metacell / neuron-ui

NEURON User Interface

NEURON-UI

This repository hosts an experimental prototype for a new user interface for NEURON based on web technologies.

Install using Docker (self-contained, the simplest)

First install Docker from here.

Install NEURON-UI using Docker graphical interface (Kitematic)

Open Kitematic from Docker menu (will install Kitematic if you don't have it already)

Search for neuron-ui and create the container.

Start the container and click on Web preview to launch it. No need to ever use the command line, enjoy!

Install NEURON-UI using Docker from command line

docker pull metacell/neuron-ui
docker run -it -p 8888:8888 metacell/neuron-ui

Open your browser and connect to http://localhost:8888/geppetto.

Install NEURON-UI using pip

pip install neuron_ui
jupyter nbextension enable --py jupyter_geppetto
NEURON-UI

Install from sources (for developers and for using your own NEURON models)

git clone https://github.com/MetaCell/NEURON-UI.git
cd utilities
python install.py
cd ..
./NEURON-UI

To update sources:

python update.py

The available functionality is currently limited to the RunControl panel, a basic cell builder, a simplified point process manager that lets you inject a current clamp and space plot functionality.

This prototype is being developed in collaboration with the Neurosim Lab and the Sense Lab.

The UI connects to nrnpython through a Geppetto extension for Jupyter Notebook.

See the Wiki for more info!

neuron-ui's Issues

Request: allow closing/minimizing NEURON example model(s) dialog

takes up too much space in laptop browser windows

Request: support running models with MPI

Request support for running models with MPI - and allow selecting number of cores, etc.

Request: widgets with png images

Request: widgets that allow matplotlib drawings/canvas

Request: widgets that allow matplotlib drawings/canvases from within the browser

Request: Programmatic/API control of NEURON-UI

Request: Programmatic/API control of NEURON-UI supporting both Python & Javascript calls/interfaces. Python calls of Javascript functions useful too.

installation difficulty

I have ubuntu 16.4
Python 2.7.12 (default, Nov 19 2016, 06:48:10)
[GCC 5.4.0 20160609] on linux2

python install.py
got a long was but stopped at
You are using pip version 8.1.1, however version 9.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Installing Geppetto Jupyter Extension ...
Traceback (most recent call last):
File "install.py", line 76, in
run_nbextension_install(False)
File "install.py", line 10, in run_nbextension_install
from notebook.nbextensions import install_nbextension_python, enable_nbextension_python, install_nbextension
ImportError: No module named notebook.nbextensions

pip install --upgrade pip
was successful but
$ python install.py
Cloning Geppetto Jupyter (Python package)...
fatal: destination path 'org.geppetto.frontend.jupyter' already exists and is not an empty directory.
Checking out development branch for Geppetto Jupyter ...
M src/geppettoJupyter/geppetto
Already on 'development'
Your branch is up-to-date with 'origin/development'.
error: pathspec 'integratingPlot' did not match any file(s) known to git.
Cloning Geppetto Neuron Configuration ...
fatal: destination path 'geppetto-neuron' already exists and is not an empty directory.
Already on 'master'
Your branch is up-to-date with 'origin/master'.
Enabling Geppetto Neuron Configuration ...
...
Installing Geppetto Jupyter Extension ...
Enabling geppettoJupyter extensions ...
Installing geppettoJupyter extension ...
Traceback (most recent call last):
File "install.py", line 76, in
run_nbextension_install(False)
File "install.py", line 22, in run_nbextension_install
install_nbextension_python('geppettoJupyter', symlink=develop)
File "/home/hines/.local/lib/python2.7/site-packages/notebook/nbextensions.py", line 239, in install_nbextension_python
destination=dest, logger=logger
File "/home/hines/.local/lib/python2.7/site-packages/notebook/nbextensions.py", line 140, in install_nbextension
ensure_dir_exists(nbext)
File "/home/hines/.local/lib/python2.7/site-packages/ipython_genutils/path.py", line 167, in ensure_dir_exists
os.makedirs(path, mode=mode)
File "/usr/lib/python2.7/os.py", line 150, in makedirs
makedirs(head, mode)
File "/usr/lib/python2.7/os.py", line 157, in makedirs
mkdir(name, mode)
OSError: [Errno 13] Permission denied: '/usr/local/share/jupyter'

run on windows ?

can it will be run on windows os ?
i have win 10 , alongwith ANaCONDA is installed with python .
soes it will work?
if yes than how ?

thank you
waiting for your rresponse

Request: tabbed widget support

Add a widget which supports tabs. Each tab has its own interface components.

Fonts Roboto Missing

Referenced by material.css, without it there is an error.
By inspecting the browser console found the error causing Python console not to work.