---
tags: Geobio course
title: Geobio 2022 Bioinformatics Weekend
---

# Geobio 2022 Bioinformatics Weekend!

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> This page will serve as our main hub for our bioinformatics weekend, holding links to all things we are going to look at and do :+1:
---

[toc]

## Who am I?
- [Mike Lee](https://astrobiomike.github.io/research/)
- A biologist-turned-bioinformatician that focuses on microbes
- "Non-traditional" academic path
- 18-25 years old -> wannabe musician
- started my undergrad at 25
- started PhD at 30
- Formal Education
- A.S. General Science (Ocean County College, NJ, USA, 2011)
- B.S. Biology (Kean University, NJ, USA, 2013)
- Ph.D. Biology (University of Southern California, CA, USA, 2018)
- Transitioned to exclusively bioinformatics during grad school
- Post-doc with NASA Ames doing genomics with microbial isolates recovered from the ISS (2018-2020)
- Joined BMSIS and NASA GeneLab in 2019
- My primary position now is as a GeneLab bioinformatician out of NASA Ames in northern CA

**Feel free to reach out to me anytime 🙂**
* Email: [e-mail]
* Twitter: [@AstrobioMike](https://twitter.com/AstrobioMike)
* Message or tag me in the slack group

## Discussion pages

- [5 things I wish I knew when I started getting into bioinformatics](https://astrobiomike.github.io/about/#five-things-i-wish-i-knew-when-i-started-getting-into-bioinformatics)
- [An overview of amplicon and metagenomics sequencing](https://astrobiomike.github.io/misc/amplicon_and_metagen)
- [Recovering genomes from metagenomes](https://astrobiomike.github.io/genomics/metagen_anvio)
- [Why learn Unix?](https://astrobiomike.github.io/unix/unix-intro)
- [quick terminology sidebar](https://astrobiomike.github.io/unix/#some-terminology)

## Hands-on pages

- [Unix crash course](https://astrobiomike.github.io/unix/unix-intro)
- [Getting started](https://astrobiomike.github.io/unix/getting-started)
- [Working with files and directories](https://astrobiomike.github.io/unix/working-with-files-and-dirs)
- [Redirectors and wildcards](https://astrobiomike.github.io/unix/wild-redirectors)
- [Six glorious commands](https://astrobiomike.github.io/unix/six-glorious-commands)
- [Variables and for loops](https://astrobiomike.github.io/unix/for-loops)
- [A short introduction to R](https://astrobiomike.github.io/R/basics)
- after being logged into our servers, we need to run this to activate the appropriate environment:
- `conda activate r_dada2`
- if error:
- `conda init bash`
- `source ~/.bashrc`

- then we want to run this to establish a connection between the server RStudio and our browsers:
- `rstudio-server-wrapper.sh`
- This will should print a link to our terminal that we can go to in our browser to access our RStudio environment :+1:
- [16S amplicon processing](https://hackmd.io/@astrobiomike/2022-geobio-16S-processing-tutorial)
- [16S amplicon analysis](https://hackmd.io/@astrobiomike/2022-geobio-16S-analysis-tutorial)