BioRuby (Ruby)

• BioRuby represents an ecosystem of related biology tools written in the Ruby programming language

• Unlike with BioJulia, BioRuby tools are installed together as classes/modules into a single bio gem

• Launched in 2000 with two major releases covering the Ruby1/2/3 transitions

• Primarily composed of wrapper classes/modules for common bioinformatics, molecular biology applications

A few similar applications between BioJulia and BioRuby:

Application	BioJulia packages	BioRuby classes/modules
Sequence alignment	BioSequences, BioAlignments	Bio::Sequence, Bio::Alignment
Input/Output	FASTX, XAM, BigWig, etc.	Bio::Fasta, Bio::Fastq, etc.

A few package/ecosystem equivalents between Julia and Ruby:

Application	Julia	Ruby
Data manipulation/analysis	DataFrames, CSV, Query	daru, CSV
Plotting/visualization	Plots, Makie, TidierPlots	Chartkick, gruff
Statistical analysis	Statistics, HypothesisTests, GLM, Distributions	Statsample, distribution
Machine learning	Flux, SciML	Rumale, TensorStream
Numerical mathematics	LinearAlgebra	NMatrix, minimization, integration
Notebook/report generator	IJulia, Pluto	IRuby
Web applications	Genie, Franklin	Hanami, Jekyll

A few notable differences between Julia and Ruby:

Julia	Ruby
High-level, general-purpose compiled language	High-level, general-purpose interpreted language
Dynamically typed with multiple dispatch and optional type annotations	Dynamically typed with optional type annotations (Sorbet, RBS)
Built-in parallelism via threads, coroutines (Tasks)	Built-in parallelism via threads, fibers
Lisp-like (homoiconic, macro-based) metaprogramming	Primarily runtime metaprogramming
Single implementation available (JuliaLang)	Multiple implementations available (TruffleRuby, mruby, etc.)

To transition from Ruby to Julia:

• Read the Julia manual for an in-depth look at its internals and features

• Consult the Running External Programs section in the manual for running Ruby scripts or other programs from Julia