Search found 26 matches

by itaru
Sun Jul 18, 2021 6:42 pm
Forum: Reaction-diffusion in NEURON
Topic: Pass ._ref_concentration to pc.source_var()?
Replies: 5
Views: 112

Re: Pass ._ref_concentration to pc.source_var()?

Hi Ted,
Yes that's the paper I was trying to refer. I'll try your second suggestion and see it works well within my Python script.

Thanks,
Itaru.
by itaru
Sat Jul 17, 2021 9:05 am
Forum: Reaction-diffusion in NEURON
Topic: Pass ._ref_concentration to pc.source_var()?
Replies: 5
Views: 112

Re: Pass ._ref_concentration to pc.source_var()?

Hi Ted, I'm trying to pass an astrocyte's Ca2+ concentration (which is modeled by RxD) to the neighboring pyramidal cells and interneurons via point process synapses that inhibit and excite the two types describing the cai to i conversion equations as described Ma et al. 2013. As I also want to buil...
by itaru
Thu Jul 15, 2021 8:57 am
Forum: Reaction-diffusion in NEURON
Topic: Pass ._ref_concentration to pc.source_var()?
Replies: 5
Views: 112

Pass ._ref_concentration to pc.source_var()?

Is this supported? I'd like to pass calcium ion concentration info of astrocytes to neighboring pyramidal cells.
by itaru
Tue Jul 06, 2021 7:05 pm
Forum: Reaction-diffusion in NEURON
Topic: RxD code performance
Replies: 0
Views: 28

RxD code performance

Hi,
Has anyone tried to profile RxD code on a platform that provides the tool?
by itaru
Mon Jul 05, 2021 2:51 am
Forum: Reaction-diffusion in NEURON
Topic: RxD with ParallelContext
Replies: 3
Views: 65

Re: RxD with ParallelContext

I looked in the "test/rxd" directory, but could not find usage examples of RxD + the ParallelContext class. As I am having a problem incorporating
RxD statements into my Python script, examples would be appreciated.
by itaru
Thu Jul 01, 2021 1:09 am
Forum: Reaction-diffusion in NEURON
Topic: Question about: example calcium wave
Replies: 1
Views: 30

Re: Question about: example calcium wave

Sorry, there's a reference to the paper on the model.
by itaru
Wed Jun 30, 2021 6:18 am
Forum: Reaction-diffusion in NEURON
Topic: RxD with ParallelContext
Replies: 3
Views: 65

Re: RxD with ParallelContext

More examples are appreciated, should I look for them in the upstream RxD folder?
by itaru
Wed Jun 30, 2021 5:56 am
Forum: Reaction-diffusion in NEURON
Topic: Question about: example calcium wave
Replies: 1
Views: 30

Question about: example calcium wave

Hi,
Is this based upon what model, I'd like to extend this example so that I can use the Li-Rinzel '94 model.
by itaru
Sun Jun 27, 2021 4:08 am
Forum: Reaction-diffusion in NEURON
Topic: RxD with ParallelContext
Replies: 3
Views: 65

RxD with ParallelContext

Hi all,
I am looking at the Calcium Wave Tutorial at: https://neuron.yale.edu/neuron/docs/rea ... lcium-wave , this works on my MacBook Pro perfectly with the latest official release of NEURON. Now I am wondering if RxD is designed to work well with ParallelContexts?
by itaru
Thu Jun 10, 2021 5:15 pm
Forum: NEURON hacks
Topic: nrnivmodl translation rules
Replies: 5
Views: 195

Re: nrnivmodl translation rules

Sure Ted I will re-read the NEURON Book's relevant chapters; sometimes even as an end-user I'd like to really see the C code can generate an optimized piece of code.
by itaru
Thu Jun 10, 2021 4:21 am
Forum: NEURON hacks
Topic: nrnivmodl translation rules
Replies: 5
Views: 195

Re: nrnivmodl translation rules

latter; those translated C codes still look to me not human readable in my humble opinion.
I'd like to know the process so I can write clearer .mod files.
by itaru
Mon Jun 07, 2021 2:30 am
Forum: NEURON hacks
Topic: nrnivmodl translation rules
Replies: 5
Views: 195

nrnivmodl translation rules

Hi,
Is there documentation to explain how mod files are translated into C files?
I've been using today's master branch of NEURON.
by itaru
Mon Mar 22, 2021 9:34 pm
Forum: NEURON Announcements
Topic: 8.0 release plan?
Replies: 3
Views: 401

Re: 8.0 release plan?

True. Thanks.
by itaru
Sun Mar 21, 2021 4:56 am
Forum: NEURON Announcements
Topic: 8.0 release plan?
Replies: 3
Views: 401

8.0 release plan?

Hi all,
I'd like to know more about the up-coming 8.0 release.

Thanks,
Itaru.
by itaru
Wed Jan 20, 2021 10:50 pm
Forum: Parallel NEURON
Topic: Efficient way of debugging Python scripts with MPI library
Replies: 4
Views: 394

Re: Efficient way of debugging Python scripts with MPI library

Hi Ted,
I take all of your suggestions. I kept adding an exit() call to check where MPI library starts to failing, but took a while
to understand that I was accessing a cell that is not associated with the rank it was made; I was wishing some handy tool
like a debugger.

Itaru.