Search found 25 matches

by JustasB
Fri Sep 13, 2019 11:09 pm
Forum: Parallel NEURON
Topic: Minimal Working Example of MPI Gap Junctions (in python)
Replies: 17
Views: 8699

Re: Minimal Working Example of MPI Gap Junctions (in python)

In case others are having a similar problem, I was receiving Segmentation Fault errors under MPI with gap junctions when I had h.cvode.cache_efficient(1). Under h.cvode.cache_efficient(0), the simulation ran without the error.
by JustasB
Thu Sep 05, 2019 10:31 pm
Forum: Parallel NEURON
Topic: Is it possible to associate multiple gids with the same segment?
Replies: 1
Views: 122

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

I'm working with dendro-dendritic synapses where my pre- cell can have multiple pre-synaptic locations. Depending on section nseg, nearby pre- section(x) locations might be referring to the same segment. When I try to associate multiple gids with a given pre- segment, on the post- end only the synap...
by JustasB
Wed Jun 12, 2019 8:43 pm
Forum: NEURON + Python
Topic: Guidance on plotting cell's geometry in Python?
Replies: 4
Views: 6975

Re: Guidance on plotting cell's geometry in Python?

For anyone else who has a similar need to visualize cell model shape beyond what is available in NEURON, I've made tools that I used for such purpose available online. Consider the following options: Use a tool like hoc2swc to convert your cell model to the SWC morphology format. Then you can use an...
by JustasB
Fri Jun 07, 2019 11:19 am
Forum: Anatomically detailed models
Topic: converting hoc to swc
Replies: 7
Views: 5997

Re: converting hoc to swc

If it's useful to anyone else, I packaged the code that exports NEURON cells to SWC files into a pip-install'able Python package: hoc2swc.

Description and instructions can be found here: https://github.com/JustasB/hoc2swc
by JustasB
Sat Mar 23, 2019 2:31 pm
Forum: Suggestions and Feedback
Topic: Possible off-by-one bug in ModelView > Export to NeuroML
Replies: 9
Views: 2320

Re: Possible off-by-one bug in ModelView > Export to NeuroML

Interesting. So it looks like the "orphan root" s2d section was what caused the original problem to appear. The s2d might be safe to remove -- it's only referenced in the create statements, and I found no references to it elsewhere in the project. As you mentioned, it's not connected to anything els...
by JustasB
Thu Mar 21, 2019 11:36 pm
Forum: Suggestions and Feedback
Topic: Possible off-by-one bug in ModelView > Export to NeuroML
Replies: 9
Views: 2320

Re: Possible off-by-one bug in ModelView > Export to NeuroML

I noticed another, very similar parent-id-off-by-one issue with another model but now in a single cell instantiation scenario. The underlying cause might be the same. Steps to reproduce: Use this HOC file: https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=114665&file=/plast/gc-plast.hoc#t...
by JustasB
Thu Mar 21, 2019 5:53 pm
Forum: Suggestions and Feedback
Topic: Possible off-by-one bug in ModelView > Export to NeuroML
Replies: 9
Views: 2320

Re: Possible off-by-one bug in ModelView > Export to NeuroML

I get the same "parent id off-by-one" issue when instantiating multiple instances of a cell made using CellBuilder. Here is the HOC template (soma + a spiraling dendrite): https://pastebin.com/J64KfDmZ Then I instantiate it twice with: h.load_file('TestCell.hoc') c1 = h.TestCell() c2 = h.TestCell() ...
by JustasB
Thu Mar 21, 2019 4:10 pm
Forum: Suggestions and Feedback
Topic: Possible off-by-one bug in ModelView > Export to NeuroML
Replies: 9
Views: 2320

Re: Possible off-by-one bug in ModelView > Export to NeuroML

Ah, that's an interesting case. I did notice the two pieces in Shape plot, but I wasn't familiar enough with the model to tell if the oddity was intentional or not. I looked for the "multi-create" issue in the source code of the models that I have locally and was able to find a few other models wher...
by JustasB
Wed Mar 20, 2019 9:48 pm
Forum: Suggestions and Feedback
Topic: Possible off-by-one bug in ModelView > Export to NeuroML
Replies: 9
Views: 2320

Possible off-by-one bug in ModelView > Export to NeuroML

I'm running into an issue where when I try to export a model to NeuroML, it generates an XML file that refers to an incorrect parent segment (parent id is off-by-one). Below are the steps to reproduce the issue: # Download a model from ModelDB: https://github.com/ModelDBRepository/116094/archive/mas...
by JustasB
Wed Mar 20, 2019 9:15 pm
Forum: Suggestions and Feedback
Topic: StackOverflow-like site for NEURON?
Replies: 1
Views: 14198

Re: StackOverflow-like site for NEURON?

Having gone through the process of proposing the new Stack Exchange site, the main lesson I learned is that proposals for new Stack Exchange sites are more suitable for large communities with high volumes of questions. In general, the broader the topic of a proposed Stack Exchange site, the more lik...
by JustasB
Fri Apr 06, 2018 8:09 pm
Forum: NEURON + Python
Topic: Cannot get Vector.play() and NetCon/NetStim work with CVODE and SaveState.restore()
Replies: 4
Views: 2082

Re: Cannot get Vector.play() and NetCon/NetStim work with CVODE and SaveState.restore()

Strangely, writing a post here has made it easier to solve my own problem! The problem appears to be with the NetStim.start time, before the restore, being set to 0. If I set the NetStim.start equal to the h.t value after the restore, the crash dissapears. So I believe I've found a workaround. It is...
by JustasB
Fri Apr 06, 2018 7:41 pm
Forum: NEURON + Python
Topic: Cannot get Vector.play() and NetCon/NetStim work with CVODE and SaveState.restore()
Replies: 4
Views: 2082

Cannot get Vector.play() and NetCon/NetStim work with CVODE and SaveState.restore()

I am having trouble using Vector.play() and NetCon/NetStim together with CVODE and SaveState.restore(). I run the simulation until my model reaches steady state, then I save with SaveState.save(), and then I inject an arbitrary current into the cell after SaveState.restore(). A NetCon/NetStim combin...
by JustasB
Mon Mar 05, 2018 5:00 pm
Forum: Other questions
Topic: Two issues with cvode.event when using cvode.active(1)
Replies: 7
Views: 2104

Re: Two issues with cvode.event when using cvode.active(1)

so it has NOT YET been documented in the Programmer's Reference! even though it appears in several blocks of example code in the Programmer's Reference!! Haha. Understood. Thank you for the explanation. I will make sure I use cvode_active() whenever I use cvode. Just an update, the problematic mode...
by JustasB
Mon Mar 05, 2018 3:40 pm
Forum: Other questions
Topic: Two issues with cvode.event when using cvode.active(1)
Replies: 7
Views: 2104

Re: Two issues with cvode.event when using cvode.active(1)

Hmmm I had tried cvode_active() in the original code, but without the test section it still produced the same error. However, test section + cvode_active(1) both issues disappear. Thank you for the suggestion. I will try it in my full script. In the hot tip about using cvode_active() , you mention t...