{"id":20074681,"url":"https://github.com/greenelab/connectivity-search-analyses","last_synced_at":"2025-05-05T21:32:03.490Z","repository":{"id":54825275,"uuid":"63903430","full_name":"greenelab/connectivity-search-analyses","owner":"greenelab","description":"hetnet connectivity search research notebooks (previously hetmech)","archived":false,"fork":false,"pushed_at":"2023-03-30T12:27:01.000Z","size":53834,"stargazers_count":9,"open_issues_count":6,"forks_count":5,"subscribers_count":7,"default_branch":"main","last_synced_at":"2025-04-11T19:16:46.213Z","etag":null,"topics":["hetionet","hetmat","hetmech","hetnet","hetnet-connectivity-search","matrix","mechanism","networks","numpy","scipy","theory-in-practice"],"latest_commit_sha":null,"homepage":"","language":"Jupyter 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Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Hetnet connectivity search prototyping and data repository\n\n[![Build Status](https://travis-ci.org/greenelab/connectivity-search-analyses.svg?branch=main)](https://travis-ci.org/greenelab/connectivity-search-analyses)\n\nConnectivity Search (formerly called Hetmech for _hetnet mechanisms_) is a project to extract mechanistic connections between nodes in hetnets.\nThe project aims to identify the relevant network connections between query nodes.\nThe method is designed to operate on hetnets (networks with multiple node or relationship types).\n\n**Note: the `hetmech` python package has been renamed to `hetmatpy` and relocated to [`hetio/hetmatpy`](https://github.com/hetio/hetmatpy).**\nThis repository is now used as a historical archive,\nas well as a dataset storage, method prototyping, and exploratory data analysis repository.\n\nMany findings from this repository are described in the [Connectivity Search Manuscript](https://greenelab.github.io/connectivity-search-manuscript/ \"Hetnet connectivity search provides rapid insights into how two biomedical entities are related\").\nThe manuscript source code is available in [`greenelab/connectivity-search-manuscript`](https://github.com/greenelab/connectivity-search-manuscript).\n\n## Environment\n\nThis repository uses [conda](http://conda.pydata.org/docs/) to manage its environment as specified in [`environment.yml`](environment.yml).\nInstall the environment with:\n\n```sh\n# install new hetmech environment\nconda env create --file=environment.yml\n\n# update existing hetmech environment\nconda env update --file=environment.yml\n```\n\nThen use `conda activate hetmech` and `conda deactivate` to activate or deactivate the environment.\n\nNote that the environment is tested with the conda `channel_priority strict` configuration.\nLocally, you can run the following commands to configure conda (as per https://conda-forge.org docs),\nbut note that it affects your conda config beyond this environment:\n\n```shell\nconda config --add channels conda-forge\nconda config --set channel_priority strict\n```\n\nAnother option is to install conda with [miniforge](https://github.com/conda-forge/miniforge).\n\n## Acknowledgments\n\nThis work was supported through a research collaboration with [Pfizer Worldwide Research and Development](https://www.pfizer.com/partners/research-and-development).\nThis work was funded in part by the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through Grants [GBMF4552](https://www.moore.org/grant-detail?grantId=GBMF4552) to Casey Greene and [GBMF4560](https://www.moore.org/grant-detail?grantId=GBMF4560) to Blair Sullivan.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fconnectivity-search-analyses","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgreenelab%2Fconnectivity-search-analyses","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fconnectivity-search-analyses/lists"}