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My own preference would be to make Erev be the dependent variable and that is what I have done in this implementation of an event-driven synaptic mechanism based on the NMODL code in your first post. I have inserted explanatory comments where this implementation differs from your original code. NEU...

You are experiencing why "available upon reasonable request" is no substitute for requiring model authors to make source code available through a publically accessible online resource, in close temporal proximity to the date of acceptance for publication.

The core issue that bothers me Before proceeding further, it would be useful to read the relevant sections of chapter 7 of The NEURON Book (if you don't have the book, you might want to get this preprint of chapter 7 https://www.neuron.yale.edu/ftp/ted/book/revisions/chap7indexedref.pdf ). As I und...

1) NEURON will first update . . . Not quite. For implementational details and sequence of execution, see chapter 7 of The NEURON Book. If you don't have the book, you might want to pick up this preprint of that chapter https://www.neuron.yale.edu/ftp/ted/book/revisions/chap7indexedref.pdf This thre...

Excellent tips, Robert. Probably will be helpful for many other readers of this thread. Now an important design decision for ipv1313: The values of ecl, ehco3, Pr (the fraction of synaptic conductance that is attributable to hco3), and Erev are not independent of each other, because Erev = Pr * ehco...

No need to apologize. Everybody makes stupid mistakes. Never use euler--it is not suitable for the equations that describe models with the anatomical and biophysical complexities of real neurons, which are stiff and often require a very small dt for stability. cnexp is the NMODL name for NEURON's im...

I want to change the NMODL integration of ODEs from cnexp to sparse Note for others who might read this thread: this change won't do anything useful. Anyone can help about this? The error message points to the line that contains the error. Compare that line with the corresponding line in hh.mod. A ...

Use of pointers to communicate the fact that "a presynaptic spike has occurred" to a synaptic mechanism attached to a postsynaptic cell was state of the art 27 years ago. Since about 20 years ago, the best practice for implementing spike-triggered synaptic transmission has been to use even...

I did not find any parameters or mechanisms to add or change. That's why you need to see the actual source code that those authors used in their simulations. Where did the first figure in your most recent Forum post come from? A simulation on your PC or Mac? If yes, then what you're looking at show...

Aha--Araya's lab just published another article that combines experimentation with modeling that involved the same model cell, so it is quite likely that they will be able to find the source code. Mitchell DE, Miranda-Rottmann S, Blanchard M, Araya R. Altered integration of excitatory inputs onto th...

The first author is not necessarily the "corresponding author" i.e. the one who takes primary responsibility for communications. Depending on the journal, the corresponding author's identity is usually indicated at the beginning of the paper e.g. near the author list or Abstract, or at the...

Avoid Euler

For clear guidance on what integration method to specify in NMODL code, see Integration methods for SOLVE statements in the NEURON Forum's Hot tips area.

Do what you like, but if your time and effort are worth anything, think hard before using this anatomical data in your models. Especially since so much morphometric data is available from NeuroMorpho.org that is not affected by these artifacts. And if you use flawed anatomical data, when it comes ti...

Most of the information appears not to have been updated in years. That's because most of what needed to be documented hasn't changed in decades. Many changes are expected in NEURON version 9, especially metadata features that will be particularly useful for code introspection; this will doubtless ...

That paper would correspond to ModelDB entry 2488 (modeldb.yale.edu/2488, modeldb.science/2488). The associated source code does not include any swc files. The "Overview" page of the ModelDB entry mentions http://www.cnl.salk.edu/~zach/methods.html and http://www.cnl.salk.edu/~zach/ , but ...