Interface between Scientific Databases and MineCraft
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The Cellcraft Project

Setup your computer for using Cellcraft

Start a Docker Image and create a MongoDB where to store the biological information of your minecraft world (Run only once!!)

docker pull mongo:latest
  • For accessing the mongo shell
docker run --name mongo -d mongo --net=host # run -p 27017:27017 --name mongo -d mongo

docker exec -it mongo /bin/bash
db = db.getSiblingDB('admin');
db.createUser({ user: 'admin', pwd: 'admin', roles: [ { role: "userAdminAnyDatabase", db: "admin" } ] });
db = db.getSiblingDB('cellcraft');
db.createUser({ user: "cellcraft", pwd: "cellcraft", roles: [{role: "readWrite", db: "cellcraft"}]});
db = db.getSiblingDB('test');
db.createUser({ user: "test", pwd: "test", roles: [{role: "readWrite", db: "test"}]});
  • Check if user and was correctly created
docker exec -it mongo bash
mongo cellcraft -u cellcraft -p cellcraft
  • To backup the database into "cellcraft-backup" folder (backup the database regularly)
docker exec -it mongo bash
mongodump --db cellcraft --out cellcraft/mongo_storage/data/cellcraft-backup

Setup your python environment

  • Install pyenv and run setup the cellcraft pyenv
brew install pyenv-virtualenv
echo 'eval "$(pyenv init -)"' >> ~/.bash_profile
source ~/.bash_profile
pyenv install 3.6.2
pyenv global 3.6.2
source ~/.bash_profile

pyenv virtualenv 3.6.2 cellcraft
pyenv activate cellcraft
Install python packages from requirements
pip install -r requirements.txt

Setup the Mincraft server and connect it to cellcraft

Installation of Minecraft Client

  • Download Minecraft server
  • Run client once with correct version (1.12)
  • Download forge installer (version 1.12) from (Notice that you need to have the Java Developer Kit installed)
  • Run forge installer and install client into minecraft folder (no change needed)

Installation of Minecraft Server with RaspberryJamMod

  • Download forge installer (version 1.12) from (same then above)
  • Run forge installer and install server into the root directory of the repo

java -jar forge-version-installer.jar

  • Download from the
  • Unzip the and copy the mods folder content into the mods folder in the root directory of the repo
  • Run the forge-*-universal.jar that has been generated in the same directory

java -jar forge-version-universal.jar

  • Edit the eula.txt file generated in the same directory and change false to true

Starting the server with cellcraft

  • Start the server in the root folder of the repo with your python environment correctly setup and start the server
java -jar forge-version-universal.jar

Now you are ready to start! Join the server

  • start the client
  • choose Multiplayer
  • choose Direct Connect
  • add as server address and join server
  • run for pdb mode:
/py cellcraft -m pdb -n 3J9U -t 2 -s 4 -he -15 -C
  • or run for pdb mode from cache:
/py cellcraft -m pdb -n 3J9U -t 2 -s 4 -he -15
  • run for cellpack mode (remove -C if run structure from cache):
    • download hiv.x3d and hiv.csv from our server
/py cellcraft -m cellpack -n hiv -t 2 -s 4 -he -15 -C