Really enjoyed presenting our genomics talk "Declare, don't parse" at #SciPy2026 with Conrad Bzura! tl; dr Problem #1: Genomics is coupled to file formats, not data Problem #2: Most genomic operations aren't even "genomic" Solution: Be composable! Slides here: abdenlab.org/scipy26

High-dimensional data is hard to understand. But is it truly cursed? To help you build better intuition for high-dimensional datasets, @lekschas.de and I developed dtour, a visualization tool for smoothly navigating through data projections.

23/ Check out this viewer by @nvictus.bsky.social to get a sense of how few cohesins make enhancer-promoter bridges 🤯 abdenlab.org/cohesin-brid...

Many of you may have received pessimism from me over the years about using Hi-C to predict distal regulatory effects, mired with paradoxical optimism that cohesin loop extrusion is key. Well, the theoretical story underlying my seemingly paradoxical rambling is finally ready to be told. 👇

Elphege Nora Lab at UCSF@elphegenoralab.bsky.social · 3mo ago

Why can't we explain enhancer action despite 2 decades of chromosome conformation technologies? 😬 Our new study spearheaded by Leonid Mirny's group points to a flaw in our assumptions, and to a solution from physical principles By @timothyfoldes.bsky.social 💻& @karissalhansen.bsky.social 🧪 🧵👇

I’m excited to be co-chairing the Biological & Medical Sciences track for the #SciPy2026 conference 🎉 in July, along with Aishwarya Chander and Jacqueline Valeri. www.scipy2026.scipy.org 🗓️Call for proposals is open! ***Submission deadline: Feb 25*** 🚀 Submit here 👉 pretalx.com/scipy-2026/cfp

SciPy 2026

scipy2026.scipy.org

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_...

Nezar Abdennur - Accelerating Genomic Data Science and AI/ML with Composability | SciPy 2025

YouTube video by SciPy

youtube.com

if interested in creating anywidgets of your own, our tutorial was finally shared to youtube: www.youtube.com/watch?v=frEo...

Abdennur, Lekschas, & Manz - Bring your __repr__’s to life with anywidget | SciPy 2024

YouTube video by SciPy

youtube.com

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.

trevor manz@manzt.sh · 12mo ago

if interested in creating anywidgets of your own, our tutorial was finally shared to youtube: www.youtube.com/watch?v=frEo...

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...

Joint decomposition of Hi-C maps reveals salient features of genome architecture across tissues and development

The spatial organization of chromosomes in the nucleus is fundamental to cellular processes. Contact frequency maps from Hi-C and related chromosome conformation capture assays are increasingly availa...

biorxiv.org

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...

GitHub - jmschrei/bpnet-lite: This repository hosts a minimal version of a Python API for BPNet.

This repository hosts a minimal version of a Python API for BPNet. - jmschrei/bpnet-lite

github.com

Jacob Schreiber@jmschreiber91.bsky.social · last yr.

Last week I released bpnet-lite v0.5.0. BPNet/ChromBPNet are powerful models for understanding regulatory genomics from @anshulkundaje.bsky.social's group, and now it's way easier to go from raw data to trained models and analysis + results in PyTorch Try it out with `pip install bpnet-lite`

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...

Year in Review

Code and composition in 2024

lifeinbytes.substack.com

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