{"id":20494787,"url":"https://github.com/fhdsl/gdscn_biodigs_amr","last_synced_at":"2025-03-05T17:48:44.357Z","repository":{"id":240766219,"uuid":"803406367","full_name":"fhdsl/GDSCN_BioDIGS_AMR","owner":"fhdsl","description":"This activity guides students through an investigation of antimicrobial resistance in the BioDIGS samples using Galaxy.","archived":false,"fork":false,"pushed_at":"2024-05-22T19:51:16.000Z","size":18173,"stargazers_count":0,"open_issues_count":6,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2024-05-22T20:21:53.169Z","etag":null,"topics":["biodigs","gdscn"],"latest_commit_sha":null,"homepage":"http://hutchdatascience.org/GDSCN_BioDIGS_AMR/","language":"CSS","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc-by-4.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/fhdsl.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":"code_of_conduct.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":"docs/support.html","governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-05-20T16:57:39.000Z","updated_at":"2024-06-26T18:24:34.487Z","dependencies_parsed_at":"2024-06-28T17:34:48.981Z","dependency_job_id":null,"html_url":"https://github.com/fhdsl/GDSCN_BioDIGS_AMR","commit_stats":null,"previous_names":["fhdsl/biodigs_amr"],"tags_count":0,"template":false,"template_full_name":"jhudsl/AnVIL_Template","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fhdsl%2FGDSCN_BioDIGS_AMR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fhdsl%2FGDSCN_BioDIGS_AMR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fhdsl%2FGDSCN_BioDIGS_AMR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fhdsl%2FGDSCN_BioDIGS_AMR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/fhdsl","download_url":"https://codeload.github.com/fhdsl/GDSCN_BioDIGS_AMR/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":242076654,"owners_count":20068234,"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":["biodigs","gdscn"],"created_at":"2024-11-15T17:43:09.116Z","updated_at":"2025-03-05T17:48:44.323Z","avatar_url":"https://github.com/fhdsl.png","language":"CSS","funding_links":[],"categories":[],"sub_categories":[],"readme":"# BioDIGS: Antimicrobial Resistance\n\n[![Render Bookdown](https://github.com/fhdsl/GDSCN_BioDIGS_Soil//actions/workflows/render-all.yml/badge.svg)](https://github.com/fhdsl/GDSCN_BioDIGS_Soil//actions/workflows/render-all.yml)\n\nThis course was created from [the AnVIL Template](https://github.com/jhudsl/AnVIL_bookdown_style), which is based on [the OTTR Template](https://github.com/jhudsl/OTTR_Template)\n\nYou can see the rendered course material [here](https://hutchdatascience.org/GDSCN_BioDIGS_BGC/)\n\n# About this book\n\nThis is a companion training guide for BioDIGS, a GDSCN project that brings a research experience into the classroom. In this module, students will investigate whether metagenomic samples from the BioDIGS project contain antimicrobial resistance genes. They will run analyses using ABRicate as implemented on Galaxy. Visit the BioDIGS (BioDiversity and Informatics for Genomics Scholars) website [here](https://biodigs.org/) for more information about this collaborative, distributed research project, including how you can get involved!\n\nThe GDSCN (Genomics Data Science Community Network) is a consortium of educators who aim to create a world where researchers, educators, and students from diverse backgrounds are able to fully participate in genomic data science research. You can find more information about its mission and initiatives [here](https://www.gdscn.org/home).\n\n```{r echo=FALSE, fig.alt=\"BioDIGS logo\", out.width='300px', fig.align='center'}\nknitr::include_graphics(\"https://raw.githubusercontent.com/fhdsl/GDSCN_BioDIGS_Book/main/assets/GDSCN_style/logo_BioDIGS_final.png\")\n```\n## Target Audience\n\nThe activity in this guide are written for undergraduate students and beginning graduate students.\n\n## Platform\n\nThe activities in this guide are demonstrated on NHGRI's [AnVIL](https://anvilproject.org/) cloud computing platform. AnVIL is the preferred computing platform for the GDSCN. However, all of these activities can be done using the online [Galaxy](usegalaxy.org) portal.\n\n## Data\n\nThe data generated by the BioDIGS project is available as an R package (BioDIGSData, https://github.com/fhdsl/BioDIGSData), through the [BioDIGS website](biodigs.org), or through an [AnVIL workspace](https://anvilproject.org).\n\nData about the soil itself as well as soil metal content was generated by the [Delaware Soil Testing Program](https://www.udel.edu/canr/cooperative-extension/environmental-stewardship/soil-testing/) at the University of Delaware. Sequences were generated by the [Johns Hopkins University Genetic Resources Core Facility](https://grcf.jhmi.edu/) and by [PacBio](https://www.pacb.com/).\n\n## Encountering problems?\n\nIf you are encountering any problems with this course, please file a GitHub issue or contact Ava Hoffman (ahoffma2 at fredhutch.org) or Elizabeth Humphries (ehumphri at fredhutch.org).\n\n\u003ca rel=\"license\" href=\"http://creativecommons.org/licenses/by/4.0/\"\u003e\u003cimg alt=\"Creative Commons License\" style=\"border-width:0\" src=\"https://i.creativecommons.org/l/by/4.0/88x31.png\" /\u003e\u003c/a\u003e\u003cbr /\u003eAll materials in this course are licensed under a \u003ca rel=\"license\" href=\"http://creativecommons.org/licenses/by/4.0/\"\u003eCreative Commons Attribution 4.0 International License\u003c/a\u003e unless noted otherwise.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffhdsl%2Fgdscn_biodigs_amr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffhdsl%2Fgdscn_biodigs_amr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffhdsl%2Fgdscn_biodigs_amr/lists"}