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Computer Science Tools for Biology/Ecology/Evolution

These topics are not exactly relevant to learn how to program, but they are definitely useful in day-to-day or occasional use of a computer in Biology/Ecology/Evolution.

• Topic: Linux/Bash/Zsh
• Topic: Text-processing
• Topic: Containers
• Topic(s): Python libraries
• Topic: Conda and python environments
• Topic: Snakemake
• Topic: HPC/Slurm/Cluster [support not yet ready]
• Topic: MBB Workflows
• Topic: Awk, a programming language
• LaTeX
  • Topic: Introduction to LaTeX
  • Topic: Tikz
• Topic: Inkscape
• Topic: Mathematica, an Introduction
• Topic: C++, Use and Dangers

Topic: Linux/Bash/Zsh

Prerequisites:

• There is a linux machine that you interact with or are about to interact with.

In scope:

• What is an OS: Windows, Unix, MacOs, Linux.. Step away from your hardware.
• The shell: interact with the OS. Sh, Bash, Zsh..
• Basic commands: ls, cd, echo, cat, mkdir, rm, less, etc.
• Your terminal should be comfy: make it your own:
  • Abuse shortcuts: <tab>, <c-r>, <c-u>..
  • Custom aliases.
  • Themes and sophisticated autocompletion: OhMyZsh/p10k.
  • Configuration files: be yourself at home, anywhere, .bashrc, .zshrc, source.
• How linux is organised: /home, /, /usr, /dev, /mnt, lsblk, /opt, etc.
• Ownership and permissions: the root user, su, sudo, chown, chmod, etc.
• Think before you type.
• The multiple command inputs:
  • Arguments.
  • Standard input (stdin).
  • Environment.
• The multiple command outputs:
  • Return code.
  • Standard outputs (stdout, stderr).
  • Border effects: (print, operations..).
• Redirections and piping: >, |, &>, >>, <<, tee, etc.
• Synchronicity and parallelism: &, sleep, etc.
• A programming language:
  • Variables and interpolations.
  • Branches and short-circuiting, &&, ||, () subshells.
  • Write a shell script.
  • Functions and arguments.
  • Loops.. but at this point maybe you need a better language?
• Important system environment variables: $PATH, $PWD, $LANG, etc.
• How the shell works and the meaning of which/type.

Topic: Text-processing

Prerequisites:

• You have already issued some commands in Linux / Bash / Zsh.
• You need perform simple operations on large or numerous text files.

In scope:

• Basic text-oriented commands: cat, head, tail, tac, etc.
• Regexes
  • Exert/learn with Regex101.
  • Matches, wildcards, alternates, repetitions..
  • Substitution, captures, greediness/lazyness.
  • The different regex flavours.
  • The limit of regexes: use a proper parser for more.
• Text-oriented programs:
  • grep/rg: find the needle in a haystack.
  • sed/perl: transform needles in a haystack.
  • awk/frawk: transform the haystack.

Topic: Containers

Prerequisites:

• You are familiar with the terminal.
• You are familiar with command-line tools.
• You are familiar how to install/compile programs on linux.
• It is sometimes a nightmare for you to get all the correct dependencies you need, their exact versions, the corresponding system libraries etc. for every given project.
• You are happy with your pipeline but you are not exactly sure how to best share it so it would work on a cluster / on another machine / on everyone else's machine.

In scope:

• Introducing containers, images, recipes.
• Introducing Docker/Podman.
• Introducing Singularity/Apptainer.
• Run your own container.
• Build your own image.
• Write your own recipe.

Topic(s): Python libraries

Prerequisites:

• Programming in Python language (topic 3).
• IDE topic.

In scope (either):

• numpy/scipy: scientific computing in python.
• pandas/polars: dataframe in python.
• matplotlib: plot graphics with python.
• pytorch: machine learning out-of-the-box.
• pathlib: manipulate filesystems with python.
• subprocess: run external commands with python.

Topic: Conda and python environments

Prerequisites (either):

• You have already become upset because of python/modules versions mismatches.
• You are not confident how to best distribute your python program.

In scope:

• Manage your various python environments.

Topic: Snakemake

Prerequisites (either):

• Your are confident running linux programs one after the other.
• You are having a hard time running your whole pipeline again and again.
• You are not confident how to best distribute your pipeline.

In scope:

• Automated your pipeline recipes with Snakemake.

Topic: HPC/Slurm/Cluster [support not yet ready]

Prerequisites:

• You are confident with basic Linux/bash.
• You are not confident how to submit jobs on a shared calculation cluster.

In scope:

• Interact with shared computing resources.

Topic: MBB Workflows

Prerequisites:

• <TODO>

In scope:

• Automate your pipelines with WAW/SubWAW.

Topic: Awk, a programming language

Prerequisites:

• You are confident running basic linux / bash commands.
• You want to learn more about awk.

In scope:

• Awk model of a text file.
• Structure of the awk script.
• Power and limitations.
• Regexes.

Resources:

• The reference.

LaTeX

Topic: Introduction to LaTeX

Prerequisites:

• You have written a LaTeX document.
• You want to learn about LaTeX.

In scope:

• Setup your machine.
• What is LaTeX, how to use it.
• Write/compile your first LaTeX document.
• Customize text typeset.
• Floating environments, counters and references.
• Bibliography.
• Create your own commands to factorize your doc.

Topic: Tikz

Prerequisites:

• You are confident writing/compiling basic LaTeX documents.

In scope:

• Draw pixel-perfect vector graphics with your keyboard.
• Program your graphics.

Resources:

• The manual.

Topic: Inkscape

In scope:

• Install Inkscape.
• What is inkscape, vector-graphics vs. bitmaps.
• Draw pixel-perfect vector graphics with your mouse.
• Sophisticated inkscape features.

Topic: Mathematica, an Introduction

Requirements:

• Paid licence.

In scope:

• Symbolic calculation with the computer.
• Documentation.
• Plots.
• Functional programming.
• Syntacting sugar.
• Manipulable graphics.
• Performances and Compilation.

Topic: C++, Use and Dangers

Requirements:

• You are fluent in another language, (like topic 5 or topic 6).
• You have understood that Rust is just as fast and powerful although much safer and modern.
• You need to dive into a legacy C++ project. (like, there is really no other option)

In scope:

• Introduction.
• Resources for learning.
• Variables, references and pointers.
• Language legacy pitfals:
  • Lexical quirks.
  • Implicit semantics.
  • Integral types.
  • Move semantics.
  • Lexical macros.
• Memory safety:
  • Undefined Behaviour (UB).
  • Resource Acquisision Is Initialization (RAII).
  • « There is more to a pointer than meets the eye » ^{[1] [2] [3].}
• Build with Cmake.
• Test with Catch2.

Resources:

• LearnCpp
• CppReference