Search found 41 matches
- Thu Nov 10, 2016 10:24 am
- Forum: NEURON + Python
- Topic: How to delete NetCon objects?
- Replies: 1
- Views: 10721
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,...
- Thu Sep 29, 2016 4:25 pm
- Forum: NEURON + Python
- Topic: Python object as argument of hoc function
- Replies: 4
- Views: 12777
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 ...
- Thu Sep 29, 2016 10:26 am
- Forum: NEURON + Python
- Topic: Python object as argument of hoc function
- Replies: 4
- Views: 12777
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.adde...
- Thu Sep 22, 2016 3:34 pm
- Forum: NEURON + Python
- Topic: NetCon without point_process target
- Replies: 4
- Views: 12055
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...
- Thu Sep 22, 2016 5:50 am
- Forum: NEURON + Python
- Topic: NetCon without point_process target
- Replies: 4
- Views: 12055
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...
- Fri May 09, 2014 8:39 am
- Forum: NEURON + Python
- Topic: creating independent instances of a cell object
- Replies: 1
- Views: 2231
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....
- Fri May 02, 2014 3:51 am
- Forum: NEURON Announcements
- Topic: The NEURON Book: errata and discussion
- Replies: 37
- Views: 111321
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...
- Sun Apr 27, 2014 3:44 pm
- Forum: NEURON + Python
- Topic: Getting parents until soma
- Replies: 1
- Views: 2868
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...
- Sun Oct 27, 2013 4:48 am
- Forum: NEURON hacks
- Topic: Syntax Highlighting for GNU Linux and MS Windows
- Replies: 11
- Views: 57251
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 ...
- Thu Oct 17, 2013 7:55 am
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Segmentation violation realtime
- Replies: 3
- Views: 2668
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...
- Wed Oct 16, 2013 3:55 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Segmentation violation realtime
- Replies: 3
- Views: 2668
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 &&...
- Wed Apr 03, 2013 10:04 am
- Forum: NEURON + Python
- Topic: import neuron crash in ipython console
- Replies: 22
- Views: 17927
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?
Would you tell us when a patch to solve this issue would be available in the repository?
- Wed Apr 03, 2013 8:27 am
- Forum: NEURON + Python
- Topic: import neuron crash in ipython console
- Replies: 22
- Views: 17927
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...
- Thu Mar 01, 2012 11:20 am
- Forum: NEURON Announcements
- Topic: European NEURON Course at IST Austria
- Replies: 1
- Views: 22834
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...
- Wed Jan 25, 2012 2:54 pm
- Forum: NEURON Announcements
- Topic: European NEURON Course at IST Austria
- Replies: 1
- Views: 22834
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 Pe...