Search found 46 matches

by RBJ
Sun Apr 21, 2019 10:15 am
Forum: UNIX/Linux
Topic: No module named hoc37
Replies: 0
Views: 2

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: 9719

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: 9719

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: 204

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: 204

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...
by RBJ
Mon Feb 04, 2019 4:19 pm
Forum: Reaction-diffusion in NEURON
Topic: Unexpected 3D behaviour
Replies: 2
Views: 369

Re: Unexpected 3D behaviour

Oh that's perfect, thanks so much! I did try and debug species.py but of course I got nowhere. Just copying in the new file worked fine-I didn't need to compile.
kind Regards R.
by RBJ
Thu Jan 31, 2019 3:24 pm
Forum: Reaction-diffusion in NEURON
Topic: Unexpected 3D behaviour
Replies: 2
Views: 369

Unexpected 3D behaviour

Sorry. me again. I am confused by the output I get with 3D RXD. Figure I below shows how I get a nice as diffusion if I just add some factor to central nodes with diffusion . It seems to indicate to me I am on the right track. http://pcwww.liv.ac.uk/~rbj/NEURON/surf1.png However, now look what happe...
by RBJ
Thu Jan 31, 2019 2:59 pm
Forum: Reaction-diffusion in NEURON
Topic: 3D Dimensional RXD/CRXD
Replies: 4
Views: 484

Re: 3D Dimensional RXD/CRXD

Thank you, yes charging dx Is so easy and speeds up processing enormously. I am sorry I didn't find that myself in the documentation. Regards R.
by RBJ
Tue Jan 29, 2019 8:30 am
Forum: Reaction-diffusion in NEURON
Topic: 3D Dimensional RXD/CRXD
Replies: 4
Views: 484

Re: 3D Dimensional RXD/CRXD

Thanks there are some useful ideas. I really I want to press on with full-scale3-D simulation, however, so I can get smooth surfaces (with microdomains etc). How do I change dx? I googled for hours! Also to clarify, the 10 hours that that 3D script takes to execute is spent waiting in the Finitialis...
by RBJ
Fri Jan 25, 2019 2:51 pm
Forum: Reaction-diffusion in NEURON
Topic: 3D Dimensional RXD/CRXD
Replies: 4
Views: 484

3D Dimensional RXD/CRXD

Hello, I wonder if you could help further. Simply adding rxd.set_solve_type(dimension=3) ...to the simple rxd model you helped me with before makes my PC workstations and mac really struggle. I have not had success with the mac at all, and one PC has taken 4 hrs to complete the task (<1 minute 1D), ...
by RBJ
Tue Jan 22, 2019 11:00 am
Forum: Reaction-diffusion in NEURON
Topic: Different reaction rates in different sections
Replies: 3
Views: 377

Re: Different reaction rates in different sections

Thank you again, so I have now "processed" that new information and help. I get it. In doing so I clocked that this is 1d, and that had been confusing me. I really want to get 3d. Having read your 2018 paper, Newton et al 2018, I realised that to get 3d I should at least be adding rxd.set_solve_type...
by RBJ
Mon Jan 21, 2019 2:32 pm
Forum: Reaction-diffusion in NEURON
Topic: Different reaction rates in different sections
Replies: 3
Views: 377

Re: Different reaction rates in different sections

Thank you very much for your detailed help and speed! It will take a little while for me to process the information, but in the meantime please do use the code if it is useful. Kind Regards Richard
by RBJ
Mon Jan 21, 2019 8:20 am
Forum: Reaction-diffusion in NEURON
Topic: Different reaction rates in different sections
Replies: 3
Views: 377

Different reaction rates in different sections

Hello there, I am trying to model the dynamics of a hypothetical factor (tfact) throughout a cell using RXD. To make what I believe to be the simplest possible model have made a two section cell, with 101 segments in each. I have linked them to one another. I added an "enzyme" rate reaction to one h...
by RBJ
Tue Oct 24, 2017 2:20 pm
Forum: MSWin
Topic: the Qt platform plugin
Replies: 20
Views: 22585

Re: the Qt platform plugin

Image
All working beautifully now. Thank you so much for your help!!
Now for some science!!
by RBJ
Mon Oct 23, 2017 5:05 am
Forum: MSWin
Topic: the Qt platform plugin
Replies: 20
Views: 22585

Re: the Qt platform plugin

Thanks very much, am on Teaching duties for a while now; will feedback when I have tried this!
BW R.