Search found 5785 matches

by ted
Tue May 26, 2020 10:26 am
Forum: Other questions
Topic: running an older NEURON model in a newer NEURON version
Replies: 1
Views: 201

Re: running an older NEURON model in a newer NEURON version

After changing from one version of NEURON to another, it is necessary to recompile the mod files used by your model. First be sure to go to the NEURON Forum's Hot tips area (hint: it's under Making and using models with NEURON) and read the topic
mod files: what they are, and how to use them
by ted
Fri May 22, 2020 4:12 pm
Forum: Other questions
Topic: Unknown semantics
Replies: 4
Views: 381

Re: Unknown semantics

What an ugly implementation--spawns a pile of graphs stacked on top of each other that you have to pull apart manually. And it runs slowly, probably because of time spent updating all of those graphs. Other than that, nrngui mosinit.hoc followed by clicking on the Init & Run button works just fine, ...
by ted
Thu May 21, 2020 5:40 pm
Forum: Optimization
Topic: how to fit channel parameters
Replies: 5
Views: 1095

Re: how to fit channel parameters

That seems strange to me. I had no problems at all getting the MRF to appear and function after executing the unmodified mosinit.hoc. Well, none of the stuff you removed is essential to the model, so it looks like you should be able to procede.
by ted
Thu May 21, 2020 2:39 pm
Forum: Optimization
Topic: how to fit channel parameters
Replies: 5
Views: 1095

Re: how to fit channel parameters

So you didn't actually work through the MRF tutorials? Instead you downloaded the zip file for the model entry unzipped it cd'd into the directory HallermannEtAl2012 successfully compiled the mod files with mknrndll or nrnivmodl used NEURON to execute mosinit.hoc then clicked on NEURON Main Menu / T...
by ted
Thu May 21, 2020 2:24 pm
Forum: Other questions
Topic: Unknown semantics
Replies: 4
Views: 381

Re: Unknown semantics

What operating system are you running? Did you install NEURON from source code, or did you use a binary installer? Does neurondemo work?
by ted
Tue May 19, 2020 8:31 pm
Forum: Optimization
Topic: how to fit channel parameters
Replies: 5
Views: 1095

Re: how to fit channel parameters

Have you worked through the MRF tutorials? (see the link on the Documentation page at neuron.yale.edu)
by ted
Tue May 19, 2020 4:25 pm
Forum: NEURON hacks
Topic: Precompute initial stabilization phase of RMP
Replies: 2
Views: 383

Re: Precompute initial stabilization phase of RMP

Chapter 8 in The NEURON Book covers the topic of initialization in great detail, with several practical examples of custom initializations. The question is: which strategy is most appropriate for your particular application. If you like, we can take this discussion to email, because only this initia...
by ted
Wed May 13, 2020 1:07 pm
Forum: NEURON + Python
Topic: range morphology and mechanism syntax for sections in python
Replies: 9
Views: 1496

Re: range morphology and mechanism syntax for sections in python

the confusing syntax . . . is used throughout the documentation (for example: https://www.neuron.yale.edu/neuron/static/new_doc/modelspec/programmatic/topology/geometry.html#stylized-specification-of-geometry) There is indeed a single instance in a throwaway example. I notice that the syntax is not...
by ted
Tue May 12, 2020 1:29 pm
Forum: NEURON + Python
Topic: range morphology and mechanism syntax for sections in python
Replies: 9
Views: 1496

Re: range morphology and mechanism syntax for sections in python

have a function that calculates things and takes e.g. a segment and gets the .x value from it Exactly. The hoc secname.varname(range0:range1) = y0:y1 statements are just a way of saying that the values of secname.varname are governed by a piecewise linear function with breakpoints at xy coordinates...
by ted
Tue May 12, 2020 12:14 pm
Forum: NEURON + Python
Topic: range morphology and mechanism syntax for sections in python
Replies: 9
Views: 1496

Re: range morphology and mechanism syntax for sections in python

Although hoc allows this kind of syntax for specifying variation of a range variable along a section gbar_na16(0 : 0.168 ) = 0 : 100 nobody should ever use it. Nobody. Ever. Why? It's obscure--nobody will know what it means, as this thread so clearly demonstrates. Just because a language offers a pa...
by ted
Sun May 10, 2020 4:54 pm
Forum: Parallel NEURON
Topic: Question regarding multisplit and rank assignment
Replies: 3
Views: 640

Re: Question regarding multisplit and rank assignment

First two questions are: Is all this complexity necessary at this stage? Will it ever be? to cut down the run time How long is run time now? What do you anticipate doing that will make it longer? More cells? Cells with more complexity (more compartments, more mechanisms that involve differential equ...
by ted
Mon May 04, 2020 11:21 am
Forum: Modeling networks
Topic: Switching synaptic connections in nested for loop
Replies: 7
Views: 852

Re: Switching synaptic connections in nested for loop

My colleague who optimized these single model cells told me to let the simulation run initially for 100-200ms to let the cells "warm up". That may not be long enough if ion accumulation is involved. Another type of initialization problem is "carryover" of something from the end of one simulation to...
by ted
Sat May 02, 2020 6:12 pm
Forum: Modeling networks
Topic: Switching synaptic connections in nested for loop
Replies: 7
Views: 852

Re: Switching synaptic connections in nested for loop

I get a weird response for my very first simulation. If I run the simulation quickly (even just 1ms) and then run it again, the response is normal. How do you know which result is "normal"? Both look abnormal to me, in that no cell appears to be initialized to steady state, nor does any cell settle...
by ted
Mon Apr 27, 2020 6:17 pm
Forum: Anatomically detailed models
Topic: morphology altered when Import3d exports to CellBuilder
Replies: 4
Views: 955

Re: morphology altered when Import3d exports to CellBuilder

Your bitmaps are looking down the Y axis onto the XZ plane (X axis horizontal, Z axis vertical, Y axis orthogonal to the plane of the image). I can't comment about the original morphometric data without seeing it for myself. However, I can tell you that in the imported model, what you are probably c...
by ted
Mon Apr 27, 2020 10:24 am
Forum: Anatomically detailed models
Topic: morphology altered when Import3d exports to CellBuilder
Replies: 4
Views: 955

Re: morphology altered when Import3d exports to CellBuilder

Rotation around the y axis. You're looking at the same thing, but from different angles.