4D Genome Browser project

The 4D Genome Browser is a toolkit for querying and visualizing genomics data through the web. It consists of a few different components:

• A web server that responds to queries for data and serves either raw JSON data or webpages displaying visualizations of the data.
• A python library for making requests to such a server
• A Javascript browser library for visualizing data.

Data is formatted into "projects". A project consists of all of the input data files and a project.json file describing the files along with settings for viewing them. A project can then be "compiled", having all of its data incorporated into an SQLite database. This database is what the web server queries to serve data. A "release" of a project consists of a copy of the server code, the projectg directory, the project database, static files (including a minified version of the javascript library) along with a copy of the python library for querying the server.

To set up

Initialize Python and npm:

# Create a python virtual environment
python3 -m venv venv/
source venv/bin/activate
pip3 install -r requirements.txt

# Init npm
cd client-js/
npm install

To run the application locally (with Python Flask)

• Make a release, then run the release server:

  ./bin/make_release <project>

• Execute the testing server in a release directory

  python3 release/<project>/server/gtkserver.py --port 8000

For example, to run the test.01 project in this repository:

./bin/make_release test.01
python3 release/test.01/server/gtkserver.py --port 8000

From there, open a web browser to localhost:8000 to view the project page:

Clicking on the grey zone or the image of the app will take you to the running instance: