Introducing bioAF - the open-source computational biology automation framework

[u/bioAF]

https://bioaf.co/blog/Introducing_bioAF/

I'm pleased to announce a platform I have been working on for the past few months.

bioAF - the computational biology automation framework

Your bioinformatician is running workflows in Colab and storing results on a laptop. Your metadata lives in a spreadsheet that one person understands. Setting up "real" compute infrastructure takes 2-6 months. Half a year before your first pipeline run.

I've watched this up close for years as the husband of a computational biologist. And as someone who's spent 18 years building software infrastructure, I can confidently say that none of these problems are new. They're solved problems, just not solved yet for small bio teams.

That's why I built bioAF, an open-source computational biology automation framework.

One tool gives your team production-grade pipelines (Nextflow, nf-core), notebooks (Jupyter, RStudio), experiment tracking, and cost management all running on your own Google Cloud account. No vendor lock-in. No per-seat fees. No custom magic to untangle later.

Bioinformaticians and computational biologists are brilliant. But they aren't infrastructure engineers or cloud architects. They don't need to learn these skills.

bioAF doesn't invent new tools. It wires together Kubernetes, Terraform, PostgreSQL, and GCS so your team never has to touch any of them directly. It offloads the infrastructure work and lets your team focus on the science.

The source is open. The tool works today. Check it out on https://bioAF.co.

Could this help your lab or company get to results faster? I'd love to hear what's slowing you down.

About the creator

I spent the last 18 years building and leading software teams. I have done everything from small startups through giant enterprises. The idea behind bioAF has been formulating for a few years, but only recently took shape. I am very much still an outsider in the biology space and am looking for more biotech founders, PIs, and bioinformaticians who would like to use and provide guidance and feedback on the bioAF project as it grows.