sysbiocurie/webmaboss repository overview

⁠WebMaboSS : a web interface for simulating Boolean models stochastically

WebMaBoSS is a web interface for the MaBoSS, the Markovian Boolean Stochastic Simulator. MaBoSS is a C++ software for simulating continuous/discrete time Markov processes, applied on a Boolean network.

WebMaBoSS allows you to store, modify, and simulate MaBoSS models. You can also import/export models in other compatible formats (SBML-qual, GINsim, BNet). Models can also be imported from public databases (BioModels, CellCollective).

WebMaBoSS is available as a docker container that can quickly be deployed locally. You will need Docker⁠ and optionally Docker-Compose⁠. A live version is deployed at https://maboss.curie.fr/WebMaBoSS/⁠.

⁠Use live version

To use the version available at https://maboss.curie.fr/WebMaBoSS/⁠, you will need to create a user account. Once created, you can immediately login and start discovering the default project.

For more information, consult the tutorials.

⁠Run locally with Docker and Docker-compose

Launch WebMaBoSS's container using :

git clone https://github.com/sysbio-curie/WebMaBoSS
cd WebMaBoSS
docker pull sysbiocurie/webmaboss:1.0.0b18
docker-compose up -d webmaboss

And then open your browser to this url : http://localhost:8000/⁠

This will use the docker image from sysbiocurie/webmaboss on DockerHub⁠. If you want to build your image locally, remove the docker pull command.

⁠Run locally with Docker

If you don't want to build the image (this can take 10-20 min), you can first download it from DockerHub⁠ :

docker pull sysbiocurie/webmaboss:1.0.0b18

Otherwise :

docker build -f docker/Dockerfile -t sysbiocurie/webmaboss:1.0.0b18 

Then launch the container of the database. Note that you should modify the password.

docker run -d --name webmaboss-db \
	--restart=always \
	-v webmaboss_db:/var/lib/mysql \
	-e MYSQL_RANDOM_ROOT_PASSWORD=yes \
	-e MYSQL_DATABASE=webmaboss \
	-e MYSQL_USER=webmaboss \
	-e MYSQL_PASSWORD=InsertAPassWordForTheDatabase \
	mariadb \
	--max_allowed_packet=268435456 

Then launch WebMaBoSS' container

docker run -d --name webmaboss \
	--restart=always \
	-v webmaboss_data:/var/webmaboss/data \
	-p 8000:8000 \
	--link webmaboss-db \
	-u www-data \
	-e DB_HOST=webmaboss-db \
	-e DB_PORT=3306 \
	-e DB_NAME=webmaboss \
	-e DB_USER=webmaboss \
	-e DB_PASSWORD=InsertAPassWordForTheDatabase \
	sysbiocurie/webmaboss:1.0.0b18 

And finally open your browser to this url : http://localhost:8000/⁠

⁠Tutorials

The directory tutorial contains two tutorials based on the two models in the default project :

• Tutorial on Cohen 2015 : Tumor Cell Invasion and Migration⁠
• Tutorial on Corral 2020 : Interplay between SMAD2 and STAT5A regulating IL-17A/F expression in Th cells⁠

⁠License

GNU Lesser General Public License v3⁠