BioJulia Package: Bio.jl



Bioinformatics and Computational Biology Infrastructure for Julia

As the flagship package of the BioJulia organisation, Bio.jl provides core julia modules containing efficient data types and algorithms, that most bioinformaticians and biologists would want to use for analyses or for building their own applications. Bio.jl is open source and the source codes are immediately available to the public.

Bio.jl provides programmable components for quick prototyping of new analyses and algorithms. These components are carefully tuned to achieve the best performance without sacrificing the usability of the dynamic programming language. The following modules are currently part of the package and actively developed as submodules:

  • Bio.Seq: Biological sequences
  • Bio.Align: Sequence alignment
  • Bio.Intervals: Genomic intervals and annotations
  • Bio.Structure: Molecular structures
  • Bio.Var: Biological variation
  • Bio.Phylo: Phylogenetics


I think BioJulia needs to be renamed to JuliaBio

See concerns here:
where BioJulia is the only org listed that does not start with Julia


Whilst in principle this could be done, and I’m willing to do this in principle if I absolutely have to, I have reservations I’d like answers to first before I’d consider it:

Whilst other julia orgs start with the name julia, and therefore someone in the julia community may say it bugs them and objectively on the criteria of consistency it should be renamed, it is only consistent from the point of view of someone inside the julia community.
As a biologist, the vast majority of biology projects in other languages begin with ‘Bio’. BioPerl, BioPython Bio++, BioRuby, BioJava, BioJS, BioSwift, BioDocker, BioLinux. In-fact the only project I know of that breaks that convention is rust-bio.

So as a biologist, who started BioJulia with other biologists with the intent of making computers and bioinformatics no longer suck for biologists that traditionally do not want to program, do I (we) say consistency with the other julia orgs is more important, or do I (we) say consistency with how projects are named in biology - biologists after all being the end users - is more important?

These reservations make me want to open it up to a vote at the very least before anything is done. But it’s been BioJulia for a long time, I’ve been promoting it at universities and academic institutes in England as BioJulia for a long time…


I prefer BioJulia. Not sure why organization names have to all start with Julia.


Very minor pedantic bikeshedding: The idea of a name change probably should have been started in the other topic the ‘BioJulia community - Main Thread’, as this was supposed to be about the development of the Bio.jl package specifically.


Good point, I wasn’t aware of the precedent in other languages. Feel free to delete the posts.