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UID:pretalx-scipy2025-PRSN9R@cfp.scipy.org
DTSTART;TZID=PST:20250709T104500
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DESCRIPTION:The practice of data science in genomics and computational biol
 ogy is fraught with friction. This is largely due to a tight coupling of b
 ioinformatic tools to file input/output. While omic data is specialized an
 d the storage formats for high-throughput sequencing and related data are 
 often standardized\, the adoption of emerging open standards not tied to b
 ioinformatics can help better integrate bioinformatic workflows into the w
 ider data science\, visualization\, and AI/ML ecosystems. Here\, we presen
 t two bridge libraries as short vignettes for composable bioinformatics. F
 irst\, we present Anywidget\, an architecture and toolkit based on modern 
 web standards for sharing interactive widgets across all Jupyter-compatibl
 e runtimes\, including JupyterLab\, Google Colab\, VSCode\, and more. Seco
 nd\, we present Oxbow\, a Rust and Python-based adapter library that unifi
 es access to common genomic data formats by efficiently transforming queri
 es into Apache Arrow\, a standard in-memory columnar representation for ta
 bular data analytics. Together\, we demonstrate the composition of these l
 ibraries to build a custom connected genomic analysis and visualization en
 vironments. We propose that components such as these\, which leverage scie
 ntific domain-agnostic standards to unbundle specialized file manipulation
 \, analytics\, and web interactivity\, can serve as reusable building bloc
 ks for composing flexible genomic data analysis and machine learning workf
 lows as well as systems for exploratory data analysis and visualization.
DTSTAMP:20260607T110923Z
LOCATION:Room 317
SUMMARY:Accelerating Genomic Data Science and AI/ML with Composability - Tr
 evor Manz\, Nezar Abdennur
URL:https://cfp.scipy.org/scipy2025/talk/PRSN9R/
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