Lecture 2: Computing Basics

Brian J. Smith

2026-01-20

Computing Basics

Basic Computer Operations

flowchart LR
 subgraph B["Process"]
        RAM["RAM"]
        CPU["CPU"]
        HDD["HDD"]
  end
    CPU <--> RAM & HDD
    A["Inputs"] --> B
    B --> C["Outputs"]
    
Figure 1: A very simplified diagram of a computer.

What’s the difference between Random Access Memory (RAM) and a hard disk drive (HDD)?

Operating Systems

What does an operating system do?

What are some example operating systems?

Operating Systems

  • Windows
  • Unix-like
    • macOS
    • (iOS)
    • Linux
    • (Android)

Operating Systems

Windows Unix
CLI cmd.exe bash
Directory separator \ /
Root directory C:\ ~/

File Structure

  • Hierarchical databases

Example file structure

File structure

  • Absolute vs. relative paths

What’s the difference between an absolute and relative path?

When should you use each one?

File structure

Absolute path:

C:/Users/bsmith/Teaching/UI 2026-01 Spring/BCB5200/BCB5200_Website/lectures/01_intro.qmd

Relative path:

./lectures/01_intro.qmd

File structure

Relative paths

. points to the current directory

.. points to the parent directory

File structure

|---C:/
|---|---Users/
|---|---|---bsmith/
|---|---|---|---Documents/
|---|---|---|---|---Website/
|---|---|---|---|---|---index.html
|---|---|---|---|---|---img/
|---|---|---|---|---|---|---img1.png
|---|---|---|---|---|---|---img2.png
|---|---|---|---Pictures/
|---|---|---|---|---img3.png

From index.html:

  • How do I get to img1?
    • C:/Users/bsmith/Documents/Website/img/img1.png
    • img/img1.png
    • ./img/img1.png

File structure

|---C:/
|---|---Users/
|---|---|---bsmith/
|---|---|---|---Documents/
|---|---|---|---|---Website/
|---|---|---|---|---|---index.html
|---|---|---|---|---|---img/
|---|---|---|---|---|---|---img1.png
|---|---|---|---|---|---|---img2.png
|---|---|---|---Pictures/
|---|---|---|---|---img3.png

From index.html:

  • How do I get to img2?
    • img/img2.png

File structure

|---C:/
|---|---Users/
|---|---|---bsmith/
|---|---|---|---Documents/
|---|---|---|---|---Website/
|---|---|---|---|---|---index.html
|---|---|---|---|---|---img/
|---|---|---|---|---|---|---img1.png
|---|---|---|---|---|---|---img2.png
|---|---|---|---Pictures/
|---|---|---|---|---img3.png

From index.html:

  • How do I get to img3?
    • ../../Pictures/img3.png
    • C:/Users/bsmith/Pictures/img3.png

RStudio Projects

RStudio Project Example

“There are only two hard things in computer science: cache invalidation and naming things.”

— Phil Karlton (Netscape)

git and GitHub

  • git is version control software git Logo 

git Screenshot

git and GitHub

  • GitHub is a platform for git repositories GitHub Logo 

GitHub Screenshot

Software Setup

Installing software

  • R
  • RStudio
  • git

RStudio Setup

RStudio ‘Tools’ Menu

RStudio Setup

RStudio ‘Global Options’

RStudio Setup

RStudio ‘Workspace’ Settings

I highly recommend that you setup your workspace so that it does not automatically save/restore.

git Setup

Reproducible Data Science

Dr. Simona Picardi, CNR, University of Idaho

https://ecorepsci.github.io/reproducible-science/version-control-git.html#configuring-git

Questions?



BCB5200 Home