How can I rerun and customize my notebooks?
Step 1.
Install Docker
  • Download, install and run Docker on your computer from the official Docker website.
Step 2.
Generate your Notebook
Step 3.
Launch a Docker Container
  • Launch the maayanlab/biojupies-notebooks Docker container and provide the UID of the selected notebook.
Step 4.
Customize your Notebook
  • Access your local Jupyter server to run, edit and save your notebook. See below for more information.
Reusing BioJupies Notebooks
All notebooks generated using BioJupies can be downloaded, rerun and saved, allowing users to fully customize the analyses of RNA-seq data on their local computers.
To achieve this, we provide a pre-configured Docker container containing a fully functional Jupyter server with all the Python and R libraries necessary to run the notebooks.
Launching the Docker Container
To run a BioJupies notebook on your local computer, follow the instructions on the leftabove. We recommend users gain a basic understanding of Docker and Jupyter before proceeding.
To complete steps 3 and 4, follow the instructions below:
  1. Open a new Terminal window.
  2. Pull the latest version of the Docker container by entering the following command: docker pull maayanlab/biojupies-notebooks
  3. Launch the Docker container by entering the following command. docker run -it -p 8888:8888 -v ${PWD}:/notebooks -e NOTEBOOK_UID=<NOTEBOOK_UID> maayanlab/biojupies-notebooks
    Note: replace <NOTEBOOK_UID> with the ID of the notebook you wish to run (e.g. JxSg0C23W).
  4. Open a new browser window.
  5. Access your Jupyter Server by visiting localhost:8888.
  6. Execute, customize and save your notebook using Jupyter.
  7. Once you are done, stop the Docker container by pressing Ctrl+C on the previously opened Terminal window.
  1. Open the Docker Quickstart Terminal.
  2. Pull the latest version of the Docker container by entering the following command: docker pull maayanlab/biojupies-notebooks
  3. Launch the Docker container by entering the following command. docker run -it -p 8888:8888 -e NOTEBOOK_UID=<NOTEBOOK_UID> maayanlab/biojupies-notebooks
    Note: replace <NOTEBOOK_UID> with the ID of the notebook you wish to run (e.g. JxSg0C23W).
  4. Find the IP of your Docker server .
  5. Open a new browser window.
  6. Access your Jupyter Server by visiting <DOCKER_IP>:8888.
    Note: replace <DOCKER_IP> with the IP of your server (e.g. 192.168.99.100:8888).
  7. Execute, customize and save your notebook using Jupyter.
  8. Once you are done, stop the Docker container by pressing Ctrl+C on the Docker Quickstart Terminal.
docker pull maayanlab/biojupies-notebooks

docker run -it -p 8888:8888 -e NOTEBOOK_UID=<NOTEBOOK_UID> maayanlab/biojupies-notebooks