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Merge pull request #9 from BioJulia/dev
Comparisons, Julia/BioJulia installation sections + devcontainer
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| { | ||
| "features": { | ||
| "ghcr.io/julialang/devcontainer-features/julia:1": { | ||
| "channel": "lts" | ||
| } | ||
| }, | ||
| "customizations": { | ||
| "vscode": { | ||
| "extensions": [ | ||
| "julialang.language-julia", | ||
| "tamasfe.even-better-toml", | ||
| "eamodio.gitlens" | ||
| ] | ||
| } | ||
| }, | ||
| "onCreateCommand": "julia --project=docs -e 'using Pkg; Pkg.instantiate(); Pkg.precompile();'" | ||
| } | ||
|
|
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| @@ -1 +1,41 @@ | ||
| # [BioJava (Java)](@id biojava) | ||
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| - [BioJava](https://biojava.org/index.html) is a biological data processing library written in the Java programming language | ||
| - BioJava tooling is distributed via multiple classes within the same `org.biojava` package | ||
| - Launched in 2002 with six major releases covering more than 11 Java releases | ||
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| **A few equivalent applications between BioJulia and BioJava:** | ||
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| | Application | BioJulia packages | BioJava modules | | ||
| |:--------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------| | ||
| | Input/Output | [FASTX](https://biojulia.dev/FASTX.jl/stable/), [XAM](https://biojulia.dev/XAM.jl/stable/), [BigWig](https://biojulia.dev/BigWig.jl/dev/),... | `nbio.genome.io.fastq`, `nbio.ontology.obo`,... | | ||
| | Sequence alignment | [BioSequences](https://biojulia.dev/BioSequences.jl/stable/), [BioAlignments](https://biojulia.dev/BioAlignments.jl/stable/) | `nbio.sequence`, `nbio.alignment` | | ||
| | Macromolecular structures | [BioStructures](https://biojulia.dev/BioStructures.jl/stable/) | `nbio.structure` | | ||
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| **A few package/ecosystem equivalents between Julia and Java:** | ||
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| | Application | Julia | Java | | ||
| |:---------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------| | ||
| | Data manipulation/analysis | [DataFrames](https://dataframes.juliadata.org/stable/), [CSV](https://csv.juliadata.org/stable/), [Query](https://www.queryverse.org/Query.jl/stable/) | `Tablesaw` | | ||
| | Plotting/visualization | [Plots](https://docs.juliaplots.org/stable/), [Makie](https://docs.makie.org/stable/) | `JFreeChart`, `Jzy3d` | | ||
| | Statistical analysis | [Statistics](https://docs.julialang.org/en/v1/stdlib/Statistics/), [HypothesisTests](https://github.com/JuliaStats/HypothesisTests.jl) | `Statistics (Apache Commons)`, `NM Dev` | | ||
| | Machine learning | [Flux](https://fluxml.ai/Flux.jl/stable/), [SciML](https://sciml.ai/) | `Java-ML`, `Neuroph` | | ||
| | Numerical mathematics | [LinearAlgebra](https://docs.julialang.org/en/v1/stdlib/LinearAlgebra/) | `NM Dev` | | ||
| | Notebook/report generator | [IJulia](https://julialang.github.io/IJulia.jl/stable/), [Pluto](https://plutojl.org/) | `IJava` | | ||
| | Web applications | [Genie](https://genieframework.com/), [Franklin](https://franklinjl.org/) | `Grails`, `Javalin` | | ||
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| **A few notable differences between Julia and Java:** | ||
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| | Julia | Java | | ||
| |:-----------------------------------------------------------------------|:-----------------------------------------------------------------------------------------| | ||
| | High-level, general-purpose compiled language | High-level, object-oriented, two-step (compiled and interpreted) language | | ||
| | Expression-based (statements yield a value) | Statement-based (assignment as a statement) | | ||
| | Dynamically typed with multiple dispatch and optional type annotations | Statically typed with required type declarations | | ||
| | Built-in parallelism via threads, coroutines (Tasks) | Built-in parallelism via threads, streams, fibers (Project Loom) | | ||
| | Extensive metaprogramming (Lisp-like macros, homoiconicity,...) | Less extensive metaprogramming (reflection, annotations,...) | | ||
| | Included default package manager | No default package manager (dependency/build management tools include Maven, Gradle,...) | | ||
| | Single implementation available (JuliaLang) | Multiple implementations available (OpenJDK, GraalVM,...) | | ||
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| **To transition from Java to Julia:** | ||
| - Use [JavaCall.jl](https://juliainterop.github.io/JavaCall.jl/) to seamlessly integrate Java code into your Julia project | ||
| - See [Running External Programs](https://docs.julialang.org/en/v1/manual/running-external-programs/) in the Julia manual for running Java scripts or other programs from Julia |
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| # [BioPerl (Perl)](@id bioperl) | ||
| # [BioPerl (Perl5)](@id bioperl) | ||
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| - [BioPerl](https://bioperl.org/) represents an ecosystem of related molecular biology modules written in the Perl5 programming language | ||
| - Supported by the Open Bioinformatics Foundation and includes additional utilities and interfaces for common bioinformatics applications | ||
| - Launched in 2002 and has contributed to major scientific achievements including the Human Genome Project | ||
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| **A few equivalent application tools between BioJulia and BioPerl:** | ||
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| | Application | BioJulia packages | BioPerl modules/objects | | ||
| |:--------------------|:----------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------| | ||
| | Input/Output | [FASTX](https://biojulia.dev/FASTX.jl/stable/), [XAM](https://biojulia.dev/XAM.jl/stable/), [BigWig](https://biojulia.dev/BigWig.jl/dev/),... | `SeqIO` | | ||
| | Sequence alignment | [BioSequences](https://biojulia.dev/BioSequences.jl/stable/), [BioAlignments](https://biojulia.dev/BioAlignments.jl/stable/) | `AlignIO`, `SimpleAlign` | | ||
| | Data structures | [Kmers](https://biojulia.dev/Kmers.jl/stable/), [IntervalTrees](https://biojulia.dev/IntervalTrees.jl/stable/) | `Bio::Kmer`, `Bio::Tree` | | ||
| | Population Genetics | [PopGen](https://biojulia.dev/PopGen.jl/) | `PopGen` | | ||
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| **A few package/ecosystem equivalents between Julia and Perl5:** | ||
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| | Application | Julia | Perl5 | | ||
| |:---------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------| | ||
| | Data manipulation/analysis | [DataFrames](https://dataframes.juliadata.org/stable/), [CSV](https://csv.juliadata.org/stable/), [Query](https://www.queryverse.org/Query.jl/stable/) | `PDL`, `Text-CSV` | | ||
| | Plotting/visualization | [Plots](https://docs.juliaplots.org/stable/), [Gadfly](http://gadflyjl.org/stable/), [Makie](https://docs.makie.org/stable/) | `GDGraph`, `Chart-GGPlot` | | ||
| | Statistical analysis | [Statistics](https://docs.julialang.org/en/v1/stdlib/Statistics/), [HypothesisTests](https://github.com/JuliaStats/HypothesisTests.jl), [GLM](https://github.com/JuliaStats/GLM.jl) | `Statistics-Descriptive`, `PDL-Stats` | | ||
| | Numerical mathematics | [LinearAlgebra](https://docs.julialang.org/en/v1/stdlib/LinearAlgebra/), [Symbolics](https://symbolics.juliasymbolics.org/stable/) | `PDL-LinearAlgebra`, `Math-Symbolic` | | ||
| | Notebook/report generator | [IJulia](https://julialang.github.io/IJulia.jl/stable/), [Pluto](https://plutojl.org/) | `Devel-IPerl` | | ||
| | Web applications | [Genie](https://genieframework.com/), [Franklin](https://franklinjl.org/) | `Catalyst`, `Mojolicious` | | ||
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| **A few notable differences between Julia and Perl5:** | ||
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| | Julia | Perl5 | | ||
| |:-----------------------------------------------------------------------|:--------------------------------------------------------------------------------| | ||
| | High-level, general-purpose compiled language | High-level, general-purpose interpreted language | | ||
| | Dynamically typed with multiple dispatch and optional type annotations | Dynamically typed without type annotations support | | ||
| | Built-in parallelism via threads, coroutines (Tasks) | Parallelism via threads, external modules (`Coro`, `Parallel`,...) | | ||
| | Lisp-inspired metaprogramming (S-expressions, homoiconicity,...) | Macro-less metaprogramming capabilities (eval, symbol table manipulation,...) | | ||
| | Single language implementation (JuliaLang) | Family of related languages/implementations (Perl5, Perl6/Raku, ActivePerl,...) | | ||
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| **To transition from Perl5 to Julia:** | ||
| - Read the [Julia manual](https://docs.julialang.org/) for an in-depth look at its internals and features | ||
| - See [Running External Programs](https://docs.julialang.org/en/v1/manual/running-external-programs/) in the manual for running Perl scripts or other programs from Julia |
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