Week 1 - Lecture 1 - Course Intro

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## *Week 1*
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# Course Intro & Overview

### Jelmer Poelstra
### 2021/01/12

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## Today's objectives

.large[
- Get to know each other

- Get an overview of what we will cover in this course

- Get an overview of the course infrastructure
]

.large[
 
- *May start with the Unix shell if time allows*
]

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# Overview

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.pull-left[
### [Zoom practicalities](#zoom)
### [Introductions](#pers-intro)
### [Course overview](#overview)
### [Course topics](#topics)
]

.pull-right[
### [Course infrastructure](#infrastructure)
### [Homework](#homework)
### [This week](#this-week)
]

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name: zoom

## Zoom practicalities

- Be muted by default, but feel free to unmute yourself to ask questions.

- Questions can also be asked in chat.

- *[Show other Zoom icons.]*

- Having your camera turned on as much as possible is appreciated!

- "Screen real estate" &mdash; large/multiple monitors or multiple devices best.
  
- Be ready to share your screen.

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name: pers-intro

# Introductions

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## Introductions: Jelmer

.pull-left[
- Bioinformatician at MCIC in Wooster since June 2020

- Background in evolutionary genomics:
  
  - *PhD*: speciation genomics in crows, Uppsala, Sweden.
  
  - *Postdocs*: UNC Chapel Hill (cichlids) and Duke (mouse lemurs).

- In my free time, I watch birds.
]

.pull-right[

<img src=img/jelmer.jpg width="130%">

]

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## Introductions: Zach (TA)

.pull-left[
- Born and raised in pacific northwest rainforests.

- Earned a *BS* studying biology and fungal antimicrobials at Oregon
  State University.

- *PhD*: exploring how horizontal gene flow affects genome organization and
  charting the evolution and products of psilocybin genes and gene homologs.
  
- *At home*: gardening, developing software, cooking, and playing instruments.
]

.pull-right[

<img src=img/zach_inthefield.png width="100%">

]

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## Introductions: You!

- Name

- Lab and Department

- Research interests and/or current topics

- Something about you that is not work-related

---
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name: overview

# Course overview

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## The core goal of this course:

# Learning skills to do your research more reproducibly and efficiently

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## Course background: Reproducibility

- Two related ideas:
  
  1. Getting same results with an independent experiment (*replicable*)
  
  2. Getting same results given the same data (*reproducible*)

Our focus is on #2.

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## Course background: Reproducibility (cont.)

.large[
> *"The most basic principle for reproducible research is: Do everything via code."*
]

- Also important:

- Project organization and documentation (*week 2*)
  
  - *Sharing* data and code (*Github for code, week 3*)
  
  - *How* you code (*especially week 10 - Python, and 13 - Snakemake*)

- Another motivator: working reproducibly will benefit future you!

> *"Your closest collaborator is you six months ago, but you don’t reply to
> emails.”*

---

## Course background: Efficiency and automation

- Using code enables you to work efficiently and largely automatically &mdash;
  particularly useful when having to:
  
  - Do repetitive tasks
  
  - Recreate a figure or redo an analysis after adding a sample
  
  - Redo everything after uncovering a mistake in the first data processing
   step.

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name: topics

# Course topics

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.left[
### I: [The Unix shell & shell scripts](#shell)
### II: [Project organization and Markdown](#proj-org)
### III: [Version control](#git)
### IV: [Python](#python)
### V: [Automated workflow management](#snakemake)
]

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name: shell

## Course topics I: The Unix shell & shell scripts (Wk 1 & 4-6)

*Being able to work in the shell is a fundamental skill in
computational biology.*

- Week 1, (2,) 4, and 5: Working in the Unix shell.

- Week 6: Shell *scripting*.

- Week 7: Submitting shell scripts at OSC using *SLURM* directives.

---
name: proj-org

## Course topics II: Project organization and Markdown (Wk 2)

*Good project organization and documentation is a necessary starting point
for reproducible research.*

- Best practices for project organization, file naming, etc.,  
  and how to use the Unix shell for this.

- To document and report what we are doing: *Markdown*.

---
name: git

## Course topics III: Version control with Git and Github (Wk 3)

*Using version control, you can more effectively keep track of project
progress, collaborate, experiment, revisit earlier versions, and undo.*

- *Git* is the version control software we will use,  
  and *Github* is the website that hosts Git projects.

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name: python

## Course topics IV: Python (Wk 8-12)

*For data processing beyond what is best done in the shell, we need to use
a scripting language.*

- We'll use *Python*, which is very versatile and has a clear, human-readable
  syntax, making it relatively easy to learn.

- We'll also emphasize general programming concepts and best practices
  while working with Python.

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name: snakemake

## Course topics V: Automated workflow management (Wk 13)

*To be able to run an entire analysis pipeline with a single command,   
  and easily change and rerun parts of it, we need a workflow manager.*

- We'll use *Snakemake*, which uses Python syntax. With limited extra effort,
  this allows us to make big gains!

---

## Course topics & general expectations

- We will cover a pretty broad array of topics,
  so you should see this as an *Introduction* to most of these topics.

- To get the most out of this course...

- Read the readings and do the exercises.
  
  - Keep practicing and applying after the course!

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name: infrastructure

# Course infrastructure

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.pull-left[
### [CarmenCanvas website](#canvas)
### [Github website](#git-site)
### [MS Teams](#teams)
]

.pull-right[
### [OSC](#osc)
### [Github](#github)
]

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name: canvas

## Course Infrastructure: CarmenCanvas website

.center[
### https://osu.instructure.com/courses/94975
]

- **Announcements**: Primary mode of communication (notifications!)
  
- **Assignments**: Everything you should do has been made a type of "assignment"
  on CarmenCanvas.

- **Calendar**: Overview of all to-do's + sign up for office hours (**_show?_**).

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name: git-site

## Course infrastructure: Github website

.center[
### https://mcic-osu.github.io/pracs-sp21/
]

- Slide decks

- Most of the *exercises* and *assignments*  
  (but always linked from the CarmenCanvas site).

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name: teams

## Course infrastructure: MS Teams

**_Optional_**, for any course-related:

- Q&A

- Chat, sharing of tips & tricks and resources, etc.

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name: osc

## Course infrastructure: Ohio Supercomputer Center (OSC)

- **All of our work can be done at OSC, in a browser (!)**

- Including *VS Code* (our text editor) and *Jupyter Notebooks* (Python)

- Avoids local installs, different behavior for different OS's, etc.

.content-box-diy[
For *local installation*, see the optional assignment for this week.
]

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name: github

## Course infrastructure: Github

- You'll be submitting your **assignments** through Github.

- This will double as practice with version control and sharing of scripts.

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name: homework

# Homework

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.left[
### [Graded assignments](#graded)
### [Final project](#project)
### [Ungraded "assignments"](#ungraded)
]

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name: graded

## Homework: Graded assignments and final project

**Graded assignments** &ndash; three total for 10 points each, due on Tuesdays:
  
- I: Due in Week 4 (*Git and Markdown*)
  
- II: Due in Week 7 (*Shell scripting*)
  
- III: Due in Week 9/10 (*Python*)

**Final project** &ndash; Plan and implement a small computational project:

- I: *Proposal* (due week 11, 10 points)
  
  - II: *Draft* (due week 13, 10 points)
  
  - III: Lightning *presentations* on Zoom (week 15, 10 points)
  
  - IV: *Final submission* (due April 23, 20 points)

.content-box-info[
The final 20% of grade comes from in-class questions.
]

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## Homework: Ungraded "assignments"

- **Readings**, **Surveys**, **Setup** (installation etc.)

- **Exercises**

- Set of exercises for most weeks.
  
  - You don't need to hand them in,  
    but we may talk about them in class on Tuesday's.

--
 
  .content-box-diy[
  Zach is available for an *optional* group session to go through
  each week's exercises or assignment:  
  If you're interested Fill out
  [this Doodle poll](https://doodle.com/poll/6yh5sayqrahgykak)
  to set a time.
  ]

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name: this-week

# This week

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# Thoughts on CSB Chapter 0?

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## Rest of the week

- **Thursday's Zoom**: code-along of CSB Chapter 1

- **Homework**:
  
  - Readings: CSB Chapter 1
  
  - [Exercises: CSB Chapter 1](https://mcic-osu.github.io/pracs-sp21/w01_exercises.html)

- [Optional: Local software installation](https://osu.instructure.com/courses/94975/assignments/2002692?module_item_id=5406932)
  
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# Questions?

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