Bio720/lectures/Welcome_BIO720.Rmd at master · DworkinLab/Bio720 · GitHub

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---
title: "WelcomeToBio720"
author: ""
date: "`r format(Sys.time(),'%d %b %Y')`"
output:
  slidy_presentation:
    keep_md: yes
    highlight: tango
    fig_retina: 1
  ioslides_presentation: default
editor_options:
  chunk_output_type: console
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

# Welcome to BIO720!

## Introductions
- Dr. Ian Dworkin
- Dr. Brian Golding
- All y'all


## Introduce yourself
- Name

- What are you studying? Are you new to McMaster?

- What skills do you hope to develop during this class?

## Why do we use (and need) computers for modern scientific research?

## Why do we use (and need) scientific computing skills for modern scientific research?


## Learning Objectives for the course
- develop fundamental computational skills necessary for modern biological research

- Open the door for you to develop your computational skills for your needs (genomics, bioinformatics, simulations, image analysis..)

- Organizing your research around principles of reproducibility

## What this course is not
- Genomic analysis course. Covered in BIO722.

- Bioinformatics class.

- A computer science course.

- A statistics course. BIO708.

## Course organization and assignments

- Weekly problem sets

- Dr. Brian Golding with be sending out an email on how these will be peer evaluated (yes, you are evaluating each other).

## Topics

- Reproducible Research, literate programming and science (ID)

- Introduction to practical computer programming for science, using R (ID)

- Introduction to the UNIX command line (shell) and remote computing (BG)

- Putting it all together (a few examples in bioinformatics, genomics and maybe image analysis?)

## Break

## What is reproducible research

## Literate programming

Literate programming just means combining the computer code with an explanation of what and how you are doing something in a natural language.

[The wikipedia page is pretty good for this](https://en.wikipedia.org/wiki/Literate_programming)

## R markdown

- Many ways of achieving this

- At least while working in R we will use R markdown via Rstudio.
    - R studio also has a newer approach, quatro, which is pretty similar.


## R markdown

Let's do a few examples.
- Combines code snippets (R, python, c++, bash) with a very simple markup language (called markdown) that is human readable, and can be rendered.


## link to github page for the class on this
[go here](https://github.com/DworkinLab/Bio720/blob/master/IntroductionMarkdownAndVersionControl/Bio720_IntroductionMarkdown.md)