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lecture_lab07.qmd
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lecture_lab07.qmd
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---
title: "Lecture Lab 7"
author: "Leon Eyrich Jessen"
format:
revealjs:
embed-resources: true
theme: moon
slide-number: c/t
width: 1600
height: 900
mainfont: avenir
logo: images/r4bds_logo_small.png
footer: "R for Bio Data Science"
---
<!--# ---------------------------------------------------------------------- -->
<!--# SLIDE ---------------------------------------------------------------- -->
<!--# ---------------------------------------------------------------------- -->
## Collaborative Bio Data Science using GitHub via RStudio
- When doing assignments, you discovered that it was challenging to collaborate
- Collaboration is key to success, **also** when coding!
- You could:
- Write your code in a google doc and copy/paste
- Send code snippets in emails
- Use a whatsapp-group to exchange code
- ...?
<!--# ---------------------------------------------------------------------- -->
<!--# SLIDE ---------------------------------------------------------------- -->
<!--# ---------------------------------------------------------------------- -->
## Collaborative Bio Data Science using GitHub via RStudio
- When doing assignments, you discovered that it was challenging to collaborate
- Collaboration is key to success, **also** when coding!
- You could:
- Write your code in a google doc and copy/paste
- Send code snippets in emails
- Use a whatsapp-group to exchange code
- Stare at the same screen and come with 17 suggestions
- ...?
- All of which would be a recipe for inevitable disaster!
<!--# ---------------------------------------------------------------------- -->
<!--# SLIDE ---------------------------------------------------------------- -->
<!--# ---------------------------------------------------------------------- -->
## Collaborative Bio Data Science using GitHub via RStudio
- Of course there is a better way!
- We can use... git!
- Git is a distributed version control system
- It tracks versions of files
- "Git is a distributed version control system that tracks versions of files. It is often used to control source code by programmers who are developing software collaboratively." (Wiki definition)
<!--# ---------------------------------------------------------------------- -->
<!--# SLIDE ---------------------------------------------------------------- -->
<!--# ---------------------------------------------------------------------- -->
## Collaborative Bio Data Science using GitHub via RStudio
- Of course there is a better way!
- We can use... git!
- Git is a distributed version control system
- It tracks versions of files
- "Git is a distributed version control system that tracks versions of analyses. It is often used to control analysis code by bioinformaticians who are developing pipelines collaboratively." (R4BDS definition)
<!--# ---------------------------------------------------------------------- -->
<!--# SLIDE ---------------------------------------------------------------- -->
<!--# ---------------------------------------------------------------------- -->
## Collaborative Bio Data Science using GitHub via RStudio
- Bonus info: The brain child of... Linus Torvalds
- Tracking changes in the Linux kernel
<!--# ---------------------------------------------------------------------- -->
<!--# SLIDE ---------------------------------------------------------------- -->
<!--# ---------------------------------------------------------------------- -->
## Okay, so... Git versus GitHub
- Think along the lines of `R` versus `RStudio`, engine and interface
:::: {.columns}
::: {.column width="50%"}
{fig-align="center" width="80%"}
:::
::: {.column width="50%"}
{fig-align="center" width="80%"}
:::
::::
<!--# ---------------------------------------------------------------------- -->
<!--# SLIDE ---------------------------------------------------------------- -->
<!--# ---------------------------------------------------------------------- -->
## Okay, so... What does it "do"?
- If you share code in mails, chat groups, shared docs
- You have no way of tracking what happened when to what and how
- You may sit with some results and have no idea how they came about
- This is the absolute opposite of doing reproducible bio data science
<!--# ---------------------------------------------------------------------- -->
<!--# SLIDE ---------------------------------------------------------------- -->
<!--# ---------------------------------------------------------------------- -->
## Okay, so... What does it "do"?
- Git and github:
- helps you track the EXACT changes made in your analysis project
- enables multiple collaborators
- are industry standard in largely any company doing (Bio) Data Science
- facilitates teamwork increasing productivity
- Again: Spend time initially to save time in the long run
- Remember the talk from the first lab? Using git is absolute key to doing reproducible research
<!--# ---------------------------------------------------------------------- -->
<!--# SLIDE ---------------------------------------------------------------- -->
<!--# ---------------------------------------------------------------------- -->
## Okay, so... What does it "do"?
_...and perhaps nearer to you for now_
{fig-align="center"}
<!--# ---------------------------------------------------------------------- -->
<!--# SLIDE ---------------------------------------------------------------- -->
<!--# ---------------------------------------------------------------------- -->
## Okay, so... How does your team "do" it?
{fig-align="center" width=80%}
<!--# ---------------------------------------------------------------------- -->
<!--# SLIDE ---------------------------------------------------------------- -->
<!--# ---------------------------------------------------------------------- -->
## Branching, a way of developing in parallel
{fig-align="center" width=90%}
<!--# ---------------------------------------------------------------------- -->
<!--# SLIDE ---------------------------------------------------------------- -->
<!--# ---------------------------------------------------------------------- -->
## But really, the best thing is to...
<!--# ---------------------------------------------------------------------- -->
<!--# SLIDE ---------------------------------------------------------------- -->
<!--# ---------------------------------------------------------------------- -->
## But really, the best thing is to...
- Try it out for your self
- Break and then exercises
- TODAY FOLLOWING THE EXERCISES POINT-BY-POINT IS SUPERCALIFRAGILISTICEXPIALIDOCIOUS!!!