BioJulia is a bioinformatics and computational biology infrastructure project, built with and for the julia language for technical computing.
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)
Bio.Align: Sequence alignment (provided by BioAlignments.jl)
Bio.Intervals: Genomic intervals and annotations (provided by GenomicFeatures.jl)
Bio.Structure: Molecular structures (provided by BioStructures.jl)
Bio.Var: Biological variation (provided by GeneticVariation.jl)
Bio.Phylo: Phylogenetics (provided by Phylogenies.jl)
Bio.Services: APIs to other services (provided by BioServices.jl)
Bio.Tools: A module for running command line tools (provided by BioTools.jl)
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.
Bio is a meta-package, and testing on CI infrastructure currently takes to long. Each Bio release is tested on desktop before release, but if you run into problems, please don't hesitate to contact a member of BioJulia.
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.
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.
Thank you to all our backers and sponsors!
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5 days ago