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Bio

Bioinformatics and Computational Biology Infrastructure for Julia

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Bio

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Description

BioJulia is a bioinformatics and computational biology infrastructure project, built with and for the julia language for technical computing.

This package Bio is the flagship package of the project. Bio is actually better described as a meta-package. It actually consolidates many other smaller packages in the BioJulia package ecosystem and makes them easier to install and use together, with less worry about version compatiblity and dependencies.

Bio has the current feature modules:

  • Bio.Seq: A biological sequences module (provided by BioSequences.jl)
    • Biological symbols (DNA, RNA and amino acid)
    • Biological sequences
    • Sequence search algorithms
    • Readers for FASTA, FASTQ and .2bit file formats
  • Bio.Align: Sequence alignment (provided by BioAlignments.jl)
    • Alignment data structures
    • Pairwise alignment algorithms
    • Reader for SAM and BAM file formats
  • Bio.Intervals: Genomic intervals and annotations (provided by GenomicFeatures.jl)
    • Genomic intervals with annotations
    • Readers for BED, bigWig, bigBed and GFF3 file formats
  • Bio.Structure: Molecular structures (provided by BioStructures.jl)
    • Macromolecular structures (e.g. proteins)
    • Reader for PDB file format
  • Bio.Var: Biological variation (provided by GeneticVariation.jl)
    • Mutation counting
    • Genetic and evolutionary distances
    • Readers for VCF and BCF file formats
  • Bio.Phylo: Phylogenetics (provided by Phylogenies.jl)
    • Phylogenetic trees
  • Bio.Services: APIs to other services (provided by BioServices.jl)
    • Entrez utilities (E-utilities)
  • Bio.Tools: A module for running command line tools (provided by BioTools.jl)
    • Run BLAST and parse its output

Installation

Install Bio from the Julia REPL:

using Pkg
add("Bio")
# Pkg.add("Bio") for julia prior to v0.7

If you are interested in the cutting edge of the development, please check out the master branch to try new features before release.

Testing

Bio is tested against Julia 0.6 and current 0.7-dev on Linux, OS X, and Windows.

Latest release Latest build status

Contributing

We appreciate contributions from users including reporting bugs, fixing issues, improving performance and adding new features.

Take a look at the CONTRIBUTING file provided with every BioJulia package package for detailed contributor and maintainer guidelines.

Financial contributions

We also welcome financial contributions in full transparency on our open collective. Anyone can file an expense. If the expense makes sense for the development of the community, it will be "merged" in the ledger of our open collective by the core contributors and the person who filed the expense will be reimbursed.

Backers & Sponsors

Thank you to all our backers and sponsors!

Love our work and community? Become a backer.

backers

Does your company use BioJulia? Help keep BioJulia feature rich and healthy by sponsoring the project Your logo will show up here with a link to your website.

Questions?

If you have a question about contributing or using BioJulia software, come on over and chat to us on Discord, or you can try the Bio category of the Julia discourse site.

First Commit

01/23/2014

Last Touched

4 days ago

Commits

762 commits