{"id":17099048,"url":"https://github.com/dhimmel/serg-pycode","last_synced_at":"2025-07-03T20:32:29.690Z","repository":{"id":82487829,"uuid":"304333967","full_name":"dhimmel/serg-pycode","owner":"dhimmel","description":"Python code related to networks from Daniel Himmelstein's PhD in the Sergio Baranzini Lab at UCSF","archived":false,"fork":false,"pushed_at":"2020-10-17T17:17:52.000Z","size":1416,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-23T18:12:43.322Z","etag":null,"topics":["baranzini-lab","hetnets","phd","ucsf"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dhimmel.png","metadata":{"files":{"readme":"readme.md","changelog":null,"contributing":null,"funding":null,"license":"license.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-10-15T13:24:50.000Z","updated_at":"2023-05-11T13:05:44.000Z","dependencies_parsed_at":null,"dependency_job_id":"59c5f793-dd88-4386-9421-da4749f85f6a","html_url":"https://github.com/dhimmel/serg-pycode","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/dhimmel/serg-pycode","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fserg-pycode","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fserg-pycode/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fserg-pycode/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fserg-pycode/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dhimmel","download_url":"https://codeload.github.com/dhimmel/serg-pycode/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fserg-pycode/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263399430,"owners_count":23460701,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["baranzini-lab","hetnets","phd","ucsf"],"created_at":"2024-10-14T15:08:52.144Z","updated_at":"2025-07-03T20:32:29.664Z","avatar_url":"https://github.com/dhimmel.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Python code related to networks from Daniel Himmelstein's PhD in the Sergio Baranzini Lab\n\nThis repository contains Python code, written by Daniel Himmelstein from 2012-2015 during his PhD in the [Baranzini Lab](https://baranzinilab.ucsf.edu/) at UCSF.\nThis includes code that contributed to the following studies:\n\n\u003c!-- \nmanubot cite --format=markdown \\\n  doi:10.1371/journal.pcbi.1004259 \\\n  doi:10.12688/f1000research.6836.2 \\\n  doi:10.6084/m9.figshare.4724797\n--\u003e\n\n1. **Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes**   \nDaniel S. Himmelstein, Sergio E. Baranzini  \n*PLOS Computational Biology* (2015-07-09) \u003chttps://doi.org/98q\u003e   \nDOI: [10.1371/journal.pcbi.1004259](https://doi.org/10.1371/journal.pcbi.1004259) · PMID: [26158728](https://www.ncbi.nlm.nih.gov/pubmed/26158728) · PMCID: [PMC4497619](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4497619)\n\n2. **iCTNet2: integrating heterogeneous biological interactions to understand complex traits**   \nLili Wang, Daniel S. Himmelstein, Adam Santaniello, Mousavi Parvin, Sergio E. Baranzini  \n*F1000Research* (2015-09-28) \u003chttps://doi.org/ghfv3v\u003e   \nDOI: [10.12688/f1000research.6836.2](https://doi.org/10.12688/f1000research.6836.2) · PMID: [26834985](https://www.ncbi.nlm.nih.gov/pubmed/26834985) · PMCID: [PMC4706053](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4706053)\n\n3. **The hetnet awakens: understanding complex diseases through data integration and open science** [Thesis]   \nDaniel Himmelstein  \n*figshare* (2017) \u003chttps://doi.org/b2nz\u003e   \nDOI: [10.6084/m9.figshare.4724797](https://doi.org/10.6084/m9.figshare.4724797) · ISBN: [9781339919881](https://worldcat.org/isbn/9781339919881)\n\nCode related to [Project Rephetio](https://doi.org/10.7554/eLife.26726 \"Systematic integration of biomedical knowledge prioritizes drugs for repurposing. eLife. 2017\") is released separately, and largely post-dates this repository.\n\nThe code to create the PLOS Comp Bio (2015) network, i.e. `het.io-dag`, is in [`projects/gene_disease_hetnet/createnet.py`](projects/gene_disease_hetnet/createnet.py) ([access data here](https://github.com/dhimmel/het.io-dag-data/tree/master/downloads#network)).\n\n## History\n\nThis repository originally used mercurial and was hosted on BitBucket at `https://bitbucket.org/dhimmel/serg`.\nUnfortunately, BitBucket [deleted](https://community.atlassian.com/t5/Bitbucket-articles/What-to-do-with-your-Mercurial-repos-when-Bitbucket-sunsets/ba-p/1155380) mercurial repos in 2020 without an automated migration path.\nOn 2020-10-15, dhimmel realized this source code was no longer online.\n\nThe repo could not be retrieved from BitBucket, but dhimmel had a local copy in `~/Documents/serg/pycode`.\nThe local copy matched the version archived by [Software Heritage](https://archive.softwareheritage.org/browse/directory/2361a3289af5749822df1c2b5addb5c73f36cab1/?branch=default\u0026origin_url=https://bitbucket.org/dhimmel/serg\u0026snapshot=179679a99b43c5549e9f89bafc6551200d3bb712).\nUsing the [hg-fast-export](https://github.com/frej/fast-export/tree/ead75895b058d16ffc7330dab78054c94a189377) utility, dhimmel exported the repository to git and uploaded it to \u003chttps://github.com/dhimmel/serg-pycode\u003e.\n\nThis code is uploaded to GitHub for archiving and historical purposes.\nThe extent this python code was used to perform certain studies and analyses requires a bit of investigation.\nThe repository is not actively maintained nor accepting feature requests.\nHowever, questions about existing code or analyses are welcome via GitHub Issues.\nFurthermore, any documentation contributions are appreciated.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdhimmel%2Fserg-pycode","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdhimmel%2Fserg-pycode","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdhimmel%2Fserg-pycode/lists"}