Search found 5673 matches

by ted
Sat Sep 28, 2019 9:48 pm
Forum: Getting started
Topic: monitor the attenuation of the peak value of the action potential with distance from the ion channel
Replies: 9
Views: 618

Re: monitor the attenuation of the peak value of the action potential with distance from the ion channel

It sounds like you're starting a modeling project and need to work closely with a collaborator on it for two reasons. First, to define exactly what you are thinking about. A big problem is that this sentence doesn't make sense: "How can I apply a stimulus at a specific ion channel (Has to be ion cha...
by ted
Sat Sep 28, 2019 9:23 pm
Forum: ModelDB and other online sources of models
Topic: Model 3808 can't use Create Your Own\Single Cell
Replies: 1
Views: 457

Re: Model 3808 can't use Create Your Own\Single Cell

It's 22 year old legacy code. What's surprising is that any of it works at all.
by ted
Sat Sep 28, 2019 9:18 pm
Forum: ModelDB and other online sources of models
Topic: Model 135839 error issue
Replies: 1
Views: 254

Re: Model 135839 error issue

Everything works fine for me under Win 10, using the latest standard distribution installer for NEURON, i.e. version 7.7.2 7.7 (2b7985ba) 2019-06-20.
by ted
Sat Sep 28, 2019 8:53 pm
Forum: Other questions
Topic: MOD Files Compile But Fail To Load
Replies: 8
Views: 919

Re: MOD Files Compile But Fail To Load

Here is the response when running neurondemo: That's all that happened? No GUI tools appeared on screen? Clicking on the "Release" radio button did what? After clicking on "Release", clicking on the Init & Run button did what? With regard to your own source code, where are you putting it before you...
by ted
Fri Sep 27, 2019 11:23 am
Forum: NEURON + Python
Topic: Use NEURON's native GUI tools with Python!
Replies: 2
Views: 11131

Re: Use NEURON's native GUI tools with Python!

For some time now, all you have to do is specify a name when you use Python to create a section, and you do it like this: namestring = h.Section(name = ' namestring ') This creates a new section that has the Python name namestring and the hoc name _pysec. namestring . The hoc name can be used in an...
by ted
Fri Sep 27, 2019 10:55 am
Forum: Other questions
Topic: MOD Files Compile But Fail To Load
Replies: 8
Views: 919

Re: MOD Files Compile But Fail To Load

Some questions.
First, did this machine ever have a previous version of NEURON installed, and if so, did mechanisms load properly then?
Second, what happens when you execute the command
neurondemo
from the command line?
by ted
Thu Sep 26, 2019 6:38 pm
Forum: Getting started
Topic: reuse modelDB:84589
Replies: 2
Views: 445

Re: reuse modelDB:84589

Tom Morse, curator of ModelDB, has revised this model entry so that it works under MSWin and is easier to launch (including enabling "auto-launch" to work). He has also revised the README.html file accordingly. Many thanks, Tom!
by ted
Thu Sep 26, 2019 2:00 pm
Forum: Getting started
Topic: intracellular sodium ion accumulation
Replies: 2
Views: 415

Re: intracellular sodium ion accumulation

Since you're working with hoc, you should read this ASAP: Hines, M.L. and Carnevale, N.T. The NEURON Simulation Environment Neural Computation 9:1179-1209, 1997. https://neuron.yale.edu/neuron/static/papers/nc97/nctoc.htm You might want to download the preprint, which is available from a link on tha...
by ted
Thu Sep 26, 2019 10:09 am
Forum: NEURON + Python
Topic: running hoc files accompanied by comand line arguments, in Python
Replies: 2
Views: 434

Re: running hoc files accompanied by comand line arguments, in Python

The answer is "don't". That's a lousy user interface--it's inconvenient, tedious, prone to user error, not very readable, and guarantees irreproducibility ("now, what command line did I use to get this interesting result?"). And it's a great way to make sure that nobody else wants to use your code. ...
by ted
Tue Sep 24, 2019 12:19 pm
Forum: NEURON + Python
Topic: error in saving a voltage trace into a figure
Replies: 2
Views: 423

Re: error in saving a voltage trace into a figure

Good question. Many people make similar mistakes. Here's a chance to learn a lot. What am I doing wrong? Misdiagnosing the cause of the problem because of failure to localize the problem. In medicine, the first step in diagnosis is to localize the cause of the problem. This is also true for diagnosi...
by ted
Tue Sep 24, 2019 11:38 am
Forum: MSWin
Topic: Downloading NEURON5.9
Replies: 1
Views: 802

Re: Downloading NEURON5.9

I'm trying to download the old version of NEURON5.9 in order to run a legacy model, but I'm not quite sure about which folder should I download from https://neuron.yale.edu/ftp/neuron/versions/v5.9/ There are no folders at that location. Download the installer that is appropriate for your hardware ...
by ted
Fri Sep 20, 2019 10:47 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Solving 8 interdependent differential equations
Replies: 6
Views: 664

Re: Solving 8 interdependent differential equations

This is not a problem of "magic numbers." There's a bug, either a subtle syntax error in your NMODL code or in NEURON itself. I'll need to work with your NMODL file in a toy model. If the NMODL file can be used by itself in a single compartment model, that's all I'll need. If it requires other mecha...
by ted
Fri Sep 20, 2019 10:39 am
Forum: NEURON + Python
Topic: Filter Mechanism params by NMODL PARAMETER
Replies: 8
Views: 745

Re: Filter Mechanism params by NMODL PARAMETER

Brilliant up to a point. The NMODL source code will tell you the default values of parameters. However, it won't tell you the actual value of any parameter used in a particular model implementation, because those can be changed by hoc or Python assignment statements. Also, if mechanism X's PARAMETER...
by ted
Thu Sep 19, 2019 10:58 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Solving 8 interdependent differential equations
Replies: 6
Views: 664

Re: Solving 8 interdependent differential equations

I'd suggest changing
SOLVE blrrate METHOD cnexp
to
SOLVE blrrate METHOD derivimplicit
because many of the state variables have very small values and should not become negative.
by ted
Thu Sep 19, 2019 10:27 am
Forum: NEURON + Python
Topic: Filter Mechanism params by NMODL PARAMETER
Replies: 8
Views: 745

Re: Filter Mechanism params by NMODL PARAMETER

mech contains parameters like 'gbar', 'g', 'ica' and so on. Not what I see. Given soma = h.Section(name='soma') soma.insert('hh') then for seg in soma: for mech in seg: print(mech) returns k_ion na_ion hh but no mention of gnabar, gkbar, gl. or el, which are declared in hh.mod's PARAMETER block.