Search found 31 matches

by ziemek
Wed Jan 08, 2020 7:26 pm
Forum: Modeling networks
Topic: Simulation with external feedback
Replies: 1
Views: 77

Simulation with external feedback

I want to perform multiple runs for the same simulation. Between runs I want to give new stimulations to my neurons, but do not reset the simulation - the network (and its state) must remain the same. The motivation for this comes from the artificial neural network field (ANN). Just like for ANN you...
by ziemek
Fri Jan 03, 2020 1:15 pm
Forum: Reaction-diffusion in NEURON
Topic: Cell membrane with PMCA pump
Replies: 2
Views: 85

Re: Cell membrane with PMCA pump

Thank you for the fast and very detailed response! :) Currently I don't care so much about extracellular space so I wonder if there is any other way to pump out Ca2+? Because I assume that the extracellular computation maybe much more expensive. Also I would like to specify explicitly 2 reactions: c...
by ziemek
Fri Jan 03, 2020 10:56 am
Forum: Reaction-diffusion in NEURON
Topic: Cell membrane with PMCA pump
Replies: 2
Views: 85

Cell membrane with PMCA pump

Hi! I would like to model PMCA pump on the cell membrane. In the Calcium wave example there is a serca pump model: cyt_er_membrane = rxd.Region(h.allsec(), geometry=rxd.DistributedBoundary(1)) serca = rxd.MultiCompartmentReaction(ca[cyt], ca[er], gserca / ((kserca / (1000. * ca[cyt])) ** 2 + 1), mem...
by ziemek
Fri Jan 03, 2020 10:53 am
Forum: Reaction-diffusion in NEURON
Topic: Checking the units
Replies: 2
Views: 47

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: 47

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: 140

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: 134

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: 134

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: 109

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: 219

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: 130

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: 219

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: 130

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: 219

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: 179

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.