JuliaCon 2026

Building modeling and analysis pipelines is a common task when doing molecular modeling and bioinformatics. However, keeping such pipelines reproducible and sharable is not an easy task. Thankfully, Julia's interoperability and reproducibility make it the best glue language for building such pipelines.
Julia allows us to have everything expressed in a single high-level programming language with performance that pairs that of low-level ones. But, while it solves the two-language problem, it is unlikely that advanced tools, fruit of years of research and development, will be translated to Julia. Therefore, to be able to build on the shoulders of giants and avoid reinventing the wheel, we need a language that can also run and manage outside tools, and Julia is such a language.
Julia's can easily interoperate with well-established languages in bioinformatics, such as Python and R, thanks to packages such as PythonCall, using CondaPkg to keep the Python environment reproducible, and RCall. But the Julia ecosystem also offers prebuilt, cross-platform native binaries for command-line tools through versioned JLL packages. That allows integrating such tools, possibly developed using languages such as C, C++, Fortran, or Rust, among others, into Julia workflows. Currently, many of the classical and more popular bioinformatics packages are available as JLL packages.
In this talk, I will present AlphaConformers, a Julia package for the modeling of protein alternative conformations. It takes advantage of Julia’s Pkg environments and already available JLL packages for common bioinformatics tools, such as FoldSeek and USalign. Therefore, we will showcase the power of Julia for the development of bioinformatics pipelines and workflows.