Search found 26 matches

by davidsterratt
Wed Sep 24, 2014 6:14 am
Forum: Reaction-diffusion in NEURON
Topic: Patch to geometry.py
Replies: 3
Views: 6126

Re: Patch to geometry.py

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...
by davidsterratt
Tue Sep 23, 2014 11:19 am
Forum: Reaction-diffusion in NEURON
Topic: Patch to geometry.py
Replies: 3
Views: 6126

Patch to geometry.py

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 ...
by davidsterratt
Sun Jul 13, 2014 4:59 pm
Forum: Reaction-diffusion in NEURON
Topic: Overriding _w_currents() in rxd.py
Replies: 4
Views: 6702

Re: Overriding _w_currents() in rxd.py

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...
by davidsterratt
Sun Jul 13, 2014 4:58 pm
Forum: Reaction-diffusion in NEURON
Topic: Overriding _w_currents() in rxd.py
Replies: 4
Views: 6702

Re: Overriding _w_currents() in rxd.py

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.
by davidsterratt
Tue Jul 08, 2014 6:36 pm
Forum: Reaction-diffusion in NEURON
Topic: Overriding _w_currents() in rxd.py
Replies: 4
Views: 6702

Re: Overriding _w_currents() in rxd.py

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...
by davidsterratt
Tue Jul 08, 2014 11:43 am
Forum: Reaction-diffusion in NEURON
Topic: Overriding _w_currents() in rxd.py
Replies: 4
Views: 6702

Overriding _w_currents() in rxd.py

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...
by davidsterratt
Thu Feb 07, 2013 7:16 am
Forum: Other questions
Topic: Optimal d_lambda for measuring propagation speed
Replies: 13
Views: 5329

Re: Optimal d_lambda for measuring propagation speed

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....
by davidsterratt
Wed Feb 06, 2013 12:03 pm
Forum: Other questions
Topic: Optimal d_lambda for measuring propagation speed
Replies: 13
Views: 5329

Re: Optimal d_lambda for measuring propagation speed

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...
by davidsterratt
Wed Jan 30, 2013 7:48 am
Forum: Other questions
Topic: Optimal d_lambda for measuring propagation speed
Replies: 13
Views: 5329

Re: Optimal d_lambda for measuring propagation speed

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...
by davidsterratt
Mon Jan 28, 2013 12:35 pm
Forum: Other questions
Topic: distributing mechanisms randomly
Replies: 12
Views: 2695

Re: distributing mechanisms randomly

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!
by davidsterratt
Fri May 20, 2011 1:10 pm
Forum: Other questions
Topic: Optimal d_lambda for measuring propagation speed
Replies: 13
Views: 5329

Re: Optimal d_lambda for measuring propagation speed

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...
by davidsterratt
Fri May 13, 2011 7:58 am
Forum: Other questions
Topic: Optimal d_lambda for measuring propagation speed
Replies: 13
Views: 5329

Re: Optimal d_lambda for measuring propagation speed

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(...
by davidsterratt
Wed May 04, 2011 10:41 am
Forum: Other questions
Topic: distributing mechanisms randomly
Replies: 12
Views: 2695

Re: distributing mechanisms randomly

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...
by davidsterratt
Tue May 03, 2011 12:08 pm
Forum: Other questions
Topic: Optimal d_lambda for measuring propagation speed
Replies: 13
Views: 5329

Re: Optimal d_lambda for measuring propagation speed

Thanks very much for your very helpful reply Ted. I've tried responding to all your queries, but I've run out of time today, so the later ones aren't addressed very well. Strange results indeed. Do you get similar results if you simply forall nseg*=3 a few times? It does vary a bit, though it looks ...
by davidsterratt
Mon May 02, 2011 9:53 am
Forum: Other questions
Topic: distributing mechanisms randomly
Replies: 12
Views: 2695

Re: distributing mechanisms randomly

I have a somewhat complicated hoc object that allows you to place point processes with a probability that depends on the diameter and length of the segment within a section, and of the perpendicular distance of the segment to some plane, which could be the cell body layer. Please let me know if you'...