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The ODE for each segment is of the form transmembrane capacitive current + transmembrane ionic current = sum of all currents arriving in the segment from adjacent segments + sum of all currents that enter the segment from all point processes that generate currents Notice that current in these equati...

The primary utility of multisplit is to achieve load balance in network simulations, and that is useful only when the network contains a very few model cells that are very large. Otherwise the performance boost will not be worth the programmer's effort required to restructure your model. Few single ...

Runtime depends on model complexity. A crude but effective measure of complexity is the total number of ODEs. For every segment there is one ODE for the cable equation, plus one ODE for each state variable of every mechanism associated with that segment that requires numerical integration. This incl...

About this Forum: If you need to paste code, be sure to surround it with the proper markup (that's what the < / > formatting button is for). Otherwise things like leftsquarebracket i rightsquarebracket will be treated as formatting instructions (interpreted as "italic"). Here's how to fix ...

I asked because DBS protocols use biphasic, charge-balanced waveforms. Vector play works for arbitrary waveforms. If the conductive medium is nondispersive ("purely resistive"), then the time course of extracelluar potential vx(x,y,z) will be of the form A(x,y,z)*f(t) where f is a function...

Haven't been much help yet--you've done all the work so far. Implementing stimulation will be easy if you only need a single rectangular pulse--the IClamp class will do for that. But what if your stimulus current should have a more complex time course, e.g. two or more monophasic rectangular pulses,...

To provide specific advice, I will have to know what you're trying to do. All that is clear from the example code is that 1. it assumes that soma2 and dend2 have the same nseg value. This is unlikely to be true. 2. it assumes that this nseg value changes on every pass through the "for seg in se...

To give specific advice, I'll have to reproduce the error for myself. Can you email the mod file in question to ted dot carnevale at yale dot edu?

I have 100's of ion channel mechanisms and i would like to be able to choose which ones I insert in my model This isn't hard. In your model setup code use conditional statements code whose execution is controlled e.g. by command line switches or statements in a text file. That way you'll have a tex...

Given a point neuron, extracellular stimulation can be represented by a current source attached to the model cell, but the question then is: how to determine the amplitude and time course of that current? Amplitude is clearly a function of assumed location of the model cell in the conductive medium,...

Regardless of the programming language, it is generally not a good idea to embed magic numbers (numerical constants) in code. Instead, it is best to use a variable whose value will not be changed during a simulation. In NMODL you could define a symbolic constant by declaring its name and assigning a...

It's not a good idea to do that, unless you enjoy setting booby traps for yourself and anyone who tries to reuse your code. Specification of the mechanisms used by a model should be made by hoc or Python statements.

Are you asking about a statement in a hoc or Python file, or in a mod file?

General comments: NEURON is a great tool, but should the project's emphasis be on the tool or on some scientific question? Examples of the former would focus on topics related to applied math (e.g. efficient methods for solving large sets of differential equations) or computer science (dealing with ...

The difference between what you expected to happen, and what actually happened, has nothing to do with software, let alone software bugs. You have rediscovered a consequence of Maxwell's equations and Gauss's law. Suggested reading in this Forum: https://www.neuron.yale.edu/phpBB/viewtopic.php?p=107...