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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...

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...

Thanks for the help! :)

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!

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...

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...

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...

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...

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.

That's the exact answer I was looking for, thanks so much!

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...

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...

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...

Thanks for the help, the way you described hoc's references from Python's code work well for me.

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...