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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 =...

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....

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...

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...

Tank you a lot! That solves the problem!

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...