Search found 62 matches

by RBJ
Sat Feb 12, 2022 8:18 am
Forum: MSWin
Topic: Error after install NEURON 8 using rxd
Replies: 3
Views: 362

Re: Error after install NEURON 8 using rxd

...and another detail I have noticed that might mean something is that when running (specifically when finalizing h.finitialize(-58)) just as it dies and throws that error... I noticed a file such as this is created every time:
rxddll868f2402-8c05-11ec-a8db-f48c5065050d.c
by RBJ
Thu Feb 10, 2022 6:57 am
Forum: OS X
Topic: PyCharm "ModuleNotFoundError: No module named 'neuron'"
Replies: 1
Views: 471

Re: PyCharm "ModuleNotFoundError: No module named 'neuron'"

I am just a bystander here, but since I do have NEURON (7.6) working well with PyCharm, using an Anaconda environment on one of our Macs, I thought perhaps I would paste up the all important configuration I have: Script path: /Users/richardbarrett-jolley/Documents/NEURON25/model.py Parameters: None ...
by RBJ
Wed Feb 09, 2022 2:24 pm
Forum: MSWin
Topic: Error after install NEURON 8 using rxd
Replies: 3
Views: 362

Re: Error after install NEURON 8 using rxd

Thank you, so NEURON 8.0, This is Python 3.8 calling a NEURON model from within an ANACONDA (py3.8) environment. With Spyder in fact. (but same with a simple terminal in the same environment). gcc looks good? Using built-in specs. COLLECT_GCC=/usr/bin/gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-pc-c...
by RBJ
Wed Feb 09, 2022 8:03 am
Forum: MSWin
Topic: Error after install NEURON 8 using rxd
Replies: 3
Views: 362

Error after install NEURON 8 using rxd

The error itself is this: Could not find module 'C:\Users\Richard\model\rxddll201f5865-89a7-11ec-9fad-f48c5065050d.so' (or one of its dependencies). Try using the full path with constructor syntax. Then this: ld: error: c:/nrn/mingw/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/10.2.0/../../../../x86_64...
by RBJ
Wed Jul 28, 2021 5:54 am
Forum: NEURON + Python
Topic: Preproducing updating PlotShape() figures in
Replies: 1
Views: 878

Preproducing updating PlotShape() figures in

Hi All, I have had some success with accessing the PlotShape() function through Python in Jupyter and up dating it so I can see a pretty coloured wave of Vm traversing my test model (based on your own tutorials). To moviefy this, I can screen record it, however, usually with Python in other projects...
by RBJ
Fri Jun 26, 2020 9:51 am
Forum: NEURON Announcements
Topic: How to cite NEURON
Replies: 2
Views: 28528

Re: How to cite NEURON

Hi there, Noticed that "https://neuron.yale.edu/neuron/nrnpubs" is a Page Not Found... should point to-> https://www.neuron.yale.edu/neuron/publications/biblio Also, unless you have a way to automate this or "Crowd source it" this may be a fantastical idea, but I wondered if you ...
by RBJ
Sat Nov 30, 2019 9:36 am
Forum: Reaction-diffusion in NEURON
Topic: Making a Nucleus
Replies: 1
Views: 1277

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...
by RBJ
Sat Nov 30, 2019 9:29 am
Forum: Reaction-diffusion in NEURON
Topic: Node.d (Diffusion) for Node3D objects
Replies: 2
Views: 1473

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: 1473

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: 2980

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 ...
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: 2980

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: 9502

Re: No module named hoc37

Ah ha!!
so now I loaded python with simply

Code: Select all

python3

Code: Select all

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: 9502

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: 9502

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: 9502

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...