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A web-based GUI application for NEST simulator (legacy, moved to https://github.com/nest-desktop/nest-desktop)

Home Page: https://github.com/nest-desktop/nest-desktop

License: Other

HTML 23.08% Dockerfile 0.53% Shell 0.42% Python 0.21% JavaScript 0.27% TypeScript 70.79% SCSS 4.66% Jinja 0.03%

nest-desktop-legacy's Introduction

❗ This repository is no longer maintained and moved to https://github.com/nest-desktop/nest-desktop

NEST Desktop

An interactive desktop application for NEST simulator

Introduction

In the past few years, we have developed a web-based graphical user interface (GUI) for the NEST simulation code of the NEST Desktop. This GUI enables the rapid construction, parametrization, and instrumentation of neuronal network models typically used in computational neuroscience. The primary objective of our development was to create a tool of classroom strength that allows non-specialists to rapidly explore interesting neuroscience concepts without the need to learn a simulator control language at the same time.

To date, we have used NEST Desktop very successfully in two courses at the University of Freiburg addressing students at the bachelor, master, and graduate level with diverse background including biology, physics, computer science and electrical engineering (Single Neuron Modeling and Biophysics of Neurons and Networks). NEST Desktop replaced the Mathematica notebooks we used for many years. With the new tool, we observed much faster learning progress than before and a highly motivating effect on the side of the students.

Currently, NEST Desktop requires NEST Server with a full NEST installation, limiting uptake by a non-expert audience and limiting networks studied to such that can be simulated on a laptop. To ease the use of NEST Desktop and the range of simulations possible with NEST Desktop, we want to separate GUI from simulation kernel, rendering the GUI in the web browser of the user, while the simulation kernel is running on a centrally maintained server.

Setup

To install NEST Desktop:

pip3 install nest-desktop

Usage

To start NEST Desktop:

nest-desktop start [-h 127.0.0.1 -p 8000]

Alternatively, to start NEST Server in Python interface (e.g. IPython, Jupyter):

from nest_desktop import app
app.run(host='127.0.0.1', port=5000)

Open a web browser with this link http://127.0.0.1:8000.

Troubleshootings

With version upgrading some configurations or database might not be compatible. Sometimes it helps when you reset configurations or databases. If not, then clear the browsing data.

License MIT

nest-desktop-legacy's People

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hubbucket-team soehrl jessica-mitchell sarakonradi mwolfr jougs hardworkingchris clinssen

nest-desktop-legacy's Issues

spike count plot does not show after simulating

When clicking the run simulation button, the first display of results has the raster plot filled, but the spike-count graph below is empty. When zooming into the raster plot the spike-count graph is updated and shows reasonable peaks.

Ideally all displayed plots show up directly after simulation.

* error linking uWSGI *

ERROR: Failed building wheel for uwsgi
I got this error for linking uWSGI

It would be great if you help me with this error.
Thanks.

Danylo's Feedback

As Denis mentioned, when I uploaded the json network, I expected to see it immediately. However, the user needs to notice that the network has appeared on the left side.
I'd like to see the Trash button on the very right thin panel that clears the simulation results with a confirmation popup.
Refreshing the page removes the simulation results without notifying the user of this behavior.
Simulate button (upper right) comes with the confusing icon which is often used as the icon for settings, but not for the launching something. A more intuitive button icon would be a simple Play icon.

Other than that, it worked fine for me.

Request Header Or Cookie Too Large

Reloading resulted in

400 Bad Request
Request Header Or Cookie Too Large

on chromium.

Application is not available

When going to the URL, instead of NEST Desktop or a login window showing up I sometimes get this error message:

I noticed that eventually the tab gets redirected to the login page, when I stare at it long enough. Loging in, then sometimes works, or it just gives:

Nest server not found!

I got this error:
Simulation failed. NEST Server not found. Please check the configuration.
could you please give me a help?
I installed my nest with conda command.

Spike count histogram bars disappearing

When making the browser window narrower, the spike count histogram bars gradually become thinner. The problem here is that at some point, they disappear completely. When setting a large simulation time (e.g. 10000ms), the browser window need to be very wide in order to see any bars.

NEST-Desktop behind a proxy

Hi everyone,

I would like to use NEST-Desktop behind a proxy, but the javascript functions are looking for the assets on the wrong path. Is there a way to tell NEST-Desktop where to look for the assets?

Context:
I created a Docker image based on jupyter/datascience. I added a server proxy extension for JupyterLab and installed nest-desktop in a conda environment. (Dockerfile is here)

However, I'm able to run nest-desktop start in my JupyterLab Terminal. But if I want to open it at the path https://<my_jupyterhub_server>/user/user_name/server_name/proxy/8000/ it is looking for the assets at https://<my_jupyterhub_server>/hub/assets/... , while instead it has to use the path above.

Is there any way to configure nest-desktop in that way? I assume that there are more usecases for this, for example running NEST-Desktop behind a nginx proxy at a specific path.

Thanks,
Tim

Log from Firefox Console:
Object { headers: {…}, status: 404, statusText: "Not Found", url: "https://jupyter-jsc.fz-juelich.de/hub/assets/config/app/groups.json" ...

JupyterLab Screenshot
NEST-Desktop Screenshot