NetPyNE Q&A forum

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NetPyNE (www.netpyne.org) is a high-level python interface to NEURON that facilitates the development, parallel simulation and analysis of biological neuronal networks. This Q&A forum enables users and developers to post questions, answers and comments about the tool.

Our previous Q&A forum with many posts can be found here: https://www.neuron.yale.edu/phpBB/viewforum.php?f=45

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gyumin park, … 박규민3

Apr 22

I couldn't get a raster image for tutorial 7

Thank you for your help :) 2024년 4월 19일 금요일 오전 11시 59분 43초 UTC+9에 JC님이 작성: Hello, The issue is `

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I couldn't get a raster image for tutorial 7

Thank you for your help :) 2024년 4월 19일 금요일 오전 11시 59분 43초 UTC+9에 JC님이 작성: Hello, The issue is `

Apr 22

Eugenio Urdapilleta

Apr 15

Join the next NetPyNE bimonthly online meeting on April 18!

Hi all, We would like to invite you to the next NetPyNE bimonthly online meeting on Thursday April 18

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Join the next NetPyNE bimonthly online meeting on April 18!

Hi all, We would like to invite you to the next NetPyNE bimonthly online meeting on Thursday April 18

Apr 15

Apr 2

Plotting figures after individual sim runs in a batch simulation

Hi James, I realized I had errors in my code! So i am indeed able to execute lines after sim.analyze(

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Plotting figures after individual sim runs in a batch simulation

Hi James, I realized I had errors in my code! So i am indeed able to execute lines after sim.analyze(

Apr 2

Da Som Choi, J C2

Feb 26

NetPyNE batch simulation problem: Unable to run whole params at one time.

Hello, Are you running with the "mpi_direct" method or the "mpi_bulletin" method?

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NetPyNE batch simulation problem: Unable to run whole params at one time.

Hello, Are you running with the "mpi_direct" method or the "mpi_bulletin" method?

Feb 26

Katherine Doxey

Feb 8

Error with setting VecStim population parameters

Hi, I am attempting to input poisson distributed spike trains to synapses in a single cell model by

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Error with setting VecStim population parameters

Hi, I am attempting to input poisson distributed spike trains to synapses in a single cell model by

Feb 8

Reza, Eugenio Urdapilleta10

Jan 31

Importing my own .hoc network file into the GUI

Hi Reza, try the next .py. Attached also a pic of the GUI implementation (upload + import). Regarding

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Importing my own .hoc network file into the GUI

Hi Reza, try the next .py. Attached also a pic of the GUI implementation (upload + import). Regarding

Jan 31

Jan 24

Batch simulations using 'evol' method

Sorry, yes you are correct-- this will sample: 0.01 < prob < 0.5 0.001 < weight < 0.1 1

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Batch simulations using 'evol' method

Sorry, yes you are correct-- this will sample: 0.01 < prob < 0.5 0.001 < weight < 0.1 1

Jan 24

Irene Bettini, … J C5

Jan 24

problems implementing NetPyNE batch simulation

Thanks for the followup Irene, I'm not sure what is happening, but it seems like some resource is

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problems implementing NetPyNE batch simulation

Thanks for the followup Irene, I'm not sure what is happening, but it seems like some resource is

Jan 24

Katherine Doxey, Eugenio Urdapilleta8

Jan 11

Issue with single cell simulations (firing with no input)

This fixed it!! Thank you so much for all your help. On Thursday, January 11, 2024 at 3:42:37 PM UTC-

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Issue with single cell simulations (firing with no input)

This fixed it!! Thank you so much for all your help. On Thursday, January 11, 2024 at 3:42:37 PM UTC-

Jan 11

Maliha A, Eugenio Urdapilleta2

Jan 9

Literature on parameter estimation (coupling strengths) for neuronal networks

Hi Maliha, sure there is plenty of methods, but one certain thing is that you will need to measure

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Literature on parameter estimation (coupling strengths) for neuronal networks

Hi Maliha, sure there is plenty of methods, but one certain thing is that you will need to measure

Jan 9

zirui wang, Eugenio Urdapilleta2

Jan 9

LFP signal baseline offset, fluctuate below baseline 0

Hi Zirui, what are the coordinates of neurons in both regions? Are they unintenionally intermingled?

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LFP signal baseline offset, fluctuate below baseline 0

Hi Zirui, what are the coordinates of neurons in both regions? Are they unintenionally intermingled?

Jan 9

linjin liu, Ankur Sinha2

12/29/23

Netpyne import issue

Hello, On Thu, Dec 28, 2023 23:46:29 -0800, linjin liu wrote: > How can I import a Python file

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Netpyne import issue

Hello, On Thu, Dec 28, 2023 23:46:29 -0800, linjin liu wrote: > How can I import a Python file

12/29/23

Maliha A, Valery Bragin2

10/13/23

Specify colours in rasterplot

Hi Maliha, You can use `popColors` parameter, which takes dictionary of populations labels and colors

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Specify colours in rasterplot

Hi Maliha, You can use `popColors` parameter, which takes dictionary of populations labels and colors

10/13/23

zirui wang, Eugenio Urdapilleta2

9/12/23

how to reset kernel in netpyne

Hi Zirui, to get different results you should probably feed different trials with different seeds.

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how to reset kernel in netpyne

Hi Zirui, to get different results you should probably feed different trials with different seeds.

9/12/23

Ben Henderson, … Gin Estrella Cruz4

8/18/23

Problem with importing cells

I'm somewhat glad to hear that I'm not the only one with this problem. I've been trying

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Problem with importing cells

I'm somewhat glad to hear that I'm not the only one with this problem. I've been trying

8/18/23

8/15/23

Join the next NetPyNE bimonthly online meeting on August 17!

Hi all, We would like to invite you to the next NetPyNE bimonthly online meeting on Thursday August

unread,

Join the next NetPyNE bimonthly online meeting on August 17!

Hi all, We would like to invite you to the next NetPyNE bimonthly online meeting on Thursday August

8/15/23

yamazaki, Valery Bragin2

7/30/23

LFP calculation using VecStim

Hi yamazaki, You can use the same repo you've referenced before, but check out the branch `LFP` -

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LFP calculation using VecStim

Hi yamazaki, You can use the same repo you've referenced before, but check out the branch `LFP` -

7/30/23

yamazaki, Valery Bragin7

7/27/23

simconfig.recordLFP error

Hi Valery, Thank you for your coorperation! For example, there was an error occurring with L23_PC_cAD

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simconfig.recordLFP error

Hi Valery, Thank you for your coorperation! For example, there was an error occurring with L23_PC_cAD

7/27/23

Tomás Baima, … Eugenio Urdapilleta8

7/25/23

Why does HH netpyne model not generate a spike train if stimulus is sustained?

Hi Tomás, the issue of setting properly the values in a detailed morphology is not easy. You have to

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Why does HH netpyne model not generate a spike train if stimulus is sustained?

Hi Tomás, the issue of setting properly the values in a detailed morphology is not easy. You have to

7/25/23

Chris Fink, … J C7

7/23/23

NetPyNE hanging with MPI

Just to close the loop on this thread, I ran this with MPI on Windows Subsystem Linux, and it

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NetPyNE hanging with MPI

Just to close the loop on this thread, I ran this with MPI on Windows Subsystem Linux, and it

7/23/23

Tim Petitjean, hassan gobara2

7/19/23

Running a simulation infinitely

Hello , I didn't understand what do you mean by simulation period might affect your result

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Running a simulation infinitely

Hello , I didn't understand what do you mean by simulation period might affect your result

7/19/23

Tomás Baima, … hassan gobara3

7/13/23

LFP plotting size error

Hi Tomàs , thanks for explanation , Could you just tell me how did you make the synaptic mechs ? .

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LFP plotting size error

Hi Tomàs , thanks for explanation , Could you just tell me how did you make the synaptic mechs ? .

7/13/23

Gin Cruz, … Eugenio Urdapilleta9

7/11/23

plotting 3D morphology

Hi Shaina, I dug into your problem with this tutorial, as I also get nothing to watch when running it

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plotting 3D morphology

Hi Shaina, I dug into your problem with this tutorial, as I also get nothing to watch when running it

7/11/23

zirui wang, … Eugenio Urdapilleta3

7/10/23

how to run a single simulation step in netpyne

Yes, also if you want only to monitor the temporal progress of your simulation you can simply add

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how to run a single simulation step in netpyne

Yes, also if you want only to monitor the temporal progress of your simulation you can simply add

7/10/23

Hyun Jae Jang, … hassan gobara3

7/1/23

Recording timings from net_event

hello , i have inquiry regarding this issue as well , how would I set vector with certain molucular

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Recording timings from net_event

hello , i have inquiry regarding this issue as well , how would I set vector with certain molucular

7/1/23

6/21/23

computational neuroscience postdoc position

A postdoctoral scientist position is available at the Nathan Kline Institute (NKI) for Psychiatric

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computational neuroscience postdoc position

A postdoctoral scientist position is available at the Nathan Kline Institute (NKI) for Psychiatric

6/21/23

Tim Petitjean, … Valery Bragin4

6/9/23

real time result with the simulation

Hello Tim, Yes, you can do it using the method described in previous answer. You'll need to

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real time result with the simulation

Hello Tim, Yes, you can do it using the method described in previous answer. You'll need to

6/9/23

Ananya Muguli, Valery Bragin3

6/8/23

Recording the evolution of various state variables.

Hey Valery, Thank you so much! Your suggestion seems to work. -Best Ananya On Thu, Jun 8, 2023 at 4:

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Recording the evolution of various state variables.

Hey Valery, Thank you so much! Your suggestion seems to work. -Best Ananya On Thu, Jun 8, 2023 at 4:

6/8/23

6/5/23

Adding extracellular mechanism along with reaction diffusion

Hello, I have been meaning to simulate extracellular stimulation. I have a few RxD multi-compartment

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Adding extracellular mechanism along with reaction diffusion

Hello, I have been meaning to simulate extracellular stimulation. I have a few RxD multi-compartment

6/5/23

Ananya Muguli, … Valery Bragin6

6/2/23

Error in string functions.

Hey Valery, Thank you so much. That sorted out the issue! -Best Ananya On Tuesday, May 30, 2023 at 1:

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Error in string functions.

Hey Valery, Thank you so much. That sorted out the issue! -Best Ananya On Tuesday, May 30, 2023 at 1:

6/2/23

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