Perspective: Julia for Biologists

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Deep Learning Perspective_Julia_for_Biologists
Overview

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

Community

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Comments
  • Add `flood` demos & timing, README

    Add `flood` demos & timing, README

    This greatly expands the comparison between Python & Julia wrt abstraction in image processing. Via a new flood example, it demonstrates the limitations in available Python tools and the flexibility of simple Julia implementations.

    It also expands & increases consistency of timing measurements, and comes with a detailed README that should let readers replicate these results on their own machines.

    opened by timholy 0
  • Julia/Python comparisons using dask

    Julia/Python comparisons using dask

    For lazy array computation, the de facto champion of the Python ecosystem appears to be dask. While there's no doubt that it's an impressive package, it also effectively shows off Python's limitations.

    opened by timholy 0
Owner
Elisabeth Roesch
Researcher + Theoretical(ly) Biologist @MelbIntGen/@unimelb, Maschinenlehrerin, Bayesian statistics, Developmental biology.
Elisabeth Roesch
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