Search found 5593 matches

by ted
Wed Sep 11, 2019 12:10 pm
Forum: Suggestions and Feedback
Topic: can't load mknrndll issue
Replies: 9
Views: 509

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.
by ted
Wed Sep 11, 2019 12:07 pm
Forum: Modeling networks
Topic: Decompose LFP into components
Replies: 5
Views: 375

Re: Decompose LFP into components

Assuming that one or more cells are embedded in a conductive medium that is linear, the potential Vi at any point i in the medium is Vi = SUMMA Zx_j Im_j j where the index j ranges over all compartments in the model, Im_j is the total (i.e. ionic + capacitive) transmembrane current for compartment j...
by ted
Wed Sep 11, 2019 11:40 am
Forum: NEURON + Python
Topic: Export to .hoc with CellBuilder from Python
Replies: 2
Views: 262

Re: Export to .hoc with CellBuilder from Python

but when I try . . . I receive an empty cell in test.hoc. You're starting with a model created by executing statements in Cell_Scnn1a.hoc. Where did the CellBuilder referenced by h.CellBuild() come from? If you created it yourself, it's "empty" (except for a soma section). It's not going to know an...
by ted
Tue Sep 10, 2019 12:29 pm
Forum: Suggestions and Feedback
Topic: can't load mknrndll issue
Replies: 9
Views: 509

Re: can't load mknrndll issue

I also tried auto-launch which didn't work because this model isn't packaged in a way that allows auto-launch to work. How do I know, without even trying it? Two ways. First, auto-launch requires the presence of a mosinit.hoc file. ModelDB entry 84589 doesn't come with a mosinit.hoc file. Second, t...
by ted
Tue Sep 10, 2019 12:18 pm
Forum: Suggestions and Feedback
Topic: can't load mknrndll issue
Replies: 9
Views: 509

Re: can't load mknrndll issue

when I double click mknrndll, these massages shows: Can't load NEURON resources from D:\nrn;C:\nrn/lib/nrn.def[aults] . . . I've downloaded NEURON twice, the first time I downloaded it on D drive, and the second time on C drive. No, you INSTALLED NEURON twice, and now you have at least one broken i...
by ted
Sat Sep 07, 2019 3:37 pm
Forum: MSWin
Topic: cygwin vs msys file path changes, Windows NEURON version
Replies: 1
Views: 242

Re: cygwin vs msys file path changes, Windows NEURON version

Try checking the value returned by neuronhome().
by ted
Sat Sep 07, 2019 3:33 pm
Forum: Parallel NEURON
Topic: Is it possible to associate multiple gids with the same segment?
Replies: 1
Views: 222

Re: Is it possible to associate multiple gids with the same segment?

Yes, but why bother? Assuming that your conceptual model of spike-triggered synaptic transmission is * transmission is triggered when a presynaptic variable crosses a user-specified threshold * the presynaptic variable is the same for all postsynaptic targets of axons that arise from the presynaptic...
by ted
Sat Sep 07, 2019 12:09 pm
Forum: NEURON + Python
Topic: TypeError: sec is not a Section"
Replies: 3
Views: 332

Re: TypeError: sec is not a Section"

You got it. This would work too
print(cell.soma[0])
stim = h.IClamp(0.5, sec=cell.soma[0])
by ted
Sat Sep 07, 2019 12:07 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: mknrndll fils with undefined reference
Replies: 2
Views: 294

Re: mknrndll fils with undefined reference

Compilation of NMODL files produces .o and .c files that persist but are not required during program execution. Why? If you decide to add a new NMODL file, or revise an existing NMODL file, there's no need to recompile all the other files. If you update NEURON, there's no guarantee that the old .o f...
by ted
Thu Sep 05, 2019 1:00 pm
Forum: NEURON + Python
Topic: TypeError: sec is not a Section"
Replies: 3
Views: 332

Re: TypeError: sec is not a Section"

Before we even get started, get rid of the import neuron statement at the top of try.pi. It's not necessary, and conceivably could cause problems. If I run try.py I get the error: "stim = h.IClamp(0.5, sec=soma_py TypeError: sec is not a Section" True, and for good reason. try.py contains no stateme...
by ted
Thu Sep 05, 2019 2:26 am
Forum: NEURON Announcements
Topic: Big models and big data workshop at SFN 2019
Replies: 0
Views: 825

Big models and big data workshop at SFN 2019

NSG and HPAC – Large Scale Simulations and Data Processing A workshop on big models and big data in neuroscience, Saturday, Oct. 19, 2019 from 8:30 AM to 12:30 PM at a downtown Chicago location. Summary This workshop is intended for neuroscientists who need to use high performance computing (HPC) r...
by ted
Tue Sep 03, 2019 1:53 pm
Forum: NEURON + Python
Topic: Save model's biophysics and morphology programmatically to .hoc
Replies: 3
Views: 286

Re: Save model's biophysics and morphology programmatically to .hoc

You can use the GUI's ModelView tool to export a NeuroML specification of the model cell. This is probably doable via hoc statements. I'm not sure how compatible NEURON's current NeuroML ouput is with the current NeuroML specification. Depending on what your simplification algorithm actually does, t...
by ted
Thu Aug 29, 2019 11:33 am
Forum: Other questions
Topic: debugging/profiling NEURON execution
Replies: 3
Views: 361

Re: debugging/profiling NEURON execution

NEURON's standard run system is discussed in some detail in chapter 7 of The NEURON Book. Chapter 8 addresses simulation initialization. If you don't have the book, see these preprints:
https://www.neuron.yale.edu/ftp/ted/book/chap7.pdf
and
https://www.neuron.yale.edu/ftp/ted/book/chap8.pdf
by ted
Mon Aug 26, 2019 1:31 pm
Forum: Getting started
Topic: Current diffusion to nearby sections ?
Replies: 3
Views: 449

Re: Current diffusion to nearby sections ?

I chose to work with individual clamps for each cell, rather than having extracellular stimulation by a single electrode. In other words, using the "activation function" approach to implement stimulation. That won't work for ephaptic interactions between axons, but at least it is a way to stimulate...
by ted
Mon Aug 26, 2019 11:02 am
Forum: NEURON + Python
Topic: Issue with Exp2Syn and stimulation of multiple dendrites
Replies: 3
Views: 395

Re: Issue with Exp2Syn and stimulation of multiple dendrites

the engineering approach that is second nature when it comes to problem solving or looking for a solution One of the reasons why neuroscience needs more engineers. I generally develop code in MATLAB, where I have complete control over all implemented parameters or variables (i.e. when apply a stimu...