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README

This README would normally document whatever steps are necessary to get your application up and running.

What is this repository for?

How do I get set up?

Installation and setup

To clone the git repository, run the following

git clone git@bitbucket.org:ml6team/biographs.git

Multiscale Interactoms

The multiscale interactome is hosted by Stanford University. All data is available at http://snap.stanford.edu/multiscale-interactome/data/data.tar.gz.To download and unpack the data, first enter the root folder of the cloned repository and then run the following:

mkdir multiscale_interactome
cd multiscale_interactome
wget http://snap.stanford.edu/multiscale-interactome/data/data.tar.gz
tar -xvf data.tar.gz

Setup

Code is written in Python3. Please install the packages present in the requirements.txt file. You may use:

pip install -r requirements.txt

Next, install additional required packages using the following command:

pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-1.13.1+cu117.html
Note:

The installed versions of pyg_lib, torch_scatter, torch_sparse, torch_cluster, and torch_spline_conv must match the installed versions of torch and CUDA. If issues persist after the previous steps, try reinstalling the following packages using the following command:

pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-{TORCH}+{CUDA}.html

where TORCH should be replaced with the correct torch version (1.13.1) above, and CUDA should be replaced with the correct CUDA version (cu117) above.

Note:

If you installed your own NVIDIA Drivers / CUDA Toolkit, it may be important to manually uninstall the Pytorch CUDA tools that are downloaded when installing torch. This can be accomplished with the followin command.

pip uninstall nvidia_cublas_cu11

Miscellaneous

Accessing Google Cloud

To authorize access to google cloud, run the following:

gcloud auth login

Files can then be copied to and from from any buckets that are authorized with the same account using the following:

gsutil cp {path/to/file} gs://{bucket-name}
  • Summary of set up
  • Configuration
  • Dependencies
  • Database configuration
  • How to run tests
  • Deployment instructions

Contribution guidelines

  • Writing tests
  • Code review
  • Other guidelines

Who do I talk to?

  • Repo owner or admin
  • Other community or team contact