BiCoN-web

Web tool of the BiCoN package for network-constrained biclustering of patients and multi-omics data.

A hosted version and demo of BiCoN-web can be found under: https://exbio.wzw.tum.de/bicon/

Table of Contents

• Installing BiCoN-web
  • Configuration of BiCoN-web
    • Configuration options
  • Deploying (automatically)
  • Deploying (manually)
• Updating and maintaining BiCoN-web (setup.sh)
• Starting and stoping BiCoN-web
• Managing volumes and data
• Cite
• Contact

Installing BiCoN-web

BiCoN-web comes in an easy to use docker-compose format.

To deploy BiCoN-web in a production environment, please ensure you have a working docker (and docker-compose) environment running. You find a manual for install docker on your operating system here.

Once docker is installed and running, clone this repository using the following command:

# First clone this repository and change into the created directory
git clone https://github.com/biomedbigdata/BiCoN-web.git && cd BiCoN-web

Configuration of BiCoN-web

The docker-compose file for BiCoN-web parses its configuration from the .env file. A .env.sample file is provided but it's not recommended to edit the file directly. We suggest you to specify your configuration inside the BiCoN-web.conf file and generate the .env file with the setup.sh script.

# First create a copy of the configuration sample
cp BiCoN-web.conf.sample BiCoN-web.conf

Open the file in a text editor and change the configuration to match your use case.

Configuration options:

• DJANGO_PRODUCTION: set to either true or false
• DJANGO_ALLOWED_HOSTS: Only really relevant for production use. Please check the Django documentation for more information
• POSTGRES/RABBITMQ passwords and username: Credentials for PostgreSQL and RabbitMQ Docker containers. They can be left with the default passwords as the containers are not reachable outside of the docker-compose setup
• NGINX_PUBLISHED_PATH: If BiCoN-web should not be deployed on the root of the domain (e.g. example.com) but rather example.com/bicon, set the variable to bicon
• NGINX_PUBLISHED_PORT: The port on which the nginx reverse proxy will bind to

Deploying (automatically)

The setup.sh script generates the needed .env file and deploys the whole docker instance for you.

# Just execute the script without any arguments
deploy.sh

# Enjoy your instance of BiCoN-web

Your instance should be available on http://localhost (or the port you have specified)

Deploying (manually)

To install BiCoN-web (running it for the first time) follow these steps:

# To generate a valid .env file from your BiCoN-web.conf configuration execute:
setup.sh --configure

# Deploy and build the containers
docker-compose up -d --build

# Apply migrations to the database (make sure the containers are up an running, else you will get an error)
docker-compose exec web python manage.py migrate --noinput 

# Collect all the static files
docker-compose exec web python manage.py collectstatic --no-input

# Enjoy your instance of BiCoN-web

Your instance should be available on http://localhost (or the port you have specified)

Updating and maintaining BiCoN-web (setup.sh)

The setup.sh is also useful for deploying updated versions of BiCoN-web on existing setups.

The following arguments are available:

bash setup.sh [--configure] [--migrate-db] [--collect-static] [--update]

No arguments specified:

• equals: bash setup.sh --configure --migrate-db --collect-static
• Useful for new installations

--update

• equals: bash setup.sh --configure --migrate-db --collect-static
• Useful for updating an existing instance (with existing .env) file

--migrate-db

• Executes the Django migrate command inside the docker container

--collect-static

• Executes the Django collect static command instide the docker container

Force update cached NDEx PPI networks The cache is automatically invalidated 24h after generation or if the NDEx network has changed. In case you want to force update the cache execute this command:

docker-compose exec web python manage.py update_ppi_cache

Starting and stoping BiCoN-web

All the important files are stored inside persistent volumes and are available even after restarting the containers

Start service

Navigate to the repository folder

docker-compose up -d

Stop service

Navigate to the repository folder

docker-compose down

Managing volumes and data

The docker containers store their data in three volumes which can be backup or moved when the application needs to move to another client.

Backing up volumes

Deleting volumes / all data

CAREFULL, docker does not ask for confirmation when deleting volumes!

docker-compose down --volumes  # THIS COMMAND DELETES ALL THE STORED DATA

Cite

BiCoN was developed by the Big Data in BioMedicine group and Computational Systems Medicine group at Chair of Experimental Bioinformatics.

If you use BiCoN in your research, we kindly ask you to cite the following manuscript: Olga Lazareva, Stefan Canzar, Kevin Yuan, Jan Baumbach, David B Blumenthal, Paolo Tieri, Tim Kacprowski*, Markus List*, BiCoN: Network-constrained biclustering of patients and omics data, Bioinformatics, 2020;, btaa1076, https://doi.org/10.1093/bioinformatics/btaa1076

** joint last author

Contact

If you have difficulties using BiCoN-web, please open an issue at out GitHub repository and/or tag @kevihiiin.ypo