Search found 12 matches

by manyi
Wed May 20, 2015 12:36 am
Forum: OS X
Topic: error: cannot find the library
Replies: 1
Views: 7330

error: cannot find the library

I'm trying to install NEURON on my MacBook OS X 10.10.3, following the instruction on http://www.neuron.yale.edu/neuron/download/compilestd_osx "Make" fails at step II C. Any help? $ make Making all in src Making all in lib libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -I../include -I/usr/X11/includ...
by manyi
Wed Jun 27, 2012 5:49 am
Forum: Anatomically detailed models
Topic: parents and children of a section
Replies: 3
Views: 3491

parents and children of a section

Hi there, I have a detailed single neuron model and want to extract the parents and children of a section, let's say necks[0]. oc>psection() necks[0] { nseg=1 L=2.78238 Ra=180.122 dend[14] connect necks[0] (0), 0.857143 /* First segment only */ insert morphology { diam=0.18} insert capacitance { cm=...
by manyi
Thu Jun 14, 2012 5:24 pm
Forum: Getting started
Topic: nan in meaured voltage and current
Replies: 1
Views: 1236

nan in meaured voltage and current

I have a multicompartment neuron model and use SEClamp. When the pulse amplitude is below about +50mV, it is working perfectly. But when the pulse amplitude is larger than +60mV, the measured voltage as well as the electrode current become nan. I wonder whether it is a precision problem.
by manyi
Thu Jun 14, 2012 5:16 pm
Forum: Getting started
Topic: Transients in SEClamp
Replies: 1
Views: 1110

Transients in SEClamp

when I use SEClamp to perform an experiment, I usually got some small transient in the beginning of the simulation. But occasionally I got some very positive and very negative values (10 to the 4 order of magnitude bigger) at t=0 and it decays rapidly. Are they still transients? Is it possible to av...
by manyi
Mon May 14, 2012 9:59 am
Forum: Getting started
Topic: unit of the recorded current measured at the soma
Replies: 9
Views: 6763

Re: unit of the recorded current measured at the soma

Thanks for your patient reply. And we have further inquiries. I think we understand different things by "... what portion of that clamp current is attributable to sodium current..." I understand that in a typical experimental voltage-clamp characterization of an ion channel, the current is isolated ...
by manyi
Tue May 08, 2012 5:53 pm
Forum: Getting started
Topic: unit of the recorded current measured at the soma
Replies: 9
Views: 6763

Re: unit of the recorded current measured at the soma

Let me clarify. We have some voltage clamp data in presence of step depolarizations and ion channel blockers. Our data are current recorded at the soma with unit Ampere. We have built a model using NEURON with topology and multiple ion channels. Next goal: reproduce the experimental result in the NE...
by manyi
Tue May 08, 2012 11:57 am
Forum: Getting started
Topic: unit of the recorded current measured at the soma
Replies: 9
Views: 6763

Re: unit of the recorded current measured at the soma

The current recorded by a voltage clamp attached to the soma reflects contributions from all membrane currents throughout the entire cell, subject to filtering (signal loss) due to the properties of the membrane and cytoplasm that separates the clamp electrode from any given patch of membrane. Do y...
by manyi
Mon May 07, 2012 12:20 pm
Forum: Getting started
Topic: unit of the recorded current measured at the soma
Replies: 9
Views: 6763

Re: unit of the recorded current measured at the soma

Thanks for the detailed reply. In fact, we already have a neuron model with topology reconstructed from experimental data, and want to further compare its neuronal dynamics with physiological data. Adding only one channel and then recording the SEC i is not a good option as we want a realistic model...
by manyi
Fri May 04, 2012 11:01 am
Forum: Getting started
Topic: unit of the recorded current measured at the soma
Replies: 9
Views: 6763

unit of the recorded current measured at the soma

Hi! I want to fit some data from voltage clamp experiments. Now I have a multi-compartment model and use VClamp(0.5) as the stimulation. Somewhere in the mod files, ik is 'assigned' ASSIGNED { ik (mA/cm2) ...} In my code, vector_current.record(&soma.ik(.5)) I got a reasonable trace of the recorded c...
by manyi
Wed Apr 25, 2012 10:14 am
Forum: Modeling networks
Topic: Extract network connectivity
Replies: 5
Views: 3057

Re: Extract network connectivity

It works when 'local nil' is removed from the obfunc.
Thanks!
by manyi
Tue Apr 24, 2012 12:45 pm
Forum: Modeling networks
Topic: Extract network connectivity
Replies: 5
Views: 3057

Re: Extract network connectivity

I have the following code in a proc for i=0, nclist.count-1 { dfile.printf("%s\t%s\n", myprecell(nclist.object(i)), nclist.object(i).postcell)} obfunc myprecell(){...} is defined in the same file, just above the proc. I get the following error message and do not know what's wrong: bad stack access: ...
by manyi
Wed Apr 18, 2012 8:52 am
Forum: Modeling networks
Topic: Extract network connectivity
Replies: 5
Views: 3057

Extract network connectivity

Hi there! I want to extract the connectivity of the network. I'm using an artificial cell as Poisson input sources and a usual neuron model for neurons. When printing the pre and post cells with for i=0, nclist.count-1 {dfile.printf("%s\t%s\t%s\n", nclist.object[i].precell, nclist.object[i].postcell...