maayanlab/biojupies-notebooks repository overview

⁠Overview

BioJupies (http://biojupies.cloud⁠) is a web application that allows users to generate interactive Jupyter notebooks from raw RNA-seq data in seconds, by means of an intuitive user interface. Generated notebooks support multiple RNA-seq analysis plugins, such as differential gene expression, and querying L1000 signatures to identify small molecule perturbations that mimic or reverse input signatures.

⁠Features

The maayanlab/biojupies-notebooks Docker image allows users to download and re-run all Jupyter notebooks generated using BioJupies. The image contains:

1. A running Jupyter Server exposed on port 8888. To access the server, the user should map this port to the local host.
2. A /notebooks folder, which contains example Jupyter Notebooks.
3. A copy of the BioJupies plugins library (https://github.com/MaayanLab/biojupies-plugins⁠ ), required to run the notebooks.

⁠Running the Image

To run the image, the execute the following command:

docker run -it -p 8888:8888 maayanlab/biojupies-notebooks

After launching the image, the user can provide the UID of a BioJupies notebook they wish to download and run. The user can also leave this empty and use the example notebooks provided (this is recommended for the workshop).

The user can then access the Jupyter Server on the specified port (e.g. localhost:8888).

⁠Mounting Volumes

Optionally, if the user wishes to permanently store results on their file system, they can mount a local volume at the /notebooks path. For example:

docker run -it -p 8888:8888 -v ~/Desktop:/notebooks maayanlab/biojupies-notebooks

By running the command above, the image will download notebooks on the user's Desktop, and the Jupyter Server will be made available on port 8888.

⁠Additional Resources

Additional information on running the BioJupies docker image is available at the following links:

• Video tutorial on YouTube - https://www.youtube.com/watch?v=7WFlqIlTud4⁠
• Text tutorial on the BioJupies website - https://amp.pharm.mssm.edu/biojupies/docker⁠