DynaSim Users

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Welcome to the E-mail Archive for the DynaSim Users mailing list!

DynaSim is a toolbox for modeling and simulating dynamical systems in Matlab.

You can download the DynaSim toolbox at: https://dynasimtoolbox.org.

You can use sign up for the mailing list at http://groupspaces.com/dynasim.

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Julian Thrash

Nov 21

Deploying DynaSim to a MATLAB Packaged App Issue

Hi, I'm a new user to DynaSim and working on a project designing an app interface for a

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Deploying DynaSim to a MATLAB Packaged App Issue

Hi, I'm a new user to DynaSim and working on a project designing an app interface for a

Nov 21

Jian Carlo Nocon

10/14/21

Problem with implementing large synaptic delays

Hi all, I'm trying to implement a large synaptic delay between two populations of neurons in

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Problem with implementing large synaptic delays

Hi all, I'm trying to implement a large synaptic delay between two populations of neurons in

10/14/21

Jason Sherfey

9/15/21

Job Opportunity (Fall 2021)

Hello DynaSim Users and Developers, Is anyone interested in working with me on a small project this

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Job Opportunity (Fall 2021)

Hello DynaSim Users and Developers, Is anyone interested in working with me on a small project this

9/15/21

Gunjan Sharma, … Jason Sherfey5

3/16/21

error in ds_simulate

Thank you Jason, the code is working now. On Tuesday, March 16, 2021 at 5:00:32 AM UTC+5:30 jssh...@

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error in ds_simulate

Thank you Jason, the code is working now. On Tuesday, March 16, 2021 at 5:00:32 AM UTC+5:30 jssh...@

3/16/21

Wei, Jingjin

1/14/21

Using dynasim to generate inhibitory synaptic current at specified frequency

Hi all, I was wondering if anyone has experience generating a rhythmic inhibitory synaptic current (

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Using dynasim to generate inhibitory synaptic current at specified frequency

Hi all, I was wondering if anyone has experience generating a rhythmic inhibitory synaptic current (

1/14/21

thomas....@ugent.be

8/11/20

Is Euler in Dynasim forward or backward?

Hi all, I was wondering if the 'Euler' solver in Dynasim (dsSimulate(spec,'solver',

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Is Euler in Dynasim forward or backward?

Hi all, I was wondering if the 'Euler' solver in Dynasim (dsSimulate(spec,'solver',

8/11/20

Wei, Jingjin, … Julia Chartove6

7/23/20

Describe white noise intensity

Popping in with a general comment that it would be great if the Dynasim documentation (or some

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Describe white noise intensity

Popping in with a general comment that it would be great if the Dynasim documentation (or some

7/23/20

Bolun Chen, Jason Sherfey via DynaSim3

4/28/20

Re: [DS] Solving stochastic differential equations

Hi Jason, Thank you for the quick reply and suggestions. I'll try to implement a sde solver and

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Re: [DS] Solving stochastic differential equations

Hi Jason, Thank you for the quick reply and suggestions. I'll try to implement a sde solver and

4/28/20

Salva Ardid2

4/2/20

Re: [DS] Matrix for strength of the connection values?

Actually disregard what I said before, I don't think it is correct. On second thoughts, I think

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Re: [DS] Matrix for strength of the connection values?

Actually disregard what I said before, I don't think it is correct. On second thoughts, I think

4/2/20

yar...@gmail.com, Erik Roberts2

3/16/20

Error with rastergram

to help us help you, temporarily edit dsPlot, write a line write above it with “keyboard”, then

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Error with rastergram

to help us help you, temporarily edit dsPlot, write a line write above it with “keyboard”, then

3/16/20

Young-Ah Rho, Ardid, Salva2

2/21/20

Errors when using R2019b Matlab in the Mac OS (Mojave, Version 10.14.6)

This should be fixed in the dev branch, else please open a new issue in the github repo. For

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Errors when using R2019b Matlab in the Mac OS (Mojave, Version 10.14.6)

This should be fixed in the dev branch, else please open a new issue in the github repo. For

2/21/20

thomas....@ugent.be, Ardid, Salva4

12/4/19

Gap junction depends on the pre- and postsynaptic intracellular concentrations

Yes, that seems right. Perhaps it is different in the Dev branch, but I'm not sure. What Dynasim

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Gap junction depends on the pre- and postsynaptic intracellular concentrations

Yes, that seems right. Perhaps it is different in the Dev branch, but I'm not sure. What Dynasim

12/4/19

Wei, Jingjin, Erik Roberts3

11/18/19

dsCheckData doesn't work for data matrix

Hi Erik, In many analytic functions in dynasim, at the very begining there is this line: % Check

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dsCheckData doesn't work for data matrix

Hi Erik, In many analytic functions in dynasim, at the very begining there is this line: % Check

11/18/19

Wei, Jingjin, … Erik Roberts7

11/17/19

Warning: File '.lock_20190706105733336_10000000' not found.

i would debug it manually: run it again after putting a keyboard/debug halt before dsCreateBatch (

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Warning: File '.lock_20190706105733336_10000000' not found.

i would debug it manually: run it again after putting a keyboard/debug halt before dsCreateBatch (

11/17/19

Wei, Jingjin

11/15/19

How to change/specify the project the job is submitted to (cluster_flag=1)

Hi Dynasim community: In case you use BU clusters and know what happens with cluster_flag=1: How does

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How to change/specify the project the job is submitted to (cluster_flag=1)

Hi Dynasim community: In case you use BU clusters and know what happens with cluster_flag=1: How does

11/15/19

Erik Roberts

11/7/19

Vary Population Size Trick

To effectively vary population size: Have max population size. Have a function take a scalar for

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Vary Population Size Trick

To effectively vary population size: Have max population size. Have a function take a scalar for

11/7/19

Wei, Jingjin, … Erik Roberts3

7/25/19

Save partial data

1) for subsets of data (when save_data_flag=1): look at the options in dsExportData used in

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Save partial data

1) for subsets of data (when save_data_flag=1): look at the options in dsExportData used in

7/25/19

Wei, Jingjin, Erik Roberts2

7/5/19

Adding a mechanism twice to the same population.

no, each mech has to be unique for each population. also each param is tried for each mech,

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Adding a mechanism twice to the same population.

no, each mech has to be unique for each population. also each param is tried for each mech,

7/5/19

Wei, Jingjin

6/15/19

Issue: vary both population size doesn't work properly with dsSimulate

Hi all, When varying two population sizes and maintain its ratio, I did: vary = {'(E,I)',

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Issue: vary both population size doesn't work properly with dsSimulate

Hi all, When varying two population sizes and maintain its ratio, I did: vary = {'(E,I)',

6/15/19

Wei, Jingjin, Erik Roberts2

6/13/19

dsCalcPower calculate the wrong variable

it's a regular expression, try this: dsSelectVariables(data, 'E_V$') On Jun 13, 2019, at

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dsCalcPower calculate the wrong variable

it's a regular expression, try this: dsSelectVariables(data, 'E_V$') On Jun 13, 2019, at

6/13/19

Wei, Jingjin, Jason Sherfey2

6/11/19

Reset during a simulation

Hi Jingjin, Here's one way to do it. This should work equally well for a population of cells.

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Reset during a simulation

Hi Jingjin, Here's one way to do it. This should work equally well for a population of cells.

6/11/19

Wei, Jingjin, Erik Roberts2

6/3/19

Turn on the notation of varied parameter

Not that I know of. It doesn't float over the figure so sometimes it's not visible due to

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Turn on the notation of varied parameter

Not that I know of. It doesn't float over the figure so sometimes it's not visible due to

6/3/19

Wei, Jingjin, Erik Roberts2

6/3/19

varying gAMPA and gGABAa together

Here are the ways to covary pairs and specify sets: ``` % Vary two parameters (run a simulation for

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varying gAMPA and gGABAa together

Here are the ways to covary pairs and specify sets: ``` % Vary two parameters (run a simulation for

6/3/19

Wei, Jingjin

5/31/19

dsCalcFR in dev branch

When I have more than 1 input in dsCalcFR, like dsCalcFR(data,'bin_size',100); There is an

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dsCalcFR in dev branch

When I have more than 1 input in dsCalcFR, like dsCalcFR(data,'bin_size',100); There is an

5/31/19

Wei, Jingjin, Erik Roberts2

5/31/19

Dynasim issues (qsub on newer MATLAB versions and dsPlotFR)

add 2018b to the dsCheckOptions file to try using it. We don't have it there because it's

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Dynasim issues (qsub on newer MATLAB versions and dsPlotFR)

add 2018b to the dsCheckOptions file to try using it. We don't have it there because it's

5/31/19

Julia Chartove

5/29/19

seeking mechanisms

Does anyone have working files for an A-type potassium current or a high voltage activated L-type

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seeking mechanisms

Does anyone have working files for an A-type potassium current or a high voltage activated L-type

5/29/19

Julia Chartove, Erik Roberts2

5/21/19

dynasim not saving results/ running slowly

Try this to speed things up and reduce storage space: use dev branch with: one_solve_file_flag = 1

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dynasim not saving results/ running slowly

Try this to speed things up and reduce storage space: use dev branch with: one_solve_file_flag = 1

5/21/19

Wei, Jingjin2

5/9/19

A strange error 'Undefined function or variable 'X'.'

Nevermind please ignore my last email, turned out that I deleted a line by mistake and did not spot

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A strange error 'Undefined function or variable 'X'.'

Nevermind please ignore my last email, turned out that I deleted a line by mistake and did not spot

5/9/19

Wei, Jingjin, … Jason Sherfey4

5/8/19

time_limit option in dsCalcPower

I can't confirm that right now, but I do have a workaround if that's the case. You can use

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time_limit option in dsCalcPower

I can't confirm that right now, but I do have a workaround if that's the case. You can use

5/8/19

Wei, Jingjin, … Jason Sherfey5

5/6/19

Using time t as a input in functions?

Hi Jason, I forgot to reply all, it was solved. Thanks! Best, Jingjin From: dynasim-users@

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Using time t as a input in functions?

Hi Jason, I forgot to reply all, it was solved. Thanks! Best, Jingjin From: dynasim-users@

5/6/19