Summer Hangouts: Coby Viner
Speeding up science: GNU Parallel for bioinformatics and beyond
RDDSX space outside the Collaborative Classroom
Van Pelt-Dietrich Library
This session introduces GNU Parallel—the shell utility that can launch thousands of jobs simultaneously, harnessing every CPU core (or even multiple machines) with a single command.
We’ll start with the why and a one-command install, then walk through the core syntax—argument lists, replacement strings, streaming with –pipe, and positional parameters—using concise man-page examples. A quick tour of newer features—colour-coded live output, adaptive –delay auto, memory-aware suspension, and seamless SLURM/SSH execution—leads into a benchmark of real-world speed-ups.
To ground it all, we’ll close with a concrete genomics pipeline from my own work, showing how GNU Parallel transforms long, brittle for-loops into reproducible high-throughput workflows.
Learn More About Coby Viner, DDDI Postdoctoral Fellow
DDDI’s 2025 Summer Hangouts program offers students the opportunity to participate in informal, hands-on tutorials led by our postdoctoral research fellows. These tutorials are open to students from all backgrounds and skill levels and cover various data science methods and topics.
Our Hangouts series this year will explore machine learning, statistics, optimization, and generative AI for scientific discovery across fields. Hangouts will be held twice a week on Tuesdays and Thursdays, from June 10th through June 25th. A pizza lunch will be provided.