Accelerating Genomic Data Science and AI/ML with Composability
The practice of data science in genomics and computational biology is fraught with friction. This is largely due to a tight coupling of bioinformatic tools to file input/output. While omic data is specialized and the storage formats for high-throughput sequencing and related data are often standardized, the adoption of emerging open standards not tied to bioinformatics can help better integrate bioinformatic workflows into the wider data science, visualization, and AI/ML ecosystems. Here, we present two bridge libraries as short vignettes for composable bioinformatics. First, we present Anywidget, an architecture and toolkit based on modern web standards for sharing interactive widgets across all Jupyter-compatible runtimes, including JupyterLab, Google Colab, VSCode, and more. Second, we present Oxbow, a Rust and Python-based adapter library that unifies access to common genomic data formats by efficiently transforming queries into Apache Arrow, a standard in-memory columnar representation for tabular data analytics. Together, we demonstrate the composition of these libraries to build a custom connected genomic analysis and visualization environments. We propose that components such as these, which leverage scientific domain-agnostic standards to unbundle specialized file manipulation, analytics, and web interactivity, can serve as reusable building blocks for composing flexible genomic data analysis and machine learning workflows as well as systems for exploratory data analysis and visualization.
