Search found 81 matches

by breakwave922
Fri Mar 01, 2019 3:54 pm
Forum: Parallel NEURON
Topic: multithreads for parallel NEURON code
Replies: 0
Views: 711

multithreads for parallel NEURON code

I need to do run my big-scale NEURON model some supercomputing resources (code is paralleled), but unfortunately, we are limited to get number of cores. To speedup, I was suggested to launch multiple threads by manually setting OMP_NUM_THREADS. I'm not sure NEURON can do this. My understanding is, t...
by breakwave922
Wed Feb 06, 2019 5:49 pm
Forum: Modeling networks
Topic: Is there any network model using extracellular mechanism in simulating DBS
Replies: 1
Views: 876

Is there any network model using extracellular mechanism in simulating DBS

I plan to implement deep brain stimulation (DBS) to a network model I’m working with. I’m wondering if there is any network level computational study with DBS. I noticed that some models used intracellular current injection to approximate the DBS. But I want to model it using extracellular induced f...
by breakwave922
Tue Oct 16, 2018 12:25 pm
Forum: Other questions
Topic: Using event delivery system with fixed time step method.
Replies: 7
Views: 1870

Re: Using event delivery system with fixed time step method.

2. The binary representation of dt must have a finite number of bits, AND that representation must be short enough to be handled by double precision arithmetic without error. In retrospect this is also obvious; if dt does not satisfy this criterion, sooner or later roundoff error will rear its ugly...
by breakwave922
Sun Oct 14, 2018 6:15 pm
Forum: Other questions
Topic: Using event delivery system with fixed time step method.
Replies: 7
Views: 1870

Re: Using event delivery system with fixed time step method.

Dear Ted and Hines, Since my question is similar to the thread here, I guess it's better to ask it here rather than having a new thread. I've been mired in the problem for several days... I have a network model which I already implemented calculating LFP at each time step. But to simplify, I don't h...
by breakwave922
Mon Oct 01, 2018 10:10 pm
Forum: Modeling networks
Topic: Real-time process on LFP
Replies: 4
Views: 1314

Re: Real-time process on LFP

No need to do off-line calculations. Use the Linear Circuit Builder to implement your filter, and you can filter any variable you like during a simulation. Linear Circuit Builder is definitely a good idea. Is it possible that we can use like "moving time window" to store some variables during a sim...
by breakwave922
Sun Sep 30, 2018 5:15 pm
Forum: Modeling networks
Topic: Real-time process on LFP
Replies: 4
Views: 1314

Re: Real-time process on LFP

Hi, Ted, Thanks for the reply. Is it possible that we can buffer a snippet of LFP data to the current time step, then band-pass filter these LFP data, and calculate the derivative of filtered LFP based on time step, if the derivative is negatively close to 0 (it stands for trough), we can activate C...
by breakwave922
Sat Sep 29, 2018 12:18 am
Forum: Modeling networks
Topic: Real-time process on LFP
Replies: 4
Views: 1314

Real-time process on LFP

Hi, I have a big-scale network model developed via NEURON, and with LFP calculated. What I want to do with LFP is, at each time step, I want to first band-pass filter LFP signal, and detect whether the filtered LFP signal is at trough. If it is, neurons with optogentic channel, like Chronos, will be...
by breakwave922
Fri Aug 10, 2018 2:56 pm
Forum: NEURON hacks
Topic: how to read single line from a file in HOC
Replies: 3
Views: 1121

Re: how to read single line from a file in HOC

Ted, Thanks for the reply. However, I still couldn't figure out how to read line-by-line from a file. For example, I have a txt data file with 3 lines, and data looks like: 12, 33 22, 3, 4 2, 3, 5, 7 If I want to read only 2nd line to have a vector with value [22,3,4], I tried scanf and fscan, and i...
by breakwave922
Thu Aug 09, 2018 12:07 pm
Forum: NEURON hacks
Topic: how to read single line from a file in HOC
Replies: 3
Views: 1121

how to read single line from a file in HOC

I have a txt file with a collection of vectors with different length. Vectors are stored in each line of this file.
Is there any way to read this file line by line in HOC? Because different lines have different lengths, I cannot use loadmatrix and getrow.

Thanks in advance.
by breakwave922
Wed Nov 29, 2017 10:37 pm
Forum: Parallel NEURON
Topic: summation of matrix on different computer nodes
Replies: 2
Views: 9999

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: 9999

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: 5323

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: 12337

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: 12337

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.