Search found 6352 matches
- Fri Oct 04, 2024 10:31 am
- Forum: Anatomically detailed models
- Topic: Determining distance from soma along apical dendrite
- Replies: 7
- Views: 1399
Re: Determining distance from soma along apical dendrite
You're welcome. Many of the old GUI tools are quite powerful, and particularly useful for interactive exploration of model properties and simulation results in a way that complements Python's powerful introspection features.
- Thu Oct 03, 2024 4:04 pm
- Forum: Anatomically detailed models
- Topic: Determining distance from soma along apical dendrite
- Replies: 7
- Views: 1399
Re: Determining distance from soma along apical dendrite
You're almost there. I bet you forgot to declare that cell is an objref. Easy to do, especially if you're comfortable with Python which has dynamic typing. Just to make sure, I ran a couple of tests myself. Over the past couple of days I have been switching from CentoOS 7 to Rocky Linux 9, and as of...
- Sun Sep 29, 2024 1:13 pm
- Forum: Anatomically detailed models
- Topic: Determining distance from soma along apical dendrite
- Replies: 7
- Views: 1399
Re: Determining distance from soma along apical dendrite
Import3d won't do this. NEURON's InterViews based GUI has a "Section Parameters viewer" tool (AKA "shape name" tool) that is specifically designed for interactive browsing of a model cell's sections and segments. NEURON Main Menu toolbar / Tools / Distributed Mechanisms / Viewers...
- Sun Sep 29, 2024 12:30 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Updating the derivative in a NET_RECEIVE block
- Replies: 1
- Views: 97
Re: Updating the derivative in a NET_RECEIVE block
In NMODL the assignment statement foo = bar() evaluates the value of bar() at the instant when the statement is executed, and passes that to foo. It does not make foo an alias for bar. If you want the value of foo to be calculated from function f0() when control variable c == 0, and from function f1...
- Thu Sep 26, 2024 11:20 pm
- Forum: MSWin
- Topic: NEURON cann't open hoc
- Replies: 5
- Views: 1390
Re: NEURON cann't open hoc
Thanks for the followup. To help with further diagnosis:
What version of Windows are you using? 10 or 11 or something else?
Have you updated Windows recently?
Have you updated NEURON recently?
What version of NEURON are you using?
What version of Windows are you using? 10 or 11 or something else?
Have you updated Windows recently?
Have you updated NEURON recently?
What version of NEURON are you using?
- Thu Sep 26, 2024 5:21 pm
- Forum: Getting started
- Topic: h.run vs h.continuerun(h.tstop)
- Replies: 2
- Views: 1322
Re: h.run vs h.continuerun(h.tstop)
Decide whether you want to use h.run() or the sequence h.finiitalize h.continuerun If you prefer the latter, it's probably best to avoid inserting any other statements between them. If you prefer to call h.run(), there's no point in calling h.finiitalize, because h.run() executes hoc statements that...
- Thu Sep 26, 2024 3:24 pm
- Forum: Anatomically detailed models
- Topic: Determining distance from soma along apical dendrite
- Replies: 7
- Views: 1399
Re: Determining distance from soma along apical dendrite
how does pyr.hoc know how to assign each chunk of data in oh140807_A0_idJ.asc to the appropriate section category The Neurolucida file contains not only the morphometric data that specify cell topology and geometry, but also metadata (specified by the person or algorithm that did the actual measuri...
- Thu Sep 26, 2024 12:57 pm
- Forum: MSWin
- Topic: NEURON cann't open hoc
- Replies: 5
- Views: 1390
Re: NEURON cann't open hoc
First, let me thank you for using NEURON. Now, about the problem you encountered, I need to ask a few questions. What version of Windows are you using? 10 or 11 or something else? Have you updated Windows recently? Have you updated NEURON recently? What version of NEURON are you using? (in a Command...
- Mon Sep 23, 2024 11:12 pm
- Forum: UNIX/Linux
- Topic: os.execv
- Replies: 8
- Views: 1725
Re: os.execv
Thanks for the followup! Now I have a question for you:
Given the (to me at least) relatively nonspecific and noninformative error messages, what led you to check the mod file permissions? After all, nrnivmodl completed without complaint.
Given the (to me at least) relatively nonspecific and noninformative error messages, what led you to check the mod file permissions? After all, nrnivmodl completed without complaint.
- Mon Sep 23, 2024 12:36 pm
- Forum: UNIX/Linux
- Topic: os.execv
- Replies: 8
- Views: 1725
Re: os.execv
In an empty directory launch python 3 from the command line.
In Python execute
from neuron import h
If that works, execute
soma = h.Section("soma")
If something fails, at which step did that happen, and what was the error message?
In Python execute
from neuron import h
If that works, execute
soma = h.Section("soma")
If something fails, at which step did that happen, and what was the error message?
- Fri Sep 20, 2024 11:44 am
- Forum: Employment and educational opportunities
- Topic: NSF-Simons NITMB Fellows Program
- Replies: 0
- Views: 1564
NSF-Simons NITMB Fellows Program
NSF-Simons NITMB Fellows Program Applications due October 15, 2024 NITMB is seeking early-career researchers who have interest in transforming biological research and inspiring new mathematical discoveries. This opportunity is open to researchers who want to develop mathematical, theoretical, and c...
- Wed Sep 18, 2024 6:38 pm
- Forum: Anatomically detailed models
- Topic: Importing SWC files and best practices
- Replies: 5
- Views: 1530
Re: Importing SWC files and best practices
The Python tutorials illustrate a lot of useful things that can be done with code, and a particular approach to writing code that scales well as program complexity increases. But the KISS principle has its own advantages. Writing less code automatically means writing fewer typos and user-created bug...
- Mon Sep 16, 2024 4:35 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Conditionally Using Ions for Ion Pool Regulation
- Replies: 3
- Views: 1566
Re: Conditionally Using Ions for Ion Pool Regulation
Calcium is a key signal in many phenomena, some of which involve calcium diffusion from the site of ca entry (or site of release from organelles) to the site of ca action. Calcium accumulation mechanisms for such cases add even more overhead because more ODEs (or more complex kinetic schemes) are in...
- Fri Sep 13, 2024 2:34 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Conditionally Using Ions for Ion Pool Regulation
- Replies: 3
- Views: 1566
Re: Conditionally Using Ions for Ion Pool Regulation
Relax. Numerical integration is computationally expensive. Merely "READing" cai costs nothing by comparison. You could insert hundreds of mechanisms that READ cai into every section of a model cell, with no noticeable effect on run time--unless at least one of those mechanisms involved an ...
- Sun Sep 08, 2024 1:21 pm
- Forum: Anatomically detailed models
- Topic: Importing SWC files and best practices
- Replies: 5
- Views: 1530
Re: Importing SWC files and best practices
Start with a clear concept of what you're trying to do. For your purpose, is it sufficient to represent neurites as right cylinders, or is it important that a neurite's diameter may vary, and its centroid diverge from a straight line, from one end to the other? This decision should be strictly on a ...