Search found 57 matches

by RBJ
Sat Feb 16, 2019 6:29 am
Forum: Reaction-diffusion in NEURON
Topic: RXD lower concentration limit?
Replies: 2
Views: 1298

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: 1483

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: 1483

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: 1831

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: 1831

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: 1831

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: 1468

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: 1468

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: 1468

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: 28811

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: 28811

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.
by RBJ
Tue Oct 17, 2017 4:41 am
Forum: MSWin
Topic: the Qt platform plugin
Replies: 20
Views: 28811

Re: the Qt platform plugin

Thanks!
by RBJ
Sun Oct 01, 2017 11:47 am
Forum: MSWin
Topic: the Qt platform plugin
Replies: 20
Views: 28811

Re: the Qt platform plugin

Output of sys.dir with the Bash window (Neuron all works well) ['', 'c:\\ProgramData\\Anaconda2', 'c:\\nrn\\ningw\\bin', 'c:\\ProgramData\\Anac onda2\\scripts', 'c:\\nrn\\lib\\python', 'c:\\ProgramData\\Anaconda2\\python27.z ip', 'c:\\ProgramData\\Anaconda2\\DLLs', 'c:\\ProgramData\\Anaconda2\\lib',...
by RBJ
Sun Oct 01, 2017 9:31 am
Forum: MSWin
Topic: the Qt platform plugin
Replies: 20
Views: 28811

Re: the Qt platform plugin

Ah! Not quite sure what this means, but reading your posts over and over, I just used bash to launch python RATHER than nrniv_python and now Qt is running. So I am sure this must mean something... and in fact if we can fix this it will fix a whole series of issues I was having with Neuron Python I d...
by RBJ
Sun Oct 01, 2017 9:09 am
Forum: MSWin
Topic: the Qt platform plugin
Replies: 20
Views: 28811

Re: the Qt platform plugin

Thank you very much. Firstly, the "unset PYTHONHOME" thing. Now I have rebooted and restarted, I get your expected bash responses. bash.exe"-3.1$ nrnpyenv.sh # PYTHONHOME exists. Do nothing Now when I run: echo $PYTHONHOME echo $NRN_PYLIB echo $PYTHONPATH I get: bash.exe"-3.1$ echo $PYTHONHOME /c/Pr...