamp that will deliver a sequence of current pulses at regular intervals. Vector play seems like overkill for this.
- I want a current clamp that will generate a pulse when I send it an event, or that I can use to produce pulses at precalculated times.
- I have a set of recorded or calculated spike times. How can I use these to drive a postsynaptic mechanism?
- How can I read data from a binary PClamp file?
- How do I exit NEURON? I’m not using the GUI, and when I enter ^D at the oc> prompt it doesn’t do anything?
- Is there a list of functions that are built into NEURON?