Search found 43 matches

by ziemek
Fri Jan 03, 2020 10:53 am
Forum: Reaction-diffusion in NEURON
Topic: Checking the units
Replies: 2
Views: 426

Re: Checking the units

Thanks for the help! :)
by ziemek
Fri Jan 03, 2020 9:11 am
Forum: Reaction-diffusion in NEURON
Topic: Checking the units
Replies: 2
Views: 426

Checking the units

Hi!

I would like to control explicitly unites in RxD and I have 2 questions:
  • Is there any way to check units of parameters of RxD object?
  • What is the unit of Species d param (diffusion coefficient) ? I guess it's um^2/ms
Thanks for your help!
by ziemek
Thu Dec 19, 2019 12:43 pm
Forum: UNIX/Linux
Topic: Which environmental variables do I need to setup for NEURON to work after rpm installation without sudo with cpio
Replies: 1
Views: 678

Which environmental variables do I need to setup for NEURON to work after rpm installation without sudo with cpio

Since I have no sudo on CentOS I installed rpm package with: rpm2cpio nrn-7.7.x86_64-linux.rpm | cpio -id which installed neuron in $HOME/usr/local/nrn. I also added ~/usr/local/nrn/x86_64/bin to my $PATH. But when I execute nrnivmodl i have an error: cadif_rectangle.mod cadif_rectangle.mod make: /u...
by ziemek
Wed Dec 18, 2019 3:25 pm
Forum: Reaction-diffusion in NEURON
Topic: The best practice of Ca2+ pumps on the cell membrane implemented in RxD model
Replies: 3
Views: 586

Re: The best practice of Ca2+ pumps on the cell membrane implemented in RxD model

Yes, that was my assumption - if I have any *.mod file - it would be easier. But there are 3 things which worries me: 1. cad.mod computes cai for the inner shell (depth 0.1) defined in the mod. Since I created Ca2+ shells with RxD - they are defined as different objects - so i suppose their concentr...
by ziemek
Wed Dec 18, 2019 7:10 am
Forum: Reaction-diffusion in NEURON
Topic: The best practice of Ca2+ pumps on the cell membrane implemented in RxD model
Replies: 3
Views: 586

The best practice of Ca2+ pumps on the cell membrane implemented in RxD model

Hi! Ca2+ wave tutorial and Neymotin et al, 2015 model contain Cyt<->ER diffusion of Ca2+ through pumps implemented in RxD. So I wonder what is the best practice to implement Ca2+ pumps on the cell membrane in RxD? Should it be as well implemented in RxD, or it should based on ica current as it is in...
by ziemek
Tue Dec 17, 2019 11:54 am
Forum: UNIX/Linux
Topic: CentOS with RxD and NEURON build from source
Replies: 1
Views: 613

CentOS with RxD and NEURON build from source

Hi! I try to run NEURON on cluster for parallel computing with CentOS. I built the code from source, with iv (even though I can't use GUI through console). NEURON is working in general, but when I try to execute code with rxd - it crashes on the line: from neuron import rxd The error message looks l...
by ziemek
Thu Dec 12, 2019 5:25 am
Forum: Anatomically detailed models
Topic: Precise 3D morphology
Replies: 6
Views: 1025

Re: Precise 3D morphology

Thanks for a very precise answer. I will go through references, but in the case of Neurolucida (which I'm actually not familiar with) - does it use as well truncated cones architecture? I'm asking because whenever I see its reconstructions with spines, it seems to be very precise.
by ziemek
Wed Dec 11, 2019 5:28 am
Forum: Reaction-diffusion in NEURON
Topic: rxd, crxd and dx
Replies: 2
Views: 624

Re: rxd, crxd and dx

That's the exact answer I was looking for, thanks so much!
by ziemek
Wed Dec 11, 2019 5:23 am
Forum: Anatomically detailed models
Topic: Precise 3D morphology
Replies: 6
Views: 1025

Re: Precise 3D morphology

Yes, I see that swcPlus is not adopted, but I understand their manifesto - SWC is quite crude. Since the NEURON allows RxD and 3D mesh with small dx cubical compartments, it's reasonable to ask - how to model the cell with precision much greater then cylindrical approximation? I know that the NEURON...
by ziemek
Tue Dec 10, 2019 3:11 pm
Forum: Reaction-diffusion in NEURON
Topic: rxd, crxd and dx
Replies: 2
Views: 624

rxd, crxd and dx

Hi! I have 2 related question: What is the difference between rxd and crxd? What exactly define dx param for Region when I use: rxd.set_solve_type(dimension=3) I understand that this is the maximum size of 3D mesh element. But how exactly the mesh is defined? Does rxd create the mesh automaticaly on...
by ziemek
Tue Dec 10, 2019 2:41 pm
Forum: Anatomically detailed models
Topic: Precise 3D morphology
Replies: 6
Views: 1025

Precise 3D morphology

Is there any way to define precise 3D morphology based on vertex/triangles in x,y,z space? SWC format as well as hoc's pt3dadd() function define cylindrical compartments, which in case of small morphological elements (like precise spine geometry) may differ too much from the needs. There is SWC Plus...
by ziemek
Tue Dec 10, 2019 2:10 pm
Forum: NEURON + Python
Topic: How to access HOC arrays from Python?
Replies: 2
Views: 705

Re: How to access HOC arrays from Python?

Thanks for the help, the way you described hoc's references from Python's code work well for me.
by ziemek
Wed Dec 04, 2019 8:00 am
Forum: NEURON + Python
Topic: How to access HOC arrays from Python?
Replies: 2
Views: 705

How to access HOC arrays from Python?

I have a Migliore cell morphology which is created based on the following compartments (written in HOC): public soma, axon, dendrite, apical_dend, user5 {create axon[1]} {create soma[1]} {create dendrite[52]} {create apical_dend[70]} {create user5[49]} which are then used to build a morphology based...
by ziemek
Tue Dec 03, 2019 5:34 am
Forum: The GUI
Topic: GUI RunControl panel and Window size
Replies: 1
Views: 1373

GUI RunControl panel and Window size

I have 2 questions: How can I start RunControl panel from Python to avoid clicking each time on Tools->RunControl. Is it possible? How can I change size of the PlotShape window? I tried this: ps = h.PlotShape(True) ps.view(0,0,0,0,0,0,800,800) ps.show(0) But I'm not quite sure what view() params mea...
by ziemek
Tue Dec 03, 2019 3:35 am
Forum: The GUI
Topic: GUI 2 with Python
Replies: 1
Views: 435

GUI 2 with Python

When I look closely to the NEURON Python I found package called gui2 which seems to work with JavaScript and HTML: https://github.com/neuronsimulator/nrn/tree/e5b6aa8bb504ec9c71c86b9abd49c3de3f98729e/share/lib/python/neuron/gui2 I also noticed that you have some Notebook tutorial which utilise the n...