Common terms used in this tutorial.
A
- API (Application Programming Interface)
-
A way for programs to communicate with each other. Claude Code uses Anthropic’s API to access Claude.
- API Key
-
A secret code that authenticates your access to an API. Like a password for programs.
B
- Bash
-
A command-line shell used on Mac and Linux. Where you type terminal commands.
- BibTeX
-
A file format for storing bibliographic references, commonly used with LaTeX.
C
- CLI (Command Line Interface)
-
A text-based way to interact with your computer by typing commands.
- Claude Code
-
Anthropic’s terminal-based tool for interacting with Claude in a development environment.
- Conda
-
A package and environment manager, popular in data science and bioinformatics.
D
- DOI (Digital Object Identifier)
-
A permanent identifier for digital content, commonly used for academic papers.
E
- Environment Variable
-
A variable set in the operating system that programs can access. Used for configuration and secrets.
G
- Git
-
A version control system that tracks changes to files over time.
- GitHub
-
A website for hosting git repositories and collaborating on code.
- Glob
-
A pattern for matching file names (e.g.,
*.csv matches all CSV files).
H
- HPC (High-Performance Computing)
-
Computing clusters used for intensive computational tasks.
I
- IDE (Integrated Development Environment)
-
Software for writing code, like VS Code.
J
- JSON (JavaScript Object Notation)
-
A text format for storing structured data. Looks like:
{"key": "value"}.
L
- LaTeX
-
A document preparation system for high-quality typesetting, especially mathematical content.
- LLM (Large Language Model)
-
AI models trained on large amounts of text, like Claude.
M
- Markdown
-
A simple text formatting syntax.
**bold** becomes bold.
- MCP (Model Context Protocol)
-
A protocol for extending Claude Code with additional capabilities via plugins.
N
- Node.js
-
A JavaScript runtime. Required for Claude Code installation.
- npm (Node Package Manager)
-
A tool for installing JavaScript packages.
P
- PAT (Personal Access Token)
-
A secure token used instead of a password for Git authentication.
- PATH
-
An environment variable listing directories where the system looks for executable programs.
- pip
-
Python’s package installer.
- PubMed
-
A database of biomedical literature maintained by NCBI.
Q
- Quarto
-
A publishing system for creating documents, presentations, and websites from Markdown.
R
- Regex (Regular Expression)
-
A pattern for matching text. Example:
\d+ matches one or more digits.
- Repository (Repo)
-
A folder tracked by git, containing code and its history.
S
- Shell
-
A program that interprets commands. Bash and Zsh are common shells.
- SLURM
-
A job scheduler used on HPC clusters.
- SSH (Secure Shell)
-
A protocol for secure communication, commonly used for git and remote servers.
- Static Site
-
A website made of pre-built files (HTML, CSS, JS) without server-side processing.
T
- Terminal
-
An application for running command-line programs. Also called console or shell.
- Token
-
In AI context, a unit of text (roughly 4 characters). APIs charge by token usage.
V
- Virtual Environment (venv)
-
An isolated Python environment with its own packages.
- VS Code (Visual Studio Code)
-
A popular, free code editor made by Microsoft.
Y
- YAML
-
A human-readable data format. Often used for configuration files.
Common File Extensions
.py |
Python script |
.R |
R script |
.js |
JavaScript |
.md |
Markdown |
.qmd |
Quarto markdown |
.tex |
LaTeX document |
.bib |
BibTeX references |
.csv |
Comma-separated values |
.json |
JSON data |
.yaml/.yml |
YAML data |
.sh |
Shell script |
.ipynb |
Jupyter notebook |
Common Commands
cd |
Change directory |
ls |
List files |
pwd |
Print working directory |
mkdir |
Make directory |
cp |
Copy files |
mv |
Move/rename files |
rm |
Remove files |
git status |
Show git status |
git add |
Stage changes |
git commit |
Commit changes |
git push |
Push to remote |
pip install |
Install Python package |
conda activate |
Activate conda environment |