Search found 28 matches

by stil
Mon Jul 23, 2012 3:58 am
Forum: Anatomically detailed models
Topic: Problems instantiating templates
Replies: 9
Views: 4825

Re: Problems instantiating templates

This verb carries a pejorative connotation that makes me think of Iago in Othello. "Imply" is much more neutral.
I apologize, i was not aware of that connotation. I am not such a villain!

Many thanks for the explanations, i am now ready to go further.
by stil
Fri Jul 20, 2012 10:16 am
Forum: Anatomically detailed models
Topic: Problems instantiating templates
Replies: 9
Views: 4825

Re: Problems instantiating templates

By the way, i managed to put spines, using an external code as you proposed : {xopen("CA1_template.hoc")} {xopen("create_spines.hoc")} objref N1 N1 = new CA1() initspines(N1,N1.Radiatum_thin, 3.15) // where Radiatum_thin is a sectionlist and in "create_spines.hoc" : proc initspines(){ local i localo...
by stil
Fri Jul 20, 2012 9:50 am
Forum: Anatomically detailed models
Topic: Problems instantiating templates
Replies: 9
Views: 4825

Re: Problems instantiating templates

I took the model from (Golding et al. 2001) as it was. I only extracted pieces of the neuron for illustration purposes, and did not modify nseg. In the whole model, branches contain odd and even numbers of segments. The functional considerations about nseg that you pinpointed here did not seem to be...
by stil
Fri Jul 20, 2012 4:24 am
Forum: Anatomically detailed models
Topic: Problems instantiating templates
Replies: 9
Views: 4825

Re: Problems instantiating templates

Thank you for the answer, i will work on this. Embedding objects in other objects seemed a natural way to mee, but i might be wrong. It's best to connect the child section's 0 end to the parent's 1 end. Ok, that has advantages such as for subtree() use indeed, but does that have an effect on computa...
by stil
Thu Jul 19, 2012 10:29 am
Forum: Anatomically detailed models
Topic: Problems instantiating templates
Replies: 9
Views: 4825

Problems instantiating templates

Hello, I am building a template of CA1 neuron, on the basis of the model of Jarsky. I have a template of Synapse that i would like to instantiate on this neuron, so that i can build an encapsulated and "clean" code. My spine template : begintemplate SPINE public PSD, CYTOSOL, NECK create PSD create ...
by stil
Wed Jun 06, 2012 12:17 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: "My mechanisms don't load!"
Replies: 21
Views: 21553

Re: "My mechanisms don't load!"

Hello, I've had such a problem (dlopen failed) on a fresh install of ubuntu, when my tests were situated on a ntfs partition. I modified the /etc/fstab file so that the partition is mounted with full rights (umask=000), and execution authorized (exec option) # Partitions Windows - NTFS UUID="X4XXCAX...
by stil
Wed Apr 04, 2012 6:16 pm
Forum: NEURON + Python
Topic: accessing hoc from python
Replies: 3
Views: 1298

Re: accessing hoc from python

thanks for the link ted, i just realize that there is a dedicated section in the programmers' reference. I used documentations in http://www.davison.webfactional.com/notes/accessing-hoc-python/ , somehow kept using a regular hoc file for all the model description, and used python for all the surroun...
by stil
Wed Apr 04, 2012 3:27 am
Forum: NEURON + Python
Topic: accessing hoc from python
Replies: 3
Views: 1298

accessing hoc from python

I have this 'bug' when using python : If ido from scipy import * , and then h.load_file(whatever.hoc) , the variables written in the hoc file like x = 0.001 will be seen as 0. If i change for x = 1e-3 , or if i import import scipy as sc , and adapt the code accordingly, the hoc variables are not cei...
by stil
Tue Apr 03, 2012 5:03 pm
Forum: Getting started
Topic: why this netstim does not work ?
Replies: 1
Views: 1064

why this netstim does not work ?

Hello, I might have missed something about netstim / netcon. I am just trying to use netstim to control a series of events, as an input of a diffusion mechanism. I started with this, but the events do not seem to occur : load_file("nrngui.hoc") objref cvode // is CVODE required to be able to use Net...
by stil
Fri Feb 17, 2012 3:41 am
Forum: Anatomically detailed models
Topic: Spine3d ?
Replies: 3
Views: 1971

Re: Spine3d ?

First, congratulations on browsing through the Programmer's Reference. Most of the time, such activity reveals things that might someday be useful. oooh ! Not in this particular case, however ah. Nobody ever uses spine3d or any of its related stuff (browse for more in the documentation of Geometry ...
by stil
Thu Feb 09, 2012 1:50 pm
Forum: Anatomically detailed models
Topic: Spine3d ?
Replies: 3
Views: 1971

Spine3d ?

Hello,
While searching in the ref pages, i found spine3d in the 'section' section.
That said, i did not manage to find more informations about that keyword...
What is it? How could i use it? Is there example available? Did i miss something ?

Thanks for your help!
by stil
Mon Sep 26, 2011 10:18 am
Forum: NEURON + Python
Topic: slient mode ?
Replies: 1
Views: 894

slient mode ?

Hello, i am launching Neuron from a python script. I use my own simulation loop up to now, in order to implement a communication with another piece of code. Every time, fadvance() function is called, i have a '1' figure in return from Neuron, and every time a h('something') is achieved. Is there a w...
by stil
Tue Jul 12, 2011 10:21 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Calcium current in a POINT_PROCESS and units
Replies: 1
Views: 1753

Calcium current in a POINT_PROCESS and units

Hello all, I might have misunderstood something again, related to the computation of Calcium current using USEION declaration in a POINT_PROCESS NMODL. What i want to do is to WRITE ica, in a POINT_PROCESS AMPA5, using a fractional conductance. In the following NMODL, i think i have declared correct...
by stil
Thu Jun 23, 2011 10:21 am
Forum: Adding new mechanisms and functions to NEURON
Topic: WATCH accuracy
Replies: 6
Views: 1717

Re: WATCH accuracy

Thanks Ted, i sent it to you.

Isn't it related to the fact that the BREAKPOINT block is evaluated twice per timestep with cvode ?
It's just an intuition, i still cannot realize what happens actually ...
by stil
Thu Jun 23, 2011 10:18 am
Forum: Adding new mechanisms and functions to NEURON
Topic: NetCon : how to write the reference to 'source'
Replies: 3
Views: 1167

Re: NetCon : how to write the reference to 'source'

OK, i found out what you meant, it deals with WATCH(), for threshold detection within the POINTPROCESS, and net_send() function to dialog with the NetCon object. Hence, i have the following, with a reduced test model : the hoc instantiates one ns POINTPROCESS in PRE, one nr POINTPROCESS in POST, and...