https://github.com/ethho/epi-model-reu
Resources and code for the epidemiological models project | TACC Summer REU 2020
https://github.com/ethho/epi-model-reu
Last synced: 2 months ago
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Resources and code for the epidemiological models project | TACC Summer REU 2020
- Host: GitHub
- URL: https://github.com/ethho/epi-model-reu
- Owner: ethho
- License: mit
- Created: 2020-06-22T22:30:03.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2020-08-05T16:12:26.000Z (almost 6 years ago)
- Last Synced: 2025-03-05T15:19:36.333Z (over 1 year ago)
- Language: Jupyter Notebook
- Size: 23.9 MB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Epidemiological Models Project | TACC Summer REU 2020
This repository contains code, literature, links, data, and other resources for the epidemiological models project.
## Walk-Through Demos
* [Descriptive stats demo](./descriptive_stats_demo/eggNOG_alignment_metadata.ipynb)
* [Sequence similarity demo](./code/20200706_align_demo.ipynb)
* [Structure similarity demo](./code/20200702_ngl_demo.ipynb)
## Links
### Data Leads
* [Data Leads Google Sheet](https://docs.google.com/spreadsheets/d/1FKQZX744kTdjj02hgceGFqKhwf1taUW7aEF4IsTerak/edit#gid=0)
### Learning Resources
#### Coding Practice
* [Python practice problems tailored for biology](https://www.programmingforbiologists.org/)
#### Software Cheat Sheets
* [Python3 cheat sheet](https://github.com/wilfredinni/python-cheatsheet)
* [Linux/Unix cheat sheet](https://gist.github.com/hofmannsven/8392477)
* [Pandas cheat sheet](https://pandas.pydata.org/pandas-docs/stable/getting_started/10min.html)
* Kelly P's [Python Data Science Tutorial](https://github.com/kellyp2738/python_data_science)
* [Git cheat sheet][1]
* Learn how to write this page: a [markdown (`*.md`) cheat sheet](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet)!
#### Learning Git
* GitHub provides a list of [resources to learn git](https://try.github.io/). Notably:
* [Learn git branching interactively](https://learngitbranching.js.org/): An interactive tool that helps one _vizualize_ git branching
* A [cheat sheet][1] provided by GitHub
### More In-Depth Guides
* [Biopython guide](http://biopython.org/DIST/docs/tutorial/Tutorial.html): how to align sequences using Python
### Literature
* [COVID-19 Resources List](https://docs.google.com/spreadsheets/d/16NmqBFRV5W801Gp0xcCx7fMMW6STQwC3203E-HzMUhw/edit?usp=sharing)
* [H1N1 Resources List](https://docs.google.com/spreadsheets/d/1FKQZX744kTdjj02hgceGFqKhwf1taUW7aEF4IsTerak/edit#gid=0)
* [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)
* [Blood types correlate with COVID-19 infection outcomes](https://www.nejm.org/doi/full/10.1056/NEJMoa2020283)
* [COVID in cats, and structural homology studies between mammalian receptors](notes/20200625_reu_mentoring.md)
### Misc.
* 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)
#### Fun science side projects!
* Looking at protein crystal structures
* [Protein Data Bank](http://www.rcsb.org) (AKA PDB or RCSB): Public repository of protein structures
* [Pymol](https://pymol.org/): Free software for looking at structures from the RCSB (AKA "PDB structures")
[1]: https://github.github.com/training-kit/downloads/github-git-cheat-sheet/ "git cheat sheet"