Search found 5592 matches

by ted
Thu Sep 26, 2019 6:38 pm
Forum: Getting started
Topic: reuse modelDB:84589
Replies: 2
Views: 183

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: 159

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: 157

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: 158

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: 220

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: 332

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: 329

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: 332

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: 329

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.
by ted
Thu Sep 19, 2019 10:09 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Solving 8 interdependent differential equations
Replies: 6
Views: 332

Re: Solving 8 interdependent differential equations

Does the STATE block declare all of the variables that appear on the LHS of the ODEs?
What are the contents of the BREAKPOINT block?
Is initialization of the state variables correct?
Is PROCEDURE calcparameters() working properly?
by ted
Tue Sep 17, 2019 1:14 pm
Forum: MSWin
Topic: Cannot find executable python3 or python
Replies: 2
Views: 264

Re: Cannot find executable python3 or python

If you're not planning to use Python with NEURON or vice versa, ignore the message. Otherwise, uninstall NEURON completely--COMPLETELY--and then reinstall and accept the "add python to path" option.
by ted
Sat Sep 14, 2019 11:31 am
Forum: Suggestions and Feedback
Topic: can't load mknrndll issue
Replies: 9
Views: 508

Re: can't load mknrndll issue

Are there some other ways that I can run this model without using cmd Nope. after removing the statement { neuron_name = "d151" , I double-clicked the eaps\cells\d151.hoc file and successfully got the shape plot. cell_type = "ca1pyr" } Then I tried to load other hoc files from Neuron Main Menu\File...
by ted
Sat Sep 14, 2019 11:17 am
Forum: Modeling networks
Topic: Decompose LFP into components
Replies: 5
Views: 374

Re: Decompose LFP into components

if I calculate single channel current's (implemented as point-process) contribution to LFP As a point process? What does point process have to do with anything? Most voltage-gated channels are implemented as density mechanisms. The currents they generate have units of mA/cm2 and must be multiplied ...
by ted
Fri Sep 13, 2019 10:50 am
Forum: Modeling networks
Topic: Decompose LFP into components
Replies: 5
Views: 374

Re: Decompose LFP into components

At large distances (more than about 10 x segment length) it is reasonable to treat the segment as a point source of current located at the segment center. A more fastidious approach is to treat each segment as a line source with the same length as the segment, centered at the location of the segment...
by ted
Wed Sep 11, 2019 12:10 pm
Forum: Suggestions and Feedback
Topic: can't load mknrndll issue
Replies: 9
Views: 508

Re: can't load mknrndll issue

Sure. Forget about Windows. Use Linux instead. The code runs without complaint under Linux. Making it work under Windows is going to be a major pain.