2020-GGG298

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# Course materials for GGG298 - Tools to support data-intensive research

## UC Davis Winter 2020

[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ngs-docs/2020-GGG298/master)

### Materials availability

<a rel="license"
 href="http://creativecommons.org/publicdomain/zero/1.0/">
 <img src="http://i.creativecommons.org/p/zero/1.0/88x31.png" style="border-style: none;" alt="CC0" />
 </a>
 
 To the extent possible under law,
 <a rel="dct:publisher"
 href="http://twitter.com/ctitusbrown">
 Titus Brown</a> and
 <a rel="dct:publisher"
 href="mailto:sejoslin@ucdavis.edu">
 Shannon Joslin</a>
 have waived all copyright and related or neighboring rights to
 GGG 298, Winter 2020 at UC Davis.
This work is published from:

 United States.

### Instructors

C. Titus Brown (IOR) (<ctbrown@ucdavis.edu>), Shannon Joslin (<sejoslin@ucdavis.edu>).

### Course description

This course will provide a practical introduction to common tools used in data-intensive research, including the UNIX shell, version control with git, RMarkdown, JupyterLab, and workflows with snakemake. The associated discussion section will connect the lab practicals to foundational concepts in data science, including repeatability/reproducibility, statistics, and publication ethics.

This course is open to all graduate students. No prior computational experience is required or assumed. There will be some minimal overlap with GGG 201(b) topics. All materials will be open to the community and freely available online.

[Full syllabus](https://hackmd.io/3bDesjZaTVSiEzEueSGlDQ?view)

## Resources

Week 1: Introduction to the course, and a basic RNAseq pipeline -- [outline](https://hackmd.io/@ctb/S1_mb0fe8), [lab notes](https://github.com/ngs-docs/2020-GGG298/blob/master/Week1-intro/README.md), [reading](https://springerplus.springeropen.com/articles/10.1186/s40064-016-2888-8), [discussion notes](https://hackmd.io/vm4LdvN8SDG619N8xFsatg)

Week 2: UNIX shell for file manipulation -- [outline](https://hackmd.io/O6MaR9tMSxazAC_UCr_hTg), [lab notes](https://github.com/ngs-docs/2020-GGG298/tree/master/Week2-UNIX_for_file_manipulation), [reading](https://springerplus.springeropen.com/articles/10.1186/s40064-016-2888-8), [discussion notes](https://hackmd.io/H7EUa5DMQKmjc4yIwdWgDQ)

Week 3: Conda for software installation -- [outline](https://hackmd.io/To23drs_STONN1zdFb2hkw), [lab notes](https://github.com/ngs-docs/2020-GGG298/blob/master/Week3-conda_for_software_installation/README.md), [reading](https://undsci.berkeley.edu/lessons/pdfs/how_science_works.pdf), [discussion notes](https://hackmd.io/lAgWvrN0T5uc9ZYAQaVHqg)

Week 4: Snakemake for workflows -- [outline](https://hackmd.io/UuYTlGyVQ7WLTL-3kX3K5A), [lab notes](https://github.com/ngs-docs/2020-GGG298/tree/master/Week4-snakemake-for-workflows/README.md), [reading](http://ivory.idyll.org/blog/2014-function-of-unknown-genes.html), [discussion notes](https://hackmd.io/UuYTlGyVQ7WLTL-3kX3K5A?view)

Week 5: Project organization and more UNIX shell -- [outline](https://hackmd.io/jSF2sFcgS02yuc3gW7RqzQ), [lab notes](https://github.com/ngs-docs/2020-GGG298/tree/master/Week5-project_organization_and_UNIX_shell/README.md), [reading](https://meaningness.com/metablog/upgrade-your-cargo-cult), [discussion notes](https://hackmd.io/DYbcnnfvTeyBpABx72xJGQ)

Week 6: Git and GitHub for file tracking and sharing -- [outline](https://hackmd.io/iuqXzr0RRw-M8rLbWjvuJg?view), [lab notes](https://github.com/ngs-docs/2020-GGG298/blob/master/Week6-Git_and_GitHub_for_file_tracking_and_sharing/README.md), [discussion notes](https://hackmd.io/iuqXzr0RRw-M8rLbWjvuJg)

Week 7: Slurm and the Farm cluster for doing analysis -- [outline](https://hackmd.io/Iy-YHQuPRGWILNV5F_A5lA?view), [lab notes](https://github.com/ngs-docs/2020-GGG298/blob/master/Week7-Slurm_and_Farm_cluster_for_doing_analysis/README.md), [reading](https://hackmd.io/GOM86OhHQ-WKdwxCk1Xtyw?view#Friday-discussion---221)

Week 8: R/Rmarkdown for Reports, Documentation and beyond -- [outline](https://hackmd.io/FxdMZvJdTBy5r2Um4KeMjw), [lab notes](https://github.com/ngs-docs/2020-GGG298/blob/master/Week8-Rmarkdown_for_reports_documentation_and_beyond), [reading](https://www.worldscientific.com/doi/pdf/10.1142/9789813235533_0008), [discussion notes](https://hackmd.io/z9GLXC_WS8-MTAAZhkgCMw)

Week 9: Integrating it all: a sourmash project! -- [outline](https://hackmd.io/juznPUnSRmWJlJ00SCJsUA?view), [lab notes](https://hackmd.io/XgI03HNBRtS6kyKcycKFLA?view), [reading](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0088889), [discussion notes](https://hackmd.io/juznPUnSRmWJlJ00SCJsUA?view)

Week 10: Advanced intro UNIX and integration -- [outline](https://hackmd.io/NkDTSmHBT-Gut6yCgCSAXQ), [lab notes](https://github.com/ngs-docs/2020-GGG298/blob/master/Week10-advanced_intro_UNIX_and_integration/README.md), [reading](https://bookbook.pubpub.org/pub/zrlj0jqb)

2020-GGG298

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