In the genomics community, we have focused pretty heavily on achieving state-of-the-art predictive performance.

While undoubtedly important, how we *use* these models after training is potentially even more important.

tangermeme v1.0.0 is out now. Hope you find it useful!

My talk on #Composability in genomic software at #SciPy2025 is up on YouTube where I showcase both #anywidget and #oxbow.

Thank you to the organizers for the opportunity to present this to both computational biologists and the wider scientific computing community!

www.youtube.com/watch?v=G22_...

if interested in creating anywidgets of your own, our tutorial was finally shared to youtube:

www.youtube.com/watch?v=frEo...

Our #anywidget tutorial from last year's #SciPy conf was uploaded to youtube! Check it out for a hands-on walkthrough to create your own web-based widgets.

We're excited to share our new preprint, "Joint decomposition of Hi-C maps reveals salient features of genome architecture across tissues and development", led by Thomas Reimonn. www.biorxiv.org/content/10.1...

A huge challenge I face when doing ML + genomics analysis is *friction*: the stupid error messages (wrong device!) and dumb implementation issues that snap you out of the zone. I wrote a vignette on how tangermeme has helped me reduce this friction:

tangermeme.readthedocs.io/en/latest/ho...

(4) bpnet-lite: Load official Chrom/BPNet models into PyTorch for downstream tangermeme integration. Improved command-line tools + docs. Still concerns about perf of models trained from scratch -- will be resolved next version!

github.com/jmschrei/bpn...

bsky.app/profile/jmsc...

I'm proud to announce the latest release of 🧬 #Oxbow 🏹, with new features to make NGS data analysis more powerful, efficient, and "composable".

Learn more at: oxbow.readthedocs.io

A belated ode to 2024! lifeinbytes.substack.com/p/year-in-re...

It's @scipyconf.bsky.social submission time again! This year I am running the Bioinf/Comp Bio/Neuroscience track, covering how Python is advancing science and problem-solving in those fields. Let me know if y'all have questions, and looking forward to the submissions!

here’s a project i’ve been involved with trying to slurp up various file formats as apache arrow github.com/abdenlab/oxbow