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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Aug 26

Time-dependent background stimulation

Hi all, I'm fairly new to NetPyne, and I'm attempting to stimulate a group of cells with a

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Time-dependent background stimulation

Hi all, I'm fairly new to NetPyne, and I'm attempting to stimulate a group of cells with a

Aug 26

alex, … Maliha A8

Jul 30

recording synaptic conductance

So I've understood now that the above implementation does not lead to the result I'm aiming

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recording synaptic conductance

So I've understood now that the above implementation does not lead to the result I'm aiming

Jul 30

Jul 9

Using simLabel to run different simulations in a jupyter notebook

Hi all, I think I found a way now. I can simply assign sim1 = sim.allSimData (and similarly for sim2)

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Using simLabel to run different simulations in a jupyter notebook

Hi all, I think I found a way now. I can simply assign sim1 = sim.allSimData (and similarly for sim2)

Jul 9

Katarzyna Piekarz, … Reza3

Jun 12

self-connections

Hello there! Can you also please let me know where exactly we need to put this and how can we make it

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self-connections

Hello there! Can you also please let me know where exactly we need to put this and how can we make it

Jun 12

Arpit Shrimankar, … Reza7

Jun 12

regarding netpyni gui upload mod files

Hello guys! While I am trying to have Izhikevich mechanism, I get the following error: [ netParams.

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regarding netpyni gui upload mod files

Hello guys! While I am trying to have Izhikevich mechanism, I get the following error: [ netParams.

Jun 12

Jun 11

plotRaster() issue

Solved! Just remove the "!pip install netpyne" and clone netpyne from github from scratch.

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plotRaster() issue

Solved! Just remove the "!pip install netpyne" and clone netpyne from github from scratch.

Jun 11

Jun 11

Arbor protruding problem in direct current stimulation to cortical surface

Hello everyone, I am currently working on simulating direct current stimulation from cortical surface

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Arbor protruding problem in direct current stimulation to cortical surface

Hello everyone, I am currently working on simulating direct current stimulation from cortical surface

Jun 11

Ivan Shevchenko, … Reza5

May 31

SyncLines not working in Tutorial 7

Hi Valery Thank you for your time. I have done all the above but it seems I still have issues

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SyncLines not working in Tutorial 7

Hi Valery Thank you for your time. I have done all the above but it seems I still have issues

May 31

Reza, Eugenio Urdapilleta6

May 17

NetStim Visualisation

Hello guys! How can we show the input stimulation source? As we have netParams.stimSourceParams[

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NetStim Visualisation

Hello guys! How can we show the input stimulation source? As we have netParams.stimSourceParams[

May 17

Reza, Eugenio Urdapilleta2

May 16

Modifying the hoc values from Python

Hi Reza, maybe in the NEURON forum they can give you the best answer, but it seems that you need to

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Modifying the hoc values from Python

Hi Reza, maybe in the NEURON forum they can give you the best answer, but it seems that you need to

May 16

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

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