www.neuron.yale.edu

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 ...

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...

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. Sor...

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...

Thank you yes that nails it!

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...

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.

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...

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.

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...

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), ...

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_...

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

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 reactio...

All working beautifully now. Thank you so much for your help!!
Now for some science!!