Search found 15 matches
- Wed Jan 13, 2010 5:50 am
- Forum: NEURON + Python
- Topic: Several pyNEURON simulations via multiprocessing
- Replies: 1
- Views: 2873
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 =...
- Tue Sep 01, 2009 9:08 am
- Forum: NEURON + Python
- Topic: possible section syntax
- Replies: 10
- Views: 12118
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....
- Tue Sep 01, 2009 8:52 am
- Forum: NEURON + Python
- Topic: More NEURON + Python documentation
- Replies: 6
- Views: 44052
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...
- Wed Aug 12, 2009 10:31 am
- Forum: NEURON + Python
- Topic: Delete a section does not work
- Replies: 14
- Views: 20274
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 crash...
- Fri Mar 13, 2009 4:53 am
- Forum: NEURON + Python
- Topic: Delete a section does not work
- Replies: 14
- Views: 20274
Re: Delete a section does not work
Tank you a lot! That solves the problem!
- Wed Mar 04, 2009 4:30 am
- Forum: NEURON + Python
- Topic: Delete a section does not work
- Replies: 14
- Views: 20274
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...
- Mon Mar 02, 2009 11:12 am
- Forum: NEURON + Python
- Topic: Delete a section does not work
- Replies: 14
- Views: 20274
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...
- Wed Feb 18, 2009 8:42 am
- Forum: NEURON + Python
- Topic: Delete a section does not work
- Replies: 14
- Views: 20274
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...
- Fri Oct 24, 2008 6:36 am
- Forum: Getting started
- Topic: Initialization to steady state
- Replies: 2
- Views: 2767
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...
- Mon Oct 20, 2008 10:58 am
- Forum: Getting started
- Topic: Initialization to steady state
- Replies: 2
- Views: 2767
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...
- Tue Feb 27, 2007 5:41 am
- Forum: Anatomically detailed models
- Topic: swc-format-problems
- Replies: 7
- Views: 8944
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...
- Fri Dec 22, 2006 9:27 am
- Forum: Anatomically detailed models
- Topic: swc-format-problems
- Replies: 7
- Views: 8944
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...
- Wed Dec 20, 2006 10:11 am
- Forum: UNIX/Linux
- Topic: Compiling NEURON/interviews in UBUNTU
- Replies: 7
- Views: 15424
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...
- Thu Dec 07, 2006 2:55 am
- Forum: Anatomically detailed models
- Topic: swc-format-problems
- Replies: 7
- Views: 8944
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...
- Wed Dec 06, 2006 11:34 am
- Forum: Anatomically detailed models
- Topic: swc-format-problems
- Replies: 7
- Views: 8944
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...