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related-sciences / string-protein-network

STRING protein network dataset downloads and transformations
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datasets genes human network-biology networks ppi string

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STRING Protein Network

This repository downloads and processes protein interaction data for human genes from STRING. Currently, v11.0 of the STRING database is analyzed. More information on STRING is available in:

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets
Damian Szklarczyk, Annika L Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic, Nadezhda T Doncheva, John H Morris, Peer Bork, … Christian von Mering
Nucleic Acids Research (2018-11-22) https://doi.org/gfz2jr
DOI: 10.1093/nar/gky1131 · PMID: 30476243 · PMCID: PMC6323986

Datasets

This repository produces the following datasets:

Large files are stored using Git LFS. Properly cloning this repository requires having Git LFS installed.

License Notice

Files in the data directory are released under a CC BY 4.0 License. Files in data/string-downloads were downloaded directly from STRING. Other files in data have modifications performed by the notebooks in this repository. Please attribute STRING and https://github.com/related-sciences/string-protein-network when reusing this data.

All contents of this repository outside of the data directory are released under the Apache License Version 2.0, as specified in LICENSE.md.

Development

This repository has a corresponding Docker image with the required dependencies. See environment for the Docker image specification.

Note that the following Docker commands have a --mount argument to give the Docker container access to files in this repository. Therefore, any changes to the repository content created while running the Docker container will persist in this directory after the container is stopped.

The Docker image is automatically built and published by a GitHub Action. Even though this repository is public, GitHub requires authentication to download from its package registry. Therefore, you will need a GitHub account to pull the image.

Use the following steps to authenticate your local docker with your GitHub. Go to https://github.com/settings/tokens and create a new personal access token, selecting only the read:packages scope. You can name the token anything, for example "docker login read-only token". Then run the following command, substituting your username and token from above:

docker login --username USERNAME --password TOKEN docker.pkg.github.com

Interactive

For interactive development, run the following command:

# This command must be run with the repository root as your working directory.
# Requires docker version >= 17.06.
docker run \
  --name string-protein-network \
  --detach --rm \
  --env JUPYTER_TOKEN=jhcyibitimnrsisdstuw \
  --publish 8880:8888 \
  --mount type=bind,source="$(pwd)",target=/user/jupyter \
  docker.pkg.github.com/related-sciences/string-protein-network/string-protein-network

Then navigate to the following URL in your browser: http://localhost:8880?token=jhcyibitimnrsisdstuw

You should see a Jupyter Notebook landing page where you can open, edit, and run any of the notebooks.

When you are done, you shutdown the Jupyter notebook server and remove the Docker container by running docker stop string-protein-network in a terminal.