Search found 5513 matches

by ted
Mon Jun 24, 2019 11:06 am
Forum: Other questions
Topic: translate KINETIC block to DERIVATIVE block
Replies: 1
Views: 18

Re: translate KINETIC block to DERIVATIVE block

I am trying to compare two mod files but one is written using the KINETIC block and the other the DERIVATIVE block. Since I would like to solve the ODEs using the same method and not (SOLVE kin METHOD sparse) or (SOLVE deriv METHOD cnexp, I am thinking to rewrite the KINETIC block as the DERIVATIVE...
by ted
Mon Jun 24, 2019 10:38 am
Forum: Getting started
Topic: Plotting Input signal
Replies: 3
Views: 58

Re: Plotting Input signal

I feel like the comment you wrote asking me if I grew up on a farm is kind of inappropriate.
Then we're even. I feel that, outside of a very limited circle of close acquaintances with whom one might horse around, addressing someone with "hey" is inappropriate.
by ted
Wed Jun 19, 2019 10:04 pm
Forum: Getting started
Topic: Plotting Input signal
Replies: 3
Views: 58

Re: Plotting Input signal

Hey Hay is for horses. You grew up on a farm? plot (with hoc language from terminal or GUI of NEURON) the input signal of the current I am injecting with a PointProcessManager Actually, the PointProcessManager isn't injecting any current. What's injecting current is an instance of a point process c...
by ted
Mon Jun 17, 2019 10:46 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Loading New Artifical Cell into NEURON
Replies: 5
Views: 103

Re: Loading New Artifical Cell into NEURON

A x86_64 directory was produced with no error message. This indicates that the mod file was compiled successfully. When I cd to the directory and call nrngui, I get: . . . IntFire4r.mod . . . Under MSWin, when NEURON starts, it automatically checks the current working directory for a library called...
by ted
Sat Jun 15, 2019 9:45 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Loading New Artifical Cell into NEURON
Replies: 5
Views: 103

Re: Loading New Artifical Cell into NEURON

named the new class IntFire4r How? I used the nrnivmodl command in the terminal within the folder containing the code. Was there an error message? Was a nrnmech.dll or x86_64 directory produced? The python line -- cell1 = h.IntFire4r() returns the following error: AttributeError: 'hoc.HocObject' ob...
by ted
Sat Jun 15, 2019 9:41 pm
Forum: Getting started
Topic: How to combine GUI with hoc programming
Replies: 3
Views: 117

Re: How to combine GUI with hoc programming

Should I write a hoc file like this? That will do nothing useful. It won't get past the second line, which is in NMODL, not hoc. The third and fourth lines will not affect intra- or extracellular sodium concentration because ionic concentrations only exist in the context of sections that contain ch...
by ted
Fri Jun 14, 2019 4:25 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Loading New Artifical Cell into NEURON
Replies: 5
Views: 103

Re: Loading New Artifical Cell into NEURON

First question: what is the name of your new integrate & fire cell class?

Second question: what exactly did you do to "compile the mod files into neuron"?

Third question: how do you know that your new cell class hasn't been added to NEURON?
by ted
Fri Jun 14, 2019 11:04 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Membrane Potential Equation
Replies: 2
Views: 99

Re: Membrane Potential Equation

Good question. There is no such file. Creating a section gives you the spatially discretized cable equation with no ionic membrane current, i.e. a charge balance equation that states capacitive membrane current in a compartment = net current entering the compartment from adjacent compartments but yo...
by ted
Thu Jun 13, 2019 10:43 am
Forum: Getting started
Topic: How to combine GUI with hoc programming
Replies: 3
Views: 117

Re: How to combine GUI with hoc programming

hoc and Python are programming languages. The typical workflow for working with a programming language is REPEAT write statements in the programming language execute the statements evaluate the results UNTIL one has a collection of statements that do what one wants The first step is done by writing ...
by ted
Sun Jun 09, 2019 9:21 am
Forum: Getting started
Topic: Accessing the current between extracellular layers
Replies: 6
Views: 158

Re: Accessing the current between extracellular layers

Without more specific information about your hypothesis, it is difficult to advise you how to build a computational model that is a close match to that hypothesis. After all, you know most about your hypothesis and something (much? little?) about NEURON, but we know a lot about NEURON and almost not...
by ted
Sun Jun 09, 2019 8:50 am
Forum: Anatomically detailed models
Topic: converting hoc to swc
Replies: 7
Views: 5441

Re: converting hoc to swc

Thanks, that sounds like something that would be of interest to many.
by ted
Thu Jun 06, 2019 10:16 am
Forum: Getting started
Topic: Accessing the current between extracellular layers
Replies: 6
Views: 158

Re: Accessing the current between extracellular layers

Then you may need to represent exchange between each cell and a shared extracellular space, and/or direct exchange between cells (e.g. through gap junctions). This can be done with special mechanisms implemented in NMODL, or by using NEURON's reaction-diffusion (rxd) module. Both approaches have the...
by ted
Wed Jun 05, 2019 9:47 am
Forum: Hot tips
Topic: conversion units
Replies: 5
Views: 227

Re: conversion units

We have just seen yet another demonstration of the value of multiple eyes examining the same code.
by ted
Tue Jun 04, 2019 1:58 pm
Forum: Getting started
Topic: Accessing the current between extracellular layers
Replies: 6
Views: 158

Re: Accessing the current between extracellular layers

No.

Are you trying to create a model of interactions between a neuron and other cells that lie adjacent to it?
by ted
Tue Jun 04, 2019 1:55 pm
Forum: NEURON + Python
Topic: 'hoc.HocObject' object has no attribute 'instantiate'
Replies: 4
Views: 147

Re: 'hoc.HocObject' object has no attribute 'instantiate'

Is there any fundamental problem when trying to instantiate a cell morphology written in a hoc template format instead of swc format for example? No, but there are fundamental problems with all human-written code, specifically * it is prone to contain errors * a narrative description is generally n...