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An interactive web-based conserved synteny browser application
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README.md

JAX Synteny Browser

An interactive web-based conserved synteny browser application, The Jackson Laboratory (JAX) Synteny Browser. The browser allows researchers to highlight or selectively display genome features in the reference and/or the comparison genomes based on the biological attributes of the features. The current implementation for the browser supports the reference genomes of the laboratory mouse and human.

There is a live, working version of Synteny Browser available at: syntenybrowser.jax.org

User documentation can be found here.

Setting up/Running Synteny Browser Locally

Prerequisites

Note: if you are running Windows some of the commands below might need to be altered Before starting the setup process, you'll need:

  1. A bash terminal (Mac OS X & Linux will have this included) or a way of running shell scripts
  2. A version of Python installed on your machine
  3. The pip Python library installed on your machine (your version of Python might have Pip included by default, but if not, you'll have to install it manually)

Assuming you have all of the above items, you'll need a Python library called Virtualenv which will allow you to run Python scripts in isolated environments that can have their own dependencies, versions, and permissions without messing with those belonging to your machine. To set up Virtualenv open up a bash and navigate to the root syntenybrowser/ directory (all of the following commands are run from this directory unless otherwise noted) and install Virtualenv:

pip install virtualenv

Note: if you're running Python 3, you may have to run pip3 install virtualenv.

Getting a Database

Once Virtualenv is installed, you'll need a database. To do this, you have two options:

Option 1: Download a preloaded database

A ready-made database is available from Box here named 'syntenybrowser-db.zip' and, when decompressed, will yield a file named 'synteny.db'. This .db file will need to be located in the root syntenybrowser/ directory before running the application, otherwise the application will not run.

Option 2: Load a database yourself

(if you went with Option 1, skip to 'Setting Up the Application') To load your own database, you'll need a virtual environment that runs in Python3.6:

virtualenv venv-db -p python3.6

Once created, activate the virtual environment:

. venv-db/bin/activate

Install necessary packages:

pip install -r requirements.txt

Run the database creation script with the required parameter:

./create_database.sh synteny.db

Note: we have found that one of the scripts that queries data from an API can run into issues if you are using a VPN This will take several minutes and when it's finished, it will yield a file named 'synteny.db' in root syntenybrowser/ directory (the database file needs to be located here so don't move it). Shut down the venv-db virtual environment:

deactivate

Setting Up the Application

Next, you'll need to get the application running using your new database (if you're at this step and haven't gotten a database using one of the two available options listed above, you'll need to do that first). To do this, we'll need a separate virtual environment that runs in Python2.7:

virtualenv venv-app -p python2.7

Once created, activate the virtual environment:

. venv-app/bin/activate

Install necessary packages:

pip install -r requirements.txt

Running the Application

Make sure the the application virtual environment is running. If it isn't, start it up (if it is, skip to the next step):

. venv-app/bin/activate

Run the application:

python runserver.py

When finished, shut down the virtual environment:

deactivate

Running the Synteny Browser from the Docker Image

Prerequisites

  1. A bash terminal (Mac OS X & Linux will have this included) or a way of running shell scripts
  2. Docker installed on your machine

Pull the image

Start docker on your machine and once running, pull the image using

docker pull lamoua/synbrowser

Once the image is done pulling from DockerHub, run the container

docker run -p 5001:5001 synbrowser:latest

This should set off the container as well as start the Python Flask server. Navigating to the specified location (which should be localhost:5001 by default), should bring you to the JAX Synteny Browser interface running from the container.

Citation

The JAX Synteny Browser for Mouse-Human Comparative Genomics.

Manuscript in review

License

The JAX Synteny Browser is provided under the license found here.

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