Search found 41 matches

by Nin
Thu Nov 10, 2016 10:24 am
Forum: NEURON + Python
Topic: How to delete NetCon objects?
Replies: 1
Views: 9161

How to delete NetCon objects?

I'm collecting a list of NetCon objects in a Python list. I do it to remove old synaptic connections after a simulation and create new ones. I was wondering what is the best way to delete old NetCon objects and substitute them with new NetCon objects. I provide a basic example: def create_netcons(n,...
by Nin
Thu Sep 29, 2016 4:25 pm
Forum: NEURON + Python
Topic: Python object as argument of hoc function
Replies: 4
Views: 10687

Re: Python object as argument of hoc function

Thank you Ted and ramcdougal for your responses. Unfortunately, sections created by statements of the form name = h.Section() end up with strange hoc names that are difficult to use in hoc statements or with the InterViews-based GUI. Definitely, I like defining cell objects from a Python Class that ...
by Nin
Thu Sep 29, 2016 10:26 am
Forum: NEURON + Python
Topic: Python object as argument of hoc function
Replies: 4
Views: 10687

Python object as argument of hoc function

While accessing a python object (h.Section) is not a problem with this code: objref py, mygraph strdef cellname py = new PythonObject() mygraph = new Graph(0) mygraph.size(0, tstop, -80, 40) sprint(cellname, "%s", "py.mycell[0].soma.v") graphList[0].append( mygraph ) mygraph.addexpr(cellname, 9,1 , ...
by Nin
Thu Sep 22, 2016 3:34 pm
Forum: NEURON + Python
Topic: NetCon without point_process target
Replies: 4
Views: 9947

Re: NetCon without point_process target

Thank you Ted, for your help, the None argument made my day!. in the mean time, I tried to access cell1 object (nrn.Section) created in Python with the hoc interface and use a new NetCon: objref py py = new PythonObject() objref nc, foo nc = new NetCon( py.cell1(0.5)._ref_v, foo, 0, 0, 0 ) But it do...
by Nin
Thu Sep 22, 2016 5:50 am
Forum: NEURON + Python
Topic: NetCon without point_process target
Replies: 4
Views: 9947

NetCon without point_process target

Hi everybody, From what I understand in the NEURON book (page 335), we could use the record method of the NetCon class to collect the spikes times of a given segment. In Python, I implemented the following example: https://github.com/JoseGuzman/myIPythonNotebooks/blob/master/NEURON/NetCon%20to%20cou...
by Nin
Fri May 09, 2014 8:39 am
Forum: NEURON + Python
Topic: creating independent instances of a cell object
Replies: 1
Views: 1153

creating independent instances of a cell object

I usually define a generic cell class in Python to generate cell objects that will be treated independently in a network of neurons. For example: class DummyCell(object): def __init__(self): self.soma = h.Section( name = 'soma', cell = self ) self.dend = h.Section( name = 'dend', cell = self ) self....
by Nin
Fri May 02, 2014 3:51 am
Forum: NEURON Announcements
Topic: The NEURON Book: errata and discussion
Replies: 37
Views: 48848

Accuracy in values in the lambda rule.

In page 122 of the NEURON book, the calculation of the length constant with the lamba_DC method for the following parameters: Ra = 180 (Ohm*cm^2), diam = 1 ( um) and Cm =1 (in uF/cm^2) is expected to be approximately 225 um. However, when implementing the calculation of the length constant as a func...
by Nin
Sun Apr 27, 2014 3:44 pm
Forum: NEURON + Python
Topic: Getting parents until soma
Replies: 1
Views: 1069

Getting parents until soma

I'm trying to get a list of nrn.Section objects that contains all the parents until the soma from a given section (it could be the currently accessed section). I tried several methods of SectionList, but couldn't find anything appropriate. For example, in the following example where the soma is conn...
by Nin
Sun Oct 27, 2013 4:48 am
Forum: NEURON hacks
Topic: Syntax Highlighting for GNU Linux and MS Windows
Replies: 11
Views: 31357

Re: Syntax Highlighting for GNU Linux and MS Windows

I wrote a NMODL syntax highlight for VIM that you can download from http://www.ist.ac.at/~jguzman/pub/NMODL.vim To use it, move the file to $VIM/syntax/ and add the following to your .vimrc file " nmodl (see in $VIM/syntax/nmodl.vim) au BufRead,BufNewFile *.mod set filetype=NMODL It includes a foldi...
by Nin
Thu Oct 17, 2013 7:55 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Segmentation violation realtime
Replies: 3
Views: 1497

Re: Segmentation violation realtime

These were fantastic pieces of advice!!!! A second but possibly important issue is that it would be good for the mechanism to be compatible with variable time steps. Anything that relies on testing t in the BREAKPOINT block will not work reliably with variable time steps; events would be better. Now...
by Nin
Wed Oct 16, 2013 3:55 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Segmentation violation realtime
Replies: 3
Views: 1497

Segmentation violation realtime

I'm trying to add a mechanism consisting in a simple step function. For that I wrote: NEURON { SUFFIX step RANGE del, dur, amp RANGE nt } UNITS { (mM) = (milli/liter) } PARAMETER { del (ms) dur (ms) <0,1e9> amp (mM) } ASSIGNED { nt (mM) } INITIAL { nt = 0 } BREAKPOINT { if ( t < del + dur && t > del...
by Nin
Wed Apr 03, 2013 10:04 am
Forum: NEURON + Python
Topic: import neuron crash in ipython console
Replies: 22
Views: 11240

Re: import neuron crash in ipython console

Thanks a lot! This did it!

Would you tell us when a patch to solve this issue would be available in the repository?
by Nin
Wed Apr 03, 2013 8:27 am
Forum: NEURON + Python
Topic: import neuron crash in ipython console
Replies: 22
Views: 11240

Re: import neuron crash in ipython console

The same happens when I updated to IPython 0.13 in GNU/Linux (Debian and Ubuntu) : NEURON -- VERSION 7.3 (726:af0c90e31572) 2012-08-12 Python version 2.6 or 2.7 IPython version 0.13 But only when the notebook is called (e.g ipython notebook) but not on a standard IPython sesion: Python 2.6.6 (r266:8...
by Nin
Thu Mar 01, 2012 11:20 am
Forum: NEURON Announcements
Topic: European NEURON Course at IST Austria
Replies: 1
Views: 11828

Re: European NEURON Course at IST Austria

There are seats available for the NEURON 2012 Summer Course at the IST Austria. The registration deadline is , April 1, 2012, just 4 weeks from today, so we suggest you should apply soon if you are interested. This course will cover the same topics as the course held in San Diego and we strongly enc...
by Nin
Wed Jan 25, 2012 2:54 pm
Forum: NEURON Announcements
Topic: European NEURON Course at IST Austria
Replies: 1
Views: 11828

European NEURON Course at IST Austria

COURSE ANNOUNCEMENT What: "European Neuron Course 2012" (NEURON 2012 Course at IST) When: Monday, August 20, through Friday, August 24, 2012 Where: Institute of Science and Technology (IST Austria) Klosterneuburg, Vienna, Austria Organizers: N.T. Carnevale , M.L. Hines, Jose Guzman and Peter Jonas ...