Search found 15 matches

by PhilippRautenberg
Wed Jan 13, 2010 5:50 am
Forum: NEURON + Python
Topic: Several pyNEURON simulations via multiprocessing
Replies: 1
Views: 2017

Several pyNEURON simulations via multiprocessing

Hello everybody, I would like to run several NEURON simulations in parallel on distinct processes with help of the `multiprocessing` module: from multiprocessing import Process, Lock from random import random as rand import time def myFunction(l, idx): import neuron as n sec = n.h.Section() number =...
by PhilippRautenberg
Tue Sep 01, 2009 9:08 am
Forum: NEURON + Python
Topic: possible section syntax
Replies: 10
Views: 8818

Re: possible section syntax

Hi everybody, for some of my applications it would be handy to have a list of segments (also accross sections). To create a list like this doesn't work: import neuron soma = neuron.h.Section() soma.nseg = 10 segmentlist = [] for seg in soma: segmentlist.append(seg) for seg in segmentlist: print(seg....
by PhilippRautenberg
Tue Sep 01, 2009 8:52 am
Forum: NEURON + Python
Topic: More NEURON + Python documentation
Replies: 6
Views: 21466

Re: More NEURON + Python documentation

Hello together, I put also a pyNEURON tutorial online. See: http://neuro.paedia.info/ Many ideas and suggestions for this tutorial go back to the pyneuron workshop at the CNS in Berlin 2009. At this point I have to thank Alvaro, Andrew, Eilif, Michele, Robert, and many more people from the conferenc...
by PhilippRautenberg
Wed Aug 12, 2009 10:31 am
Forum: NEURON + Python
Topic: Delete a section does not work
Replies: 14
Views: 6366

How to delete an object like IClamp

Hello together, I got a new "delete" problem. When I delete all sections as described before, there remain still attached point process like a IClamp electrode. To problems are caused by this: If I open the gui with from neuron import gui and go to model view to plot the cell, neuron crashes with NE...
by PhilippRautenberg
Fri Mar 13, 2009 4:53 am
Forum: NEURON + Python
Topic: Delete a section does not work
Replies: 14
Views: 6366

Re: Delete a section does not work

Tank you a lot! That solves the problem!
by PhilippRautenberg
Wed Mar 04, 2009 4:30 am
Forum: NEURON + Python
Topic: Delete a section does not work
Replies: 14
Views: 6366

Re: Delete a section does not work

The problem seems to be that I can't reload a morphology that was deleted once. hoc-file little_model.hoc : proc celldef() { topol() subsets() geom() biophys() geom_nseg() } create soma[3] create dend_contra[3] create dend_ipsi[3] proc topol_0() { connect soma[1](0),soma[0](1) connect soma[2](0),som...
by PhilippRautenberg
Mon Mar 02, 2009 11:12 am
Forum: NEURON + Python
Topic: Delete a section does not work
Replies: 14
Views: 6366

Re: Delete a section does not work

Perfect, so I can now delete sections. The references (section lists - within the example below: 'region') are the problems now, indeed. But I can't delete them. for sec in h.reg_soma: sec.insert(mechanism) causes the error: NEURON: Accessing a deleted section near line 0 forall delete_section() ^ S...
by PhilippRautenberg
Wed Feb 18, 2009 8:42 am
Forum: NEURON + Python
Topic: Delete a section does not work
Replies: 14
Views: 6366

Re: Delete a section does not work

I have a similar problem: My simulation loads the morphology of a single cell. As the morphology is described within a hoc-file, I run neuron.h.load_file('file.hoc') Here, a dendrite is composed of about thousand sektions (neuron.h.dend[0]... neuron.h.dend[1000] ). To facilitate the control I also c...
by PhilippRautenberg
Fri Oct 24, 2008 6:36 am
Forum: Getting started
Topic: Initialization to steady state
Replies: 2
Views: 1784

Re: Initialization to steady state

Thank you for your answer! For my purposes the values t=-1000 and dt = 10 works now perfect. As a side note for beginners (like me): make the initialization process visible in order to enable yourself to fix it: tstop = 1e3 // ms dt = 10 steps_per_ms = 1/dt run() I also changed line 9 of the init pr...
by PhilippRautenberg
Mon Oct 20, 2008 10:58 am
Forum: Getting started
Topic: Initialization to steady state
Replies: 2
Views: 1784

Initialization to steady state

Hi all, I have a initialization problem: For initialization I usually use the script of The NEURON Book, Chapter 8.4.2. It works perfectly fine for most of my Parameters although I had to set 't = -1e11'. I need to calculate the resting potential for a big parameter space of different g_bar_kLT (low...
by PhilippRautenberg
Tue Feb 27, 2007 5:41 am
Forum: Anatomically detailed models
Topic: swc-format-problems
Replies: 7
Views: 6428

surface with spines

Thanks a lot! This is what I am planing to do now: 1. files with morphologoical data (with spines like you suggested, and swc-structure from neuromantic) 2. files with the parameters like Ra, Ri,... 3. python-script to set parameters in the parameter files for parameter search, merging with morph an...
by PhilippRautenberg
Fri Dec 22, 2006 9:27 am
Forum: Anatomically detailed models
Topic: swc-format-problems
Replies: 7
Views: 6428

I changed the read_swc.hoc and everything works just fine now! I am just not sure, whether this causes now problems. E.g. when you put all points in different seperate sections will there be a disadvantage (increasing calculation time). In my case I just model one single neuron and would like to mod...
by PhilippRautenberg
Wed Dec 20, 2006 10:11 am
Forum: UNIX/Linux
Topic: Compiling NEURON/interviews in UBUNTU
Replies: 7
Views: 9695

yes, I have been able to compile source code for other programs, and I've installed some packages not in my original Kubuntu 6.10 dist for X11, such as libx11-dev, but it doesn't seem to help. When I try to ./configure Interview I get .... checking sys/conf.h usability... no checking sys/conf.h pre...
by PhilippRautenberg
Thu Dec 07, 2006 2:55 am
Forum: Anatomically detailed models
Topic: swc-format-problems
Replies: 7
Views: 6428

Looks to me like its algorithm was constructed under the assumption that data points are obtained by an orderly recursive descent through the tree. That's the sequence that the second data set follows, whereas the first data set does more of a drunken jig. You're probably going to say that the tool...
by PhilippRautenberg
Wed Dec 06, 2006 11:34 am
Forum: Anatomically detailed models
Topic: swc-format-problems
Replies: 7
Views: 6428

swc-format-problems

Hello everybody, look at the following 2 files: ---------swc1---------- 1 1 1465.700 1934.700 97.600 0.7400 -1 2 1 1462.000 1931.400 96.700 0.8300 1 3 1 1458.300 1928.200 95.800 0.9200 2 4 1 1459.300 1935.700 97.500 0.8300 2 5 1 1454.300 1925.300 94.900 0.9800 3 6 1 1462.500 1928.700 94.700 0.8200 3...