Perspective: Julia for Biologists

1. Examples

Speed: Example 1 - Single cell data and network inference

• Domain: Single cell data
• Methodology: Network inference
• Feature: Speed for vectorisable code
• Packages: InformationMeasures.jl

Speed: Example 2 - Dynamical systems and pharmacology

• Domain: Pharmacology
• Methodology: Dynamical systems
• Feature: Speed for non linear system code
• Packages: DifferentialEquations.jl

Abstraction: Example 1 - Structural bioinformatics

• Domain: Structural bioinformatics
• Methodology: Alignments, protein structure
• Feature: Package composability
• Packages: BioStructures.jl, BioSequences.jl, Bio3DViewer.jl, MetaGraphs.jl, LightGraphs.jl

Abstraction: Example 2 - Image processing in Julia

• Domain: Cell biology and neuroscience
• Methodology: Image processing
• Feature: Code reusablility and lazy operations
• Packages: JuliaImages suite

Metaprogramming: Example - Biochemical reaction networks

• Domain: Biochemistry
• Methodology: Dynamical systems
• Feature: Metaprogramming
• Packages: DifferentialEquations.jl, Catalyst.jl, GpABC.jl, Turing.jl

2. Links for learning more about Julia

General resources

• Official website with tutorial videos and notebooks: https://julialang.org and https://julialang.org/learning/notebooks
• Download and install Julia: https://julialang.org/downloads
• Julia Academy, for free courses by core Julia developers: https://juliaacademy.com
• The Julia Programming Language youtube channel: https://www.youtube.com/c/TheJuliaLanguage

Intermediate language features

• "Developing Julia Packages" tutorial by Chris Rackauckas: https://www.youtube.com/watch?v=QVmU29rCjaA
• "The Unreasonable Effectiveness of Multiple Dispatch" talk by Stefan Karpinski: https://www.youtube.com/watch?v=kc9HwsxE1OY
• Introduction to metaprogramming workshop by David Sanders: https://www.youtube.com/watch?v=2QLhw6LVaq0

Switching to Julia

• Using old R code in your new Julia project:https://juliainterop.github.io/RCall.jl/stable/gettingstarted/

Julia for biologists

• BioJulia organisation website for bioinformatics packages and discussion: https://biojulia.net
• Package searching on JuliaHub and Julia Observer: https://juliahub.com/ui/Packages and https://juliaobserver.com/categories/Biology
• "Julia for Bioinformatics and Computational Biology" talk by Ben Ward, note this talk is from 2016 and some of the details are out of date: https://www.youtube.com/watch?v=0aa3g1NrLBM
• "On the performance and design of BioSequences compared to the Seq language" blog post by Jakob Nybo Nissen and Ben J. Ward, which discusses some design tradeoffs and benchmarking in detail: https://biojulia.net/post/seq-lang

Community

• Discourse, the main discussion forum for the Julia community: https://discourse.julialang.org
• Slack, for quick and informal correspondence with a community of over 8,000 members: https://julialang.org/slack
• Zulip, similar to Slack with unlimited message history: https://julialang.zulipchat.com
• JuliaCon, the conference for all things Julia: https://juliacon.org
• Current diversity and inclusion initiatives: https://julialang.org/diversity/current