{"id":25995204,"url":"https://github.com/ethho/epi-model-reu","last_synced_at":"2026-04-21T04:31:09.672Z","repository":{"id":89662294,"uuid":"274255439","full_name":"ethho/epi-model-reu","owner":"ethho","description":"Resources and code for the epidemiological models project | TACC Summer REU 2020","archived":false,"fork":false,"pushed_at":"2020-08-05T16:12:26.000Z","size":25013,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-05T15:19:36.333Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","has_issues":false,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ethho.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2020-06-22T22:30:03.000Z","updated_at":"2020-08-05T16:12:28.000Z","dependencies_parsed_at":null,"dependency_job_id":"bb25e144-1e7f-476d-9786-78a377c704f4","html_url":"https://github.com/ethho/epi-model-reu","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/ethho/epi-model-reu","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ethho%2Fepi-model-reu","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ethho%2Fepi-model-reu/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ethho%2Fepi-model-reu/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ethho%2Fepi-model-reu/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ethho","download_url":"https://codeload.github.com/ethho/epi-model-reu/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ethho%2Fepi-model-reu/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32076845,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-21T02:38:07.213Z","status":"ssl_error","status_checked_at":"2026-04-21T02:38:06.559Z","response_time":128,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":[],"created_at":"2025-03-05T15:19:39.914Z","updated_at":"2026-04-21T04:31:09.666Z","avatar_url":"https://github.com/ethho.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Epidemiological Models Project | TACC Summer REU 2020\n\nThis repository contains code, literature, links, data, and other resources for the epidemiological models project.\n\n## Walk-Through Demos\n\n* [Descriptive stats demo](./descriptive_stats_demo/eggNOG_alignment_metadata.ipynb)\n* [Sequence similarity demo](./code/20200706_align_demo.ipynb)\n* [Structure similarity demo](./code/20200702_ngl_demo.ipynb)\n\n## Links\n\n### Data Leads\n\n* [Data Leads Google Sheet](https://docs.google.com/spreadsheets/d/1FKQZX744kTdjj02hgceGFqKhwf1taUW7aEF4IsTerak/edit#gid=0)\n\n### Learning Resources\n\n#### Coding Practice\n\n* [Python practice problems tailored for biology](https://www.programmingforbiologists.org/)\n\n#### Software Cheat Sheets\n\n* [Python3 cheat sheet](https://github.com/wilfredinni/python-cheatsheet)\n* [Linux/Unix cheat sheet](https://gist.github.com/hofmannsven/8392477)\n* [Pandas cheat sheet](https://pandas.pydata.org/pandas-docs/stable/getting_started/10min.html)\n* Kelly P's [Python Data Science Tutorial](https://github.com/kellyp2738/python_data_science)\n* [Git cheat sheet][1]\n* Learn how to write this page: a [markdown (`*.md`) cheat sheet](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet)!\n\n#### Learning Git\n\n* GitHub provides a list of [resources to learn git](https://try.github.io/). Notably:\n   * [Learn git branching interactively](https://learngitbranching.js.org/):  An interactive tool that helps one _vizualize_ git branching\n   * A [cheat sheet][1] provided by GitHub\n\n### More In-Depth Guides\n\n* [Biopython guide](http://biopython.org/DIST/docs/tutorial/Tutorial.html): how to align sequences using Python\n\n### Literature\n\n* [COVID-19 Resources List](https://docs.google.com/spreadsheets/d/16NmqBFRV5W801Gp0xcCx7fMMW6STQwC3203E-HzMUhw/edit?usp=sharing)\n* [H1N1 Resources List](https://docs.google.com/spreadsheets/d/1FKQZX744kTdjj02hgceGFqKhwf1taUW7aEF4IsTerak/edit#gid=0)\n* [New York Times: Mutation Allows Coronavirus to Infect More Cells, Study Finds. Scientists Urge Caution](https://www.nytimes.com/2020/06/12/science/coronavirus-mutation-genetics-spike.html?searchResultPosition=1)\n* [Blood types correlate with COVID-19 infection outcomes](https://www.nejm.org/doi/full/10.1056/NEJMoa2020283)\n* [COVID in cats, and structural homology studies between mammalian receptors](notes/20200625_reu_mentoring.md)\n\n### Misc.\n\n* Never enter your GitHub password again into Terminal: how to [add your SSH keys to GitHub](https://docs.github.com/en/github/authenticating-to-github/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent)\n#### Fun science side projects!\n\n* Looking at protein crystal structures\n    * [Protein Data Bank](http://www.rcsb.org) (AKA PDB or RCSB):  Public repository of protein structures\n    * [Pymol](https://pymol.org/): Free software for looking at structures from the RCSB (AKA \"PDB structures\")\n\n\n[1]: https://github.github.com/training-kit/downloads/github-git-cheat-sheet/ \"git cheat sheet\"\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fethho%2Fepi-model-reu","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fethho%2Fepi-model-reu","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fethho%2Fepi-model-reu/lists"}