Search found 97 matches

by eacheon
Fri Dec 01, 2006 2:36 pm
Forum: Optimization
Topic: Help on pointprocess initialization with multirun fitter
Replies: 4
Views: 9860

That's exactly what caused the problem. SEClamp[0] and SEClamp[1] are different objects. ... Or maybe something references seclampList.o(0).i, then seclampList.o(0) is destroyed. Either way, you'll get a "freed" error message. Oh, thanks for the prompt answer, the quoted part are what happened in m...
by eacheon
Fri Dec 01, 2006 12:54 pm
Forum: Optimization
Topic: Help on pointprocess initialization with multirun fitter
Replies: 4
Views: 9860

From your description, it is hard for me to know exactly what you did. However, when an error message complains that something was "freed," it means that there has been an attempt to refer to an object that has been destroyed. My confusing is exactly here: in my undserstanding according to the erro...
by eacheon
Fri Dec 01, 2006 4:35 am
Forum: Optimization
Topic: Help on pointprocess initialization with multirun fitter
Replies: 4
Views: 9860

Help on pointprocess initialization with multirun fitter

Hi, I have problem with using pointprocess with multirun fitter. Here is what I did: 1. load the model. 2. load the saved multirun fitter session. 3. press "Error Value" button in window "MulRunFitter[0] Generator" it worked fine and gave me an error value of 1.0341e-07. 4. (optional) change a param...
by eacheon
Fri Dec 01, 2006 4:17 am
Forum: Optimization
Topic: Segmentation violation when load_file a .ses file
Replies: 4
Views: 10531

You might want to have a look at this discussion on how to use the standard run system: https://www.neuron.yale.edu/phpBB2/viewtopic.php?t=495&highlight=finitialize Actually I read this thread before, though I still cannot figured out why stdinit() will do but init() won;t when I work with Mutrunfi...
by eacheon
Fri Dec 01, 2006 1:33 am
Forum: Optimization
Topic: Segmentation violation when load_file a .ses file
Replies: 4
Views: 10531

If init_fit.hoc is using stdinit() instead of init(): stdinit() load_file("SEClampFit.ses") Then everything is fine. In the customized init() I created something like "rig/instrument", i.e. an SEClamp. because parameters of some instruments depend on the result of init(). Now I realized it might be ...
by eacheon
Fri Dec 01, 2006 1:20 am
Forum: Optimization
Topic: Segmentation violation when load_file a .ses file
Replies: 4
Views: 10531

hold on. I seem to find the reason. will post later.
by eacheon
Thu Nov 30, 2006 11:29 pm
Forum: Optimization
Topic: Segmentation violation when load_file a .ses file
Replies: 4
Views: 10531

Segmentation violation when load_file a .ses file

When I load my model and type manually $ /path/to/special model_setup.hoc - oc> init() oc> load_file("SEClampFit.ses") every things goes fine and a multirun fitter pops out. However when I append this load_file to a init_fit.hoc script and run the script I got the following error message (repeating ...
by eacheon
Tue Nov 28, 2006 8:21 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Realistic current clamp electrode (balance bridge artifact)
Replies: 9
Views: 12750

Re: modeling electrodes and clamp circuitry

In theory it should be the latter. Practice is another matter; do you know of an experimental method for measuring "the residual resistance of the ruptured patch" ? The experimenters retract the electrodes a little after finishing patch-recording from a cell, and do an I-V curve of the electrode, h...
by eacheon
Tue Nov 28, 2006 4:36 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Realistic current clamp electrode (balance bridge artifact)
Replies: 9
Views: 12750

Re: modeling electrodes and clamp circuitry

how do people deal with non-infinite "seal resistance"? I read some of the materials mentioned above but did not find it mentioned. Too bad nobody seems to be teaching this stuff. The answer to your question "how do people deal with . . . " is somewhere in the primary literature about patch clamp. ...
by eacheon
Mon Nov 27, 2006 7:53 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Realistic current clamp electrode (balance bridge artifact)
Replies: 9
Views: 12750

Re: modeling electrodes and clamp circuitry

The SEClamp class, which is built into NEURON, is a voltage source in series with a resistor. Think of it as a model of an electrode that has series resistance but no capacitance, attached to a "perfect single electrode clamp device." You only need to use the Linear Circuit Builder if you want to t...
by eacheon
Mon Nov 27, 2006 1:22 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Realistic current clamp electrode (balance bridge artifact)
Replies: 9
Views: 12750

Re: use the Linear Circuit Builder

Easily done with the Linear Circuit Builder. Decide how to represent your electrode and whether or not you want to include compensation circuitry. The simplest electrode model is an equivalent L circuit --lumps the series resistance into a single element, and lumps the electrode capacitance into a ...
by eacheon
Mon Nov 13, 2006 10:11 pm
Forum: Suggestions and Feedback
Topic: Missing "cm" in online references
Replies: 1
Views: 11363

Missing "cm" in online references

Hi, Not knowing where is the appropriate place for this topic, please forgive me if this is posted to the wrong place. I find there's no entry about "cm" in online references, neither "topology" nor "section". A search does not give me any result. Hope it added to the document, but correct me if I i...
by eacheon
Thu Nov 09, 2006 1:01 am
Forum: Adding new mechanisms and functions to NEURON
Topic: "NEURON's CVode method ignores conservation" and &
Replies: 1
Views: 3415

"NEURON's CVode method ignores conservation" and &

When I do nrnivmodl, what's these info meaning? Translating Ih.mod into Ih.c NEURON's CVode method ignores conservation and Translating VClamp.mod into VClamp.c Notice: This mechanism cannot be used with CVODE VECTORIZED I understand "Notice: This mechanism cannot be used with CVODE", but what does ...
by eacheon
Tue Oct 03, 2006 1:57 am
Forum: Other questions
Topic: how to read from, and record data into binary files?
Replies: 7
Views: 10218

Re: how to read from, and record data into binary files?

I am simulating an IClamp through cells and recording Voltage vs time. I have no problem recording and reading data from Ascii files, but the volume of these files becomes incredibly large very quickly. I want to save the data in binary format. Is it possible? How is it done? I am actually zipping ...
by eacheon
Thu Sep 28, 2006 12:16 am
Forum: NEURON + Python
Topic: Using nrniv with IPython
Replies: 10
Views: 10078

Using nrniv with IPython

Hello, Here's how we can use nrniv with IPython: nrniv -python argv.py argv.py as: #!/usr/bin/python import sys sys.argv = [''] from IPython.Shell import IPythonShellEmbed ipshell = IPythonShellEmbed() ipshell() This does not work with nrngui yet. Maybe IPython embeded shell does not know threads en...