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

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

Intermediate language features

Switching to Julia

Julia for biologists