Search found 72 matches

by breakwave922
Wed Nov 29, 2017 10:37 pm
Forum: Parallel NEURON
Topic: summation of matrix on different computer nodes
Replies: 2
Views: 9244

Re: summation of matrix on different computer nodes

Ted, Thanks for the reply and information. Actually, I saved each cell's membrane potential into a vector, cell by cell. Those cells are distributed among different cores, in paralleled environment. I can use .add(vec1) to sum them up, but this sum-up only applicable to cells on the same core. I wan...
by breakwave922
Sun Nov 19, 2017 3:27 am
Forum: Parallel NEURON
Topic: summation of matrix on different computer nodes
Replies: 2
Views: 9244

summation of matrix on different computer nodes

Hi, I have a big network NEURON model, which is computed in parallel environment on superclusters. For each cell, I generated a matrix to save it's membrane voltages of all compartments, so these matrix should be on different computer nodes. I need to sum-up all the matrix from all cells. Since thos...
by breakwave922
Mon Jul 03, 2017 9:59 pm
Forum: Modeling networks
Topic: possibility with constructing large-scale network
Replies: 2
Views: 4305

possibility with constructing large-scale network

Hi, I'm trying to scale my current project of simulating 1000-cell network to ~27,000-cell network in NEURON. I use to generate connectivity matrix file in matlab, with 1000*1000 elements, and saved as txt file that was later imported into NEURON for connecting cells. But if network is with 27,000 c...
by breakwave922
Thu Jun 15, 2017 3:55 pm
Forum: ModelDB and other online sources of models
Topic: couldn't find model on modeldb with accession number 151685
Replies: 7
Views: 9462

Re: couldn't find model on modeldb with accession 151685

tom_morse wrote:Shane Lee apologized for the oversight and is looking for the files.
Hi, Tom,

Did the author give feedback and codes uploaded?

Thanks.
by breakwave922
Thu Jun 08, 2017 3:02 pm
Forum: ModelDB and other online sources of models
Topic: couldn't find model on modeldb with accession number 151685
Replies: 7
Views: 9462

Re: couldn't find model on modeldb with accession 151685

tom_morse wrote:Thank you for your post. I will contact the authors and request for them to contribute their model.
Hi, Tom,

Do you have any news from the authors?

Thanks.
by breakwave922
Sat Jun 03, 2017 4:06 pm
Forum: ModelDB and other online sources of models
Topic: couldn't find model on modeldb with accession number 151685
Replies: 7
Views: 9462

couldn't find model on modeldb with accession number 151685

Is anyone here could help me to find model with accession number 151685? This model package is from paper: Lee S, Jones SR (2013) Distinguishing mechanisms of gamma frequency oscillations in human current source signals using a computational model of a laminar neocortical network. Front Hum Neurosci...
by breakwave922
Thu Aug 04, 2016 4:11 pm
Forum: LFPsim
Topic: Question about using LFPsim from modelDB(#190140)
Replies: 8
Views: 10273

Re: Question about using LFPsim from modelDB(#190140)

Given a multicompartmental model, it is easy to show that if there is any point P that satisfies the condition "all transfer resistances between P and the model's compartments are identical" then the field potential observed at P will equal Rx*Iinj where Rx is the transfer impedance between P and a...
by breakwave922
Wed Aug 03, 2016 3:48 pm
Forum: LFPsim
Topic: Question about using LFPsim from modelDB(#190140)
Replies: 8
Views: 10273

Re: Question about using LFPsim from modelDB(#190140)

Imagine we have two-compartment cell model with single segment in each compartment, and each compartment has the same length and diameter, if we set the electrode and observe the extracellular potential at any point lies in the plane that is perpendicular to the middle of the cell, will the recorde...
by breakwave922
Mon Aug 01, 2016 3:29 pm
Forum: LFPsim
Topic: Question about using LFPsim from modelDB(#190140)
Replies: 8
Views: 10273

Re: Question about using LFPsim from modelDB(#190140)

I was able to record the LFP with the same properties you expected when checking the simple test example. I'm not sure what your sentence means. Are you saying that LFPsim produced a waveform that has the properties I described? No, LFPsim produced differently. I already contact the developer to di...
by breakwave922
Sun Jul 31, 2016 10:19 pm
Forum: LFPsim
Topic: Question about using LFPsim from modelDB(#190140)
Replies: 8
Views: 10273

Re: Question about using LFPsim from modelDB(#190140)

Ted, Thanks a lot for the reply. I was able to record the LFP with the same properties you expected when checking the simple test example. In this simple test model, I have another questions: the distance r from each segment to electrode is supposed to be calculated according to segment's and electr...
by breakwave922
Fri Jul 22, 2016 10:17 pm
Forum: LFPsim
Topic: Question about using LFPsim from modelDB(#190140)
Replies: 8
Views: 10273

Question about using LFPsim from modelDB(#190140)

I'm trying to implement the LFPsim tool which can record the LFP from the single neuron into my own neuron model. LFPsim is just developed and published by Parasuram et al., 2016 http://journal.frontiersin.org/article/10.3389/fncom.2016.00065/full# , and can be downloaded from modelDB https://sensel...
by breakwave922
Tue Dec 01, 2015 4:03 pm
Forum: NEURON + Python
Topic: Introducing LFPy, a Python module for simulating LFPs
Replies: 3
Views: 4496

Re: Introducing LFPy, a Python module for simulating LFPs

Thanks, Oren. Sorry for my late response.
Another thing I want to check with you is, do you know any big neuronal network that people have been published, using LFPy in it?
Because what I read from Linden et al. 2013, is LFPy couldn't support paralleled computing of NEURON.
Thanks in advance.
by breakwave922
Fri Nov 13, 2015 11:20 pm
Forum: Modeling networks
Topic: How to run the simulation in-between?
Replies: 28
Views: 8792

Re: How to run the simulation in-between?

Hi, Hines, Yes, I didn't close the file on return from savestate.fread and savestate.fwrite. Please see following codes: ss.fwrite(f, 0) for i=0,randomlist.count-1 { f.printf("%g\n", randomlist.o(i).seq()) } f.close } proc init() { finitialize() s = new String() sprint(s.s, "svst.%04d", pc.id) f = n...
by breakwave922
Fri Nov 13, 2015 6:31 pm
Forum: Modeling networks
Topic: How to run the simulation in-between?
Replies: 28
Views: 8792

Re: How to run the simulation in-between?

Hi, Hines, Thanks for the help. Yes, I've been trying to debug this issue step-by-step. I created a small network with only 100 cells. I printed out the sequences saved and restored. But I'm not sure whether I did it correctly. Below is what I did. For the first part of the simulation, I saved the s...