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OMG: Omics Mock Generator

Generates a mock dataset of omics data (importable in EDD using the new import format): transcriptomics, proteomics, and metabolomics.

Dependencies

  • pip
  • Python 3.8
  • cobra
  • pandas
  • CPLEX

Package Installation

Please follow the next steps after cloning the repository:

$ pip install pipenv
$ pipenv install

You may want to use the --user flag in pip and prepend ~/.local/bin to your path.

Jupyter Notebook

An example Jupyter Notebook, using the OMG module, is included here. To run, build the Docker image, and run it to access a Jupyter Lab server:

DOCKER_BUILDKIT=1 docker build -t omg .
docker run --rm -p 8888:8888 -e JUPYTER_ENABLE_LAB=yes -v "$(pwd):/home/jovyan/work" omg

After the server launches, the terminal will have instructions on how to open the Jupyter Lab server from your browser, looking something like the below:

    To access the server, open this file in a browser:
        file:///home/jovyan/.local/share/jupyter/runtime/jpserver-8-open.html
    Or copy and paste one of these URLs:
        http://<container_id>:8888/lab?token=<random token value>
        http://127.0.0.1:8888/lab?token=<random token value>

Copy the last URL and open in a web browser. The notebook example.ipynb will be in the work folder. Run the example as-is, or make modifications to cells in the notebook or uploaded input files.

Contact

License

Omics Mock Generator Library (OMG) Copyright (c) 2021, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.

If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Intellectual Property Office at [email protected].

NOTICE. This Software was developed under funding from the U.S. Department of Energy and the U.S. Government consequently retains certain rights. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, distribute copies to the public, prepare derivative works, and perform publicly and display publicly, and to permit others to do so.