Neurolab

Docker image to provide HTML5 VNC interface to access Ubuntu 16.04 LXDE desktop environment with neuroscience tools installed.

Neuroscience tools provided:

• Anaconda3 with Jupyter Notebooks
• NEURON
• BMTK
• BMTOOLS

Quick Start

Run the docker container and access with port 6080

docker run -p 6080:80 -v /dev/shm:/dev/shm tylerbanks/neurolab:0.1.0

Browse http://127.0.0.1:6080/

Custom Commands

Update software

update-bmtk
update-bmtools

Run jupyter notebook

jupyter-notebook

VNC Viewer

Forward VNC service port 5900 to host by

docker run -p 6080:80 -p 5900:5900 -v /dev/shm:/dev/shm tylerbanks/neurolab:0.1.0

Now, open the vnc viewer and connect to port 5900. If you would like to protect vnc service by password, set environment variable VNC_PASSWORD, for example

docker run -p 6080:80 -p 5900:5900 -e VNC_PASSWORD=mypassword -v /dev/shm:/dev/shm tylerbanks/neurolab:0.1.0

A prompt will ask password either in the browser or vnc viewer.

HTTP Base Authentication

This image provides base access authentication of HTTP via HTTP_PASSWORD

docker run -p 6080:80 -e HTTP_PASSWORD=mypassword -v /dev/shm:/dev/shm tylerbanks/neurolab:0.1.0

SSL

To connect with SSL, generate self signed SSL certificate first if you don't have it

mkdir -p ssl
openssl req -x509 -nodes -days 365 -newkey rsa:2048 -keyout ssl/nginx.key -out ssl/nginx.crt

Specify SSL port by SSL_PORT, certificate path to /etc/nginx/ssl, and forward it to 6081

docker run -p 6081:443 -e SSL_PORT=443 -v ${PWD}/ssl:/etc/nginx/ssl -v /dev/shm:/dev/shm tylerbanks/neurolab:0.1.0

Screen Resolution

The Resolution of virtual desktop adapts browser window size when first connecting the server. You may choose a fixed resolution by passing RESOLUTION environment variable, for example

docker run -p 6080:80 -e RESOLUTION=1920x1080 -v /dev/shm:/dev/shm tylerbanks/neurolab:0.1.0

Default Desktop User

The default user is root. You may change the user and password respectively by USER and PASSWORD environment variable, for example,

docker run -p 6080:80 -e USER=doro -e PASSWORD=password -v /dev/shm:/dev/shm tylerbanks/neurolab

Deploy to a subdirectory (relative url root)

You may deploy this application to a subdirectory, for example /some-prefix/. You then can access application by http://127.0.0.1:6080/some-prefix/. This can be specified using the RELATIVE_URL_ROOT configuration option like this

docker run -p 6080:80 -e RELATIVE_URL_ROOT=some-prefix tylerbanks/neurolab

NOTE: this variable should not have any leading and trailing splash (/)

Sound (Preview version and Linux only)

It only works in Linux.

First of all, insert kernel module snd-aloop and specify 2 as the index of sound loop device

sudo modprobe snd-aloop index=2

Start the container

docker run -it --rm -p 6080:80 --device /dev/snd -e ALSADEV=hw:2,0 tylerbanks/neurolab

where --device /dev/snd -e ALSADEV=hw:2,0 means to grant sound device to container and set basic ASLA config to use card 2.

Launch a browser with URL http://127.0.0.1:6080/#/?video, where video means to start with video mode. Now you can start Chromium in start menu (Internet -> Chromium Web Browser Sound) and try to play some video.

Troubleshooting and FAQ

1. boot2docker connection issue, fcwu/docker-ubuntu-vnc-desktop#2
2. Multi-language supports, fcwu/docker-ubuntu-vnc-desktop#80
3. Autostart, fcwu/docker-ubuntu-vnc-desktop#85
4. x11vnc arguments(multiptr), fcwu/docker-ubuntu-vnc-desktop#101
5. firefox/chrome crash (/dev/shm), fcwu/docker-ubuntu-vnc-desktop#112
6. resize display size without destroying container, fcwu/docker-ubuntu-vnc-desktop#115 (comment)

License

See the LICENSE file for details.