Search found 6139 matches

by ted
Wed Mar 29, 2023 7:16 pm
Forum: NEURON + Python
Topic: Null pointer error when trying to access the pointer through python
Replies: 4
Views: 60

Re: Null pointer error when trying to access the pointer through python

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...
by ted
Wed Mar 29, 2023 4:11 pm
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 57
Views: 2486

Re: pyramidal spine-neck EPSPs

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.
by ted
Wed Mar 29, 2023 12:40 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Using NMODL integration of ODEs: sparse
Replies: 5
Views: 76

Re: Using NMODL integration of ODEs: sparse

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...
by ted
Wed Mar 29, 2023 11:41 am
Forum: Adding new mechanisms and functions to NEURON
Topic: What is the numeric integration method of cnexp?
Replies: 2
Views: 41

Re: What is the numeric integration method of cnexp?

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...
by ted
Wed Mar 29, 2023 1:30 am
Forum: NEURON + Python
Topic: Null pointer error when trying to access the pointer through python
Replies: 4
Views: 60

Re: Null pointer error when trying to access the pointer through python

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...
by ted
Tue Mar 28, 2023 11:03 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Using NMODL integration of ODEs: sparse
Replies: 5
Views: 76

Re: Using NMODL integration of ODEs: sparse

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...
by ted
Mon Mar 27, 2023 10:58 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Using NMODL integration of ODEs: sparse
Replies: 5
Views: 76

Re: Using NMODL integration of ODEs: sparse

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 ...
by ted
Mon Mar 27, 2023 1:15 am
Forum: NEURON + Python
Topic: Null pointer error when trying to access the pointer through python
Replies: 4
Views: 60

Re: Null pointer error when trying to access the pointer through python

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...
by ted
Sat Mar 25, 2023 4:54 pm
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 57
Views: 2486

Re: pyramidal spine-neck EPSPs

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...
by ted
Thu Mar 23, 2023 11:35 am
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 57
Views: 2486

Re: pyramidal spine-neck EPSPs

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...
by ted
Thu Mar 23, 2023 11:23 am
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 57
Views: 2486

Re: pyramidal spine-neck EPSPs

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...
by ted
Mon Mar 20, 2023 8:43 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Current NMODL Best Practices
Replies: 3
Views: 53

Re: Current NMODL Best Practices

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.
by ted
Mon Mar 20, 2023 8:38 pm
Forum: Anatomically detailed models
Topic: Segmentation violation error in swc
Replies: 4
Views: 79

Re: Segmentation violation error in swc

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...
by ted
Mon Mar 20, 2023 4:17 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Current NMODL Best Practices
Replies: 3
Views: 53

Re: Current NMODL Best Practices

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 ...
by ted
Mon Mar 20, 2023 3:23 pm
Forum: NEURON + Python
Topic: Unbounded Membrane Voltage Increase
Replies: 5
Views: 236

Re: Unbounded Membrane Voltage Increase

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 ...