bdb-2021

This repository contains files used in the course "Biomedical Data Bases" (BDB) at the University of Bologna, Academic Year 2020-2021, taught by prof. Davide Salomoni.

For details, see the course slides.

For more information on the course, see here.

Install Docker

Refer to the course slides for information on how to do that.

Create a local directory

We are going to create a directory local to our laptop/PC called bdb.

If you run Linux or MacOS:

mkdir $HOME/bdb

If you run Windows 10:

mkdir %USERPROFILE%\bdb

Create a docker network

docker network create bdb-net

Start the Jupyter notebook

Remember to change the password to access Jupyter (parameter JUPYTER_TOKEN in the command below). Once the docker container is started, connect to http://127.0.0.1:8888. Note that with the command below access is only permitted from the PC where docker is running.

If you run Linux or MacOS:

docker run -d --rm --name my_jupyter -v $HOME/bdb:/home/jovyan -p 127.0.0.1:8888:8888 --network bdb-net -e JUPYTER_TOKEN="bdb_password" --user root -e CHOWN_HOME=yes -e CHOWN_HOME_OPTS="-R" jupyter/datascience-notebook

If you run Windows 10:

docker run -d --rm --name my_jupyter -v %USERPROFILE%\bdb:/home/jovyan -p 127.0.0.1:8888:8888 --network bdb-net -e JUPYTER_TOKEN="bdb_password" --user root -e CHOWN_HOME=yes -e CHOWN_HOME_OPTS="-R" jupyter/datascience-notebook

Start the redis server

If you run Linux or MacOS:

Without persistence:

docker run -d --rm --name my_redis -v $HOME/bdb:/data --network bdb-net --user 1000 redis redis-server --maxmemory 32mb --maxmemory-policy allkeys-lru

With persistence:

docker run -d --rm --name my_redis -v $HOME/bdb:/data --network bdb-net --user 1000 redis redis-server --maxmemory 32mb --save 180 1 --dbfilename my_database.rdb

If you run Windows 10:

Without persistence:

docker run -d --rm --name my_redis -v %USERPROFILE%\bdb:/data --network bdb-net --user 1000 redis redis-server --maxmemory 32mb --maxmemory-policy allkeys-lru

With persistence:

docker run -d --rm --name my_redis -v %USERPROFILE%\bdb:/data --network bdb-net --user 1000 redis redis-server --maxmemory 32mb --save 180 1 --dbfilename my_database.rdb