Search found 41 matches

by Nin
Tue Mar 15, 2011 10:58 am
Forum: NEURON + Python
Topic: Plot what... from a Python class
Replies: 2
Views: 1766

Re: Plot what... from a Python class

This might help, I wanted it just simply to test that both hoc and python routines give the same results!
by Nin
Fri Mar 11, 2011 3:20 am
Forum: NEURON + Python
Topic: Plot what... from a Python class
Replies: 2
Views: 1766

Plot what... from a Python class

Hi everybody I created a cell class with Python and wanted to use the Neuron gui, so that I can play around with some parameters. In principle this is an easy job for the current accessed section, but if I want to see other compartments, I have to change the currently accessed section all the time. ...
by Nin
Wed Mar 09, 2011 1:12 pm
Forum: NEURON + Python
Topic: Method for moving IClamp
Replies: 6
Views: 4070

Re: Method for moving IClamp

You should probably test to see whether stim.loc(sec(x)) changes the currently accessed section from { whatever it was previously } to { sec }. No, it does not change the currently accessed section: In my case >>> mycell.soma.push() >>> h.cas().name() >>> '<CA3neuron.Neuron object at 0xb04220c>.som...
by Nin
Wed Mar 09, 2011 4:18 am
Forum: NEURON + Python
Topic: Method for moving IClamp
Replies: 6
Views: 4070

Re: Method for moving IClamp

This was exactly what I was looking for! Thanks a lot!!!!
by Nin
Mon Mar 07, 2011 9:51 am
Forum: NEURON + Python
Topic: Method for moving IClamp
Replies: 6
Views: 4070

Method for moving IClamp

I was wondering if is there any method to change easily the location of a point process (like IClamp) without having to create and delete an h.IClamp object in Python everytime we change the section. I am trying to simulate THE SAME current injection in different sections of a cell. def stimulator(s...
by Nin
Fri Jan 07, 2011 4:59 pm
Forum: NEURON + Python
Topic: Parallel Neuron: NetCon failed to connect different hosts
Replies: 4
Views: 3266

Re: Parallel Neuron: NetCon failed to connect different hosts

Very nice advices! I have changed the Sage notebook as you suggested, and now everything can be viewed online. Thanks again for your nice Parallel Neuron tutorials, without them, I would not have done it!!!!.
by Nin
Thu Jan 06, 2011 6:53 pm
Forum: NEURON + Python
Topic: Parallel Neuron: NetCon failed to connect different hosts
Replies: 4
Views: 3266

Re: Parallel Neuron: NetCon failed to connect different hosts

Thanks a lot Hines! I was erroneously taking the gid source of the NetCon from the current thread, and this is supposed to be taken from other gid/cell/thread. The toy model works now and to show my gratitude I wrote a mini-guide and uploaded as a Sage notebook with the model and an explanation abou...
by Nin
Wed Jan 05, 2011 5:50 pm
Forum: NEURON + Python
Topic: Parallel Neuron: NetCon failed to connect different hosts
Replies: 4
Views: 3266

Parallel Neuron: NetCon failed to connect different hosts

Hi everybody and happy new year to all of you! I am trying to create a basic ring network to run in parallel as in Hines & Carnevalle 2007 (see in http://www.neuron.yale.edu/neuron/nrnpubs ) together with the help of Thomas McTavish tutorial on https://nn.med.yale.edu:8000 to implement it in Python....
by Nin
Sun Dec 19, 2010 6:08 pm
Forum: NEURON + Python
Topic: More NEURON + Python resources
Replies: 4
Views: 16764

Re: More NEURON + Python resources

Have you released a NEURON spkg for Sage? To build the Neuron shared Python library in Sage you can: 1.- call the python scritp in /nrn/src/nrnpython/setup.py with the sage interpreter, like: # sage setup.py install 2.- Alternatively, change the Line 8 in the file setup.py. Where you find nrnpython...
by Nin
Tue Dec 14, 2010 2:43 am
Forum: Getting started
Topic: Length with the 3-D method.
Replies: 3
Views: 1846

Re: Length with the 3-D method.

Thanks a lot for your advice!!! Ted Don't change from one to the other in the middle of specifying the geometry of a section What a dumb thing from my side! I expected that both geometric methods would interact with each other in a section :P. Actually, the problem arose when I overwrote the geometr...
by Nin
Mon Dec 13, 2010 7:43 pm
Forum: Getting started
Topic: Length with the 3-D method.
Replies: 3
Views: 1846

Length with the 3-D method.

I am running some dummy tests to create cells with the 3D methods and I realized that the length of a segment changes after running pt3dadd(). Is this normal? For example, if I run this: /* dummy.hoc */ create soma access soma soma.L = 10 soma.diam = 10 // 3-D method (see page 146) soma { pt3dadd(0,...
by Nin
Sun Dec 12, 2010 10:57 am
Forum: NEURON + Python
Topic: is possible to use isinstance() with Segment objects?
Replies: 1
Views: 1267

is possible to use isinstance() with Segment objects?

Hi everybody, for debugging processes, I would like to test if an object passed as argument to a class is indeed a Segment. I though that checking it with isinstance () would be appropriate, but unfortunately this launches an error: here a minimal example: from neuron import h soma = h.Section(name ...
by Nin
Wed Dec 08, 2010 10:04 am
Forum: UNIX/Linux
Topic: Where is the mercurial repository site?
Replies: 2
Views: 3041

Re: Where is the mercurial repository site?

Thanks a lot! I agree with you about the way sometimes the information is hidden there :P. For that reason, I created a common documentation/manual project about NEURON for the people in my lab. Just if anyone else want to have a look, it is here: http://neurohost.org/compneurosci/index.html Best.
by Nin
Sun Dec 05, 2010 7:48 pm
Forum: UNIX/Linux
Topic: Where is the mercurial repository site?
Replies: 2
Views: 3041

Where is the mercurial repository site?

Hi everybody, I am planning to install the latest development version of Neuron in my notebook from the mercurial site. I tried this >> hg clone http://www.neuron.yale.edu/hg but it replied: abort: 'http://www.neuron.yale.edu/hg/' does not appear to be an hg repository! Would anybody there be so kin...
by Nin
Wed May 12, 2010 7:23 pm
Forum: Getting started
Topic: A very simple Voltage-clamp experiment
Replies: 2
Views: 5034

Re: A very simple Voltage-clamp experiment

Dear Ted, thanks a lot for your fabulous and advices. The basic model started to work nicely and I started the changes to perform more complicated simulation I am particularly thankful for your *hints* since this is something that we cannot get in the books and manuals, and required a more experienc...