www.neuron.yale.edu

Thank-you. We need all items apart from the Jacobians. This page describes (rather roughly) how we interface with NEURON 7.4:
https://github.com/davidcsterratt/Kappa ... ron-7.4.md
A Zoom call would be great - I'll contact you about it by email.

I have a student working on updating my KappaNEURON package (https://github.com/davidcsterratt/KappaNEURON) so that it works with Neuron 7.7 rather than 7.4. In 7.4, I overrode rxd callback functions, but in 7.7, it looks like I should create a SolverPlugin object and then set the solver using set_s...

Glad you like the change and thanks for putting it in your development version. I've tried pulling the NEURON code, but there seem to be no changes coming through, so I was wondering when the change might make the main NEURON repo? If not in the next few days, I'll need to supply potential testers o...

While I've been working on integrating the SpatialKappa rule-based simulator into NEURON (see work in progress at https://github.com/davidcsterratt/KappaNEURON), I've discovered what I think is a bug in share/lib/python/neuron/rxd/geometry.py . The patch below makes all functions in this file treat ...

Thanks for the clarification and the tip. Re the suggestion about changing the order of calling the blocks, I'm not sure. Intuitively I expected the callback to be like WRITE ica I'm a mod file, but it may actually suit my purposes as well if it doesn't. I'll get back to this once I'm back in the of...

Thanks for the clarification and the tip. Re the suggestion about changing the order of calling the blocks, I'm not sure. Intuitively I expected the callback to be like WRITE ica I'm a mod file, but it may actually suit my purposes as well if it doesn't.

I've now got a minimal complete (if nonsensical) example that shows my problem more clearly. There's also a possible solution, which I got to by examining the NEURON source code, in particular by doing some printf debugging in setup_tree_matrix() in treeset.c. It seems that the rhs argument feeds in...

I'm trying to override the _w_currents() callback in rxd.py so that I can add a contribution to the membrane current generated by a rule-based model that I've embedded using a subclass of a GeneralizedReaction. The following snippet works for me - almost: import neuron.rxd.rxd as nrr import random d...

I've now derived the conduction velocity from simulations using fixed dt and CVODE methods for various numbers of segments per section. Fixed dt: dt nsegall V 1 1e-03 1 55.0239 2 1e-03 3 44.5736 3 1e-03 9 41.2186 4 1e-03 27 40.0697 5 1e-03 81 39.9306 6 1e-04 1 56.0976 7 1e-04 3 45.1512 8 1e-04 9 41....

Many thanks for the reply Mike. Of course the d_lambda won't work because of xraxial (I should have thought of this!). I suppose one might be able to work out an equivalent with a bit of algebra, but perhaps the best approach is just to increase nseg and the time resolution until convergence is reac...

After a long time, I've had reason to look at this again. I've now got graphs (and a spreadsheet) of the propagation speed at various values of dt and d_lambda which I could share. However, the picture is much as described earlier in this thread. There is a difference in conduction velocity of about...

As promised over a year ago, here is my PointProcessDistributor code:
http://homepages.inf.ed.ac.uk/sterratt/node/54

I've only just packaged it up, so please let me know if there are problems; it's not the most elegant of code and the documentation could be better!

Thanks very much for your help Ted - I'm glad it's not just me who's finding the model tricky! I've modified the AXNODES mod file as you suggest. I've set up the initialisation that you suggest, and have now just finished running a simulation with a fixed time step of dt=1e-4, d_lambda=0.003 and nse...

Dear Ted, apologies for not having replied sooner. I have now made the changes you suggest, viz: Stimulus now placed at node[0] Stimulus strength now half of original Measuring distance and time between node 5 and 15 Second order spike time detection using cvode.record() Here is the code: load_file(...

OK, I will post the code on my website. I can't do it right now as the code is more involved than I recall - it requires three different types of object to work, and I need to produce a minimal example of its use rather than the gargantuan model I have at present. However, I hope to have it early ne...