Hetnet connectivity search prototyping and data repository

Connectivity Search (formerly called Hetmech for hetnet mechanisms) is a project to extract mechanistic connections between nodes in hetnets. The project aims to identify the relevant network connections between query nodes. The method is designed to operate on hetnets (networks with multiple node or relationship types).

Note: the hetmech python package has been renamed to hetmatpy and relocated to hetio/hetmatpy. This repository is now used as a historical archive, as well as a dataset storage, method prototyping, and exploratory data analysis repository.

Many findings from this repository are described in the Connectivity Search Manuscript. The manuscript source code is available in greenelab/connectivity-search-manuscript.

Environment

This repository uses conda to manage its environment as specified in environment.yml. Install the environment with:

# install new hetmech environment
conda env create --file=environment.yml

# update existing hetmech environment
conda env update --file=environment.yml

Then use conda activate hetmech and conda deactivate to activate or deactivate the environment.

Note that the environment is tested with the conda channel_priority strict configuration. Locally, you can run the following commands to configure conda (as per https://conda-forge.org docs), but note that it affects your conda config beyond this environment:

conda config --add channels conda-forge
conda config --set channel_priority strict

Another option is to install conda with miniforge.

Acknowledgments

This work was supported through a research collaboration with Pfizer Worldwide Research and Development. This work was funded in part by the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through Grants GBMF4552 to Casey Greene and GBMF4560 to Blair Sullivan.