Search found 56 matches

by RBJ
Sat Nov 30, 2019 9:36 am
Forum: Reaction-diffusion in NEURON
Topic: Making a Nucleus
Replies: 0
Views: 143

Making a Nucleus

Hi so in a previous post I mentioned that I had been defining a no go zone in the middle of my cells by creating a region with zero diffusion. I can't get that to work, so next I have tried using h.pt3dremove() to "bite" a nucleus out of the cell. That doesn't work for me: h.pt3dremove(int(x + nucle...
by RBJ
Sat Nov 30, 2019 9:29 am
Forum: Reaction-diffusion in NEURON
Topic: Node.d (Diffusion) for Node3D objects
Replies: 2
Views: 345

Re: Node.d (Diffusion) for Node3D objects

Sorry for the delay in my reply to your reply! Firstly, the nthreads thing; I am just wrong. There seems to be an optimal number of threads. Might work out to be the cores or something I don't know, but I was wrong to say it slowed it down of course. Must of been changing several things at the same ...
by RBJ
Sat Oct 26, 2019 8:20 am
Forum: Reaction-diffusion in NEURON
Topic: Node.d (Diffusion) for Node3D objects
Replies: 2
Views: 345

Node.d (Diffusion) for Node3D objects

Hi there, is this my understanding or an issue.. If I create my mode in 1D, my species.nodes have a diffusion value node.d that I can either read or write to... ...but if I do the same with 3D models, I find that node.d is unread or writable? Well it seems to be a string not a float value anyway. I ...
by RBJ
Sun Jul 07, 2019 8:52 am
Forum: Reaction-diffusion in NEURON
Topic: Modelling a channel with multiple markov states
Replies: 7
Views: 1163

Re: Modelling a channel with multiple markov states

Sorry, my RXD models use pointers to gate channelbuilder channels with temperature not Ca[er]. So that approach may work with your problem, using Ca[er] instead of temperature... but look I am just a regular NEURON user, not an expert, so lets see what the experts say :-) If "your" method works it s...
by RBJ
Sun Jul 07, 2019 4:57 am
Forum: Reaction-diffusion in NEURON
Topic: Modelling a channel with multiple markov states
Replies: 7
Views: 1163

Re: Modelling a channel with multiple markov states

...Interesting, I didn't realise that was a feature of RxD, my Markov channel models are built with Channel Builder and then imported into my code (that includes RxD). I will interested to hear the answer to this enquiry also.
Regards
by RBJ
Wed Apr 24, 2019 7:23 pm
Forum: UNIX/Linux
Topic: No module named hoc37
Replies: 11
Views: 3081

Re: No module named hoc37

Ah ha!!
so now I loaded python with simply

Code: Select all

python3

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from neuron import gui
successfully brings up the menus!!

In fact still no go through spyder, but I am sure I can work it out from here!
Thanks!
..,.and so to bed (UK)...
R.
by RBJ
Wed Apr 24, 2019 6:58 pm
Forum: UNIX/Linux
Topic: No module named hoc37
Replies: 11
Views: 3081

Re: No module named hoc37

I am sorry, I don't know the ldd `which python3` instruction, but it returned this linux-vdso.so.1 (0x00007ffdbc3fb000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007ff4e8c09000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007ff4e8818000) libdl.so.2 => /lib/x86_64-linux-gnu/...
by RBJ
Wed Apr 24, 2019 5:44 pm
Forum: UNIX/Linux
Topic: No module named hoc37
Replies: 11
Views: 3081

Re: No module named hoc37

Thanks, cp hoc.cpython-37m-x86_64-linux-gnu.so hoc.so # be sure to make a copy of hoc.so first!!! cp hoc.cpython-37m-x86_64-linux-gnu.so hoc37.so so copying that file to those two alternative hoc.so and hoc37.made no difference that I can see. However: ldd /usr/local/nrn/lib/python/neuron/hoc.cpytho...
by RBJ
Tue Apr 23, 2019 9:42 am
Forum: UNIX/Linux
Topic: No module named hoc37
Replies: 11
Views: 3081

Re: No module named hoc37

Thank you, so yes tried these: firstly python3 -v Gives: import _frozen_importlib # frozen import _imp # builtin import '_thread' # <class '_frozen_importlib.BuiltinImporter'> import '_warnings' # <class '_frozen_importlib.BuiltinImporter'> import '_weakref' # <class '_frozen_importlib.BuiltinImport...
by RBJ
Mon Apr 22, 2019 6:38 pm
Forum: UNIX/Linux
Topic: No module named hoc37
Replies: 11
Views: 3081

Re: No module named hoc37

Thank you for your reply, So firstly, no NEURON does not work from a regular python prompt. In fact it gets less far, failing to find neuron at all, because I only set PYTHONPATH within the PYTHONPATH preferences of Spyder. Same as I do on my mac. Secondly, the PYTHONPATH I am using on these UBUNTU ...
by RBJ
Sun Apr 21, 2019 10:15 am
Forum: UNIX/Linux
Topic: No module named hoc37
Replies: 11
Views: 3081

No module named hoc37

I have Neuron successful installed on OSX and Windows 7/10... but I have failed with two separate linux (Ubuntu) machines now and so I think it is time to call for help. I don't have much experience with linux, so it is highly probably I am being an idiot. I have been trying off and on for days, tho...
by RBJ
Tue Feb 19, 2019 2:07 pm
Forum: Hot tips
Topic: Turning adaptive integration ("CVODE") on and off
Replies: 3
Views: 10771

Re: Turning adaptive integration ("CVODE") on and off

Yes, sorry I realise this. That is the only way I know to turn it on and off. The post says "Instead of using... an argument of 1 or 0 to turn ..., it is better to call cvode_active() with the appropriate argument....". I thought I might be missing the alternative arguments to 1 and 0. Sorry. Kind R...
by RBJ
Tue Feb 19, 2019 3:18 am
Forum: Hot tips
Topic: Turning adaptive integration ("CVODE") on and off
Replies: 3
Views: 10771

Re: Turning adaptive integration ("CVODE") on and off

Sorry Ted, I am doubtless being really slow here; but I keep reading the first line of this post over and over and don’t follow. If one should not use cvode.active(1) etc., please can you give an explicit example of the “appropriate argument” one would use? Thanks, sorry... just want to be sure I am...
by RBJ
Mon Feb 18, 2019 5:13 pm
Forum: Reaction-diffusion in NEURON
Topic: RXD lower concentration limit?
Replies: 2
Views: 867

Re: RXD lower concentration limit?

Thank you yes that nails it!
by RBJ
Sat Feb 16, 2019 6:29 am
Forum: Reaction-diffusion in NEURON
Topic: RXD lower concentration limit?
Replies: 2
Views: 867

RXD lower concentration limit?

Hello again, I m having good success with the RXD now, and hoping to incorporate in a range of models now. I’ve hit another hiccup however. When I have a species that should be decreasing in concentration asymptotically towards zero it invariably equilibrates at somewhat above zero. For example, dro...