iiinova — where your digital self keeps evolving

Reposted by Johannes Köster

Felix Wiegand @fxwiegand.bsky.social · 09/10/2026

The plot is highly customizable by choosing marks, aggregation, color and size mappings and can be directly exported to publication ready SVG files. We also support exporting the specs back into a datavzrd view for easy reproducibilty and more tweaking.

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Felix Wiegand @fxwiegand.bsky.social · 09/10/2026

Our tool #datavzrd has just received a new release adding on the fly scatter plot creation for any two columns of your dataset. @johanneskoester.bsky.social github.com/datavzrd/dat...

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Brent Pedersen @brent-p.bsky.social · 05/10/2026

We continue to improve bedder. It does interval intersections on VCF, BED, etc and lets users write python expressions on the intersection to drive output (including modifying VCF INFO fields). It will also use an index where possible to avoid extra parsing. Give it a go: github.com/quinlan-lab/...

github.com

Release Release v0.2.1 · quinlan-lab/bedder-rs

Changes in v0.2.1 Downloads bedder-static-linux-x86_64: Static binary for Linux x86_64 (no dependencies required) bedder-static-macos-x86_64-python3.13: macOS x86_64 binary built with Python 3.13 ...

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Reposted by Johannes Köster

Polars @pola.rs · 06/10/2026

We just released Polars 2.0. It removed many of our legacy decisions makes the streaming engine our default and promotes SQL to a first class citizen within Polars. pola.rs/posts/releas...

pola.rs

Release of Polars 2.0

DataFrames for the new era

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Johannes Köster @johanneskoester.bsky.social · 02/10/2026

I have just release #rust-bio 4.1.0 containing various bug fixes (e.g. for gap extensions in pairHMMs) and support for IUPAC codes in our homopolymer aware pair HMM flavor (homopolypairHMM).

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Reposted by Johannes Köster

Felix Wiegand @fxwiegand.bsky.social · 15/09/2026

Our portable alignment viewer #alignoth now supports working with remote BAM files similar to samtools. Simply update to version 1.11 via cargo, conda or pixi and you are good to go. github.com/alignoth/ali... #bioinformatics #genomics #rustlang @johanneskoester.bsky.social

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Reposted by Johannes Köster

Felix Wiegand @fxwiegand.bsky.social · 09/09/2026

#datavzrd config files now get autocomplete and inline validation right in your editor thanks to schemastore. Just name the file *.datavzrd.yaml and Zed, VS Code and most other IDEs should pick up the schema automatically. @johanneskoester.bsky.social

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Felix Wiegand @fxwiegand.bsky.social · 26/08/2026

New in #datavzrd v2.72.0: The suggest command can now draft your report config with any OpenAI compatible LLM endpoint. Describe what you want in plain language and it writes a validated config from your tables. datavzrd.github.io #bioinformatics @johanneskoester.bsky.social

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Reposted by Johannes Köster

Robert Aboukhalil @robert.bio · 11/08/2026

Datavzrd is an awesome tool that turns CSVs into shareable reports that can sort/filter/plot your data, made by @fxwiegand.bsky.social and @johanneskoester.bsky.social You can now run Datavzrd in the browser and rebuild the reports in real time as you edit the config: sandbox.bio/playgrounds/...

sandbox.bio

Interactive datavzrd playground

Playground for creating interactive reports from tabular data using datavzrd

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Johannes Köster @johanneskoester.bsky.social · 17/08/2026

We seek for an experienced bioinformatician to perform #Snakemake based reproducible multi omics data integration in order to decipher melanoma therapy resistance. The project is a DFG funded CRC and might be extended for up to 12 years. Details can be found here: karriere.ume.de/wp-content/u...

karriere.ume.de

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Stegle Lab @steglelab.bsky.social · 05/08/2026

Two weeks left to apply! We're recruiting a PhD student with @brianfclarke.bsky.social and @junyanlu.bsky.social through HIDSS4Health - see below for details. 👇 Looking forward to your application.

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Reposted by Johannes Köster

Rob Patro @robp.bsky.social · 29/07/2026

New preprint🚨(*long* time coming)! We introduce seqproc: an efficient, flexible, and concise tool for describing and transforming sequencing-read geometry. The aim: make complex protocols easy to specify & transform without giving up speed or accuracy. www.biorxiv.org/content/10.6... 🧵

Crop of the preprint's first page. The title is "seqproc: An
efficient, flexible, and concise tool for sequence geometry description and
transformation." Authors are Noah Cape, Elan Fisher, Daniel Liu, and Rob Patro.
The abstract introduces seqproc, EFGDL, and the antisequence execution engine.

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Reposted by Johannes Köster

Prefix.dev - the Pixi company @prefix.dev · 30/07/2026

Pixi v0.75.0 now ships with an --offline mode. Install your environments directly from the shared cache, even on the train or plane! 🛫 Find out more here: pixi.prefix.dev/latest/refe...

A terminal window displays the command "pixi update --offline," suggesting functionality for updating in offline mode.

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Reposted by Johannes Köster

Felix Wiegand @fxwiegand.bsky.social · 10/07/2026

We just released a new version of #alignoth that adds support for multiple bam tracks that will get vstacked. Also many convenience features suggested by @johanneskoester.bsky.social such as automatically creating an index for bam, fasta and vcf files if they dont exit. github.com/alignoth/ali...

github.com

GitHub - alignoth/alignoth: Creating alignment plots from bam files

Creating alignment plots from bam files. Contribute to alignoth/alignoth development by creating an account on GitHub.

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Reposted by Johannes Köster

Felix Wiegand @fxwiegand.bsky.social · 26/06/2026

Another new #datavzrd feature has been released in the form of toggling columns into a narrow view. This allows compressing very wide heatmap-heavy tables into an oncoprint like overview. Thanks for the feature suggestion @johanneskoester.bsky.social datavzrd.github.io

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Johannes Köster @johanneskoester.bsky.social · 15/06/2026

It is now possible to sponsor #snakemake development. Money will go to the Essen University Medicine Foundation and be used for hackathons, computational resources, and personnel: github.com/sponsors/sna...

github.com

Sponsor @snakemake on GitHub Sponsors

Support the development of Snakemake. The money will be used for hackathons, computational resources, and depending on the amount, also personnel.

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Johannes Köster @johanneskoester.bsky.social · 12/06/2026

#rustbio 4.0 has been released. It harmonizes the error handling, improves the API, makes gap-open/extend behavior in pairwise alignment more intuitive and in-line with the literature, improves GFF parsing, and allows incremental building of the rank-select datastructure. github.com/rust-bio/rus...

github.com

Release v4.0.0 · rust-bio/rust-bio

4.0.0 (2026-06-12) ⚠ BREAKING CHANGES Replace anyhow with typed thiserror errors (#674) Change Phase conversion methods to use TryFrom for better error handling (#625) for pairwise alignment, only...

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Johannes Köster @johanneskoester.bsky.social · 11/06/2026

#Snakemake 9.23 has been released. It adds the ability to use gh/gl shorthands for specifying source files (e.g. Snakefiles) from Github oder Gitlab repositories. In addition, source retrieval from Github/Gitlab has been optimized and further secured. snakemake.github.io

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Alexander Clarkson @aphclarkson.bsky.social · 11/06/2026

A trend to keep an eye on are efforts to develop pocket AIs that can run offline on a single laptop. They're not nearly as powerful as what OpenAI or Anthropic offer, but if free offline options do enough to satisfy normie users the entire business case for so many massive data centres falls apart

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Reposted by Johannes Köster

Felix Wiegand @fxwiegand.bsky.social · 11/06/2026

After some quite time #datavzrd finally got a new release with an updated binning algorithm ensuring interesting datapoints don’t get swallowed up by one bin. Working on more more features right now!

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Johannes Köster @johanneskoester.bsky.social · 01/06/2026

Another #Snakemake release (9.22.0). We have added a new default pathvar, new semantic helpers for choosing directories or files from alternatives, extended provenance information and Python 3.14 support. In addition various bugs have been fixed. snakemake.github.io

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Reposted by Johannes Köster

Stephen Turner @stephenturner.us · 01/06/2026

I'm going to try something next month. AI deskilling is real. I'm going a month without it. blog.stephenturner.us/p/ai-dry-july

blog.stephenturner.us

AI Dry July

AI deskilling is real. I'm going a month without it. 900 words, 4 minutes reading time.

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Reposted by Johannes Köster

Dr. Stephanie @punkrockscience.bsky.social · 01/06/2026

It’s amazing how quickly we lose fluency in languages we don’t use frequently. I think many coders are going to find out the hard way that we don’t call programming languages that just for convenience. All to say I like this idea and will likely try the same (outside existing build-AI-to projects.)

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Reposted by Johannes Köster

Igor Martayan @imartayan.bsky.social · 31/05/2026

Congrats to @leoackermann.bsky.social on winning RECOMB's best poster award for his work on compressing pairwise distance matrices! Check it out here: lacker.gitlab.io/pdf/research...

lacker.gitlab.io

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Reposted by Johannes Köster

Heng Li @lh3lh3.bsky.social · 30/05/2026

Jeremy Wang developed rammap, a minimap2 rewrite in Rust. It achieves comparable or better performance than minimap2 and produces identical output to minimap2. During rewrite, Jeremy found two long-existing bugs in minimap2 which are fixed in v2.31. www.biorxiv.org/content/10.6...

biorxiv.org

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Reposted by Johannes Köster

Travis Wheeler @wheelerlab.org · 31/05/2026

Introducing nail - a Rust implementation of profile HMM sequence alignment for proteins. Near-HMMER sensitivity, but a lot faster: www.biorxiv.org/content/10.1... github.com/TravisWheele...

biorxiv.org

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Johannes Köster @johanneskoester.bsky.social · 30/05/2026

#Snakemake 9.21.1 has been released with lots of bug fixes. In addition, we had several more releases in the past 2 months with improvements for between workflow caching, profile handling, and semantic helper functions. And there is more in the pipeline! snakemake.github.io

snakemake.github.io

Snakemake

072

Reposted by Johannes Köster

Rob Patro @robp.bsky.social · 30/05/2026

Yo; @lh3lh3.bsky.social is in on the AI-assisted RIIR. The future is, literally, now :). Can't wait to try this out!

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Reposted by Johannes Köster

Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 26/03/2026

RE: fediscience.org/@snakemake/11629556… This is a big step forward: The SLURM plugin for Snakemake now supports so-called job arrays. These are cluster jobs, with ~ equal resource requirements in terms of memory and compute resources. The change in itself was big: The purpose […]

fediscience.org

Original post on fediscience.org

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Reposted by Johannes Köster

Michael Hall @mbhall88.bsky.social · 24/03/2026

🐍 For all ye #snakemake users out there who want consistent, opinionated formatting of their workflows: we have just released v1.0.0 of snakefmt 🥳 The major update is that it now sorts rule directives (e.g., input, output, resources, params, shell etc.). See github.com/snakemake/sn... for more

github.com

GitHub - snakemake/snakefmt: The uncompromising Snakemake code formatter

The uncompromising Snakemake code formatter. Contribute to snakemake/snakefmt development by creating an account on GitHub.

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Reposted by Johannes Köster

Wytamma @wytamma.bsky.social · 15/03/2026

The modern #Snakemake architecture makes this fairly easy! I just wrote a wasm executor plugin and used the API to build the dag and run the workflow in pyodide. Massive credit to @johanneskoester.bsky.social and the core team for making Snakemake to interoperable.

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Reposted by Johannes Köster

Wytamma @wytamma.bsky.social · 14/03/2026

At the #SnakemakeHackathon2026 in Munich last week I complied Snakemake to #Wasm and made a client-side webapp for creating and sharing workflows -> snakemake.github.io/snakemake-wa.... It has support for python, R, and a 32bit linux environment all running in your browser ❤️ 🐍

snakemake.github.io

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Johannes Köster @johanneskoester.bsky.social · 13/03/2026

Today, the #SnakemakeHackathon2026 at the TU Munich ended with the release of Snakemake 9.17! I want to thank all participants and my co-organizers! You have been incredibly dedicated and we improved a ton of things throughout the ecosystem.

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Johannes Köster @johanneskoester.bsky.social · 11/03/2026

The third day of the #SnakemakeHackathon2026 at #TUM is about to end. We were very productive and I have merged over 20 pull requests that fix various bugs, clean up code, add new functionality and improvide user as well as developer experience. Thanks a lot to all the participants!

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Johannes Köster @johanneskoester.bsky.social · 29/01/2026

I've just released #rust-htslib 1.0. After a long time with a pretty stable API usage of rust-htslib in production, it feels like the right time to finally move to 1.0. Most important change is probably a switch to thread-safe pointers in BAM record handling. github.com/rust-bio/rus...

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Johannes Köster @johanneskoester.bsky.social · 29/01/2026

The new #Snakemake releases in the last weeks (9.14.*-9.16) have massively improved the way Snakemake handles source files from github (wrappers, modules, scripts, envs), avoiding the github API entirely and caching (bare) git repos instead. This increases performance and avoid hitting API limits.

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Reposted by Johannes Köster

Zamin Iqbal @zaminiqbal.bsky.social · 19/01/2026

Ah - a friend told me! Use -noai after your search term bsky.app/profile/zami...

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Johannes Köster @johanneskoester.bsky.social · 15/01/2026

We have released multiple new #Varlociraptor versions in the last weeks, providing various model improvements that further reduce false positives, improve the performance, and fix bugs with the log2fc operator of Varlcoriaptor's calling grammar. varlociraptor.github.io

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Reposted by Johannes Köster

Felix Wiegand @fxwiegand.bsky.social · 08/01/2026

🚀 Our new paper on Alignoth just published in Bioinformatics! Alignoth generates self-contained interactive HTML read alignment plots from BAM files – Rust-based, portable, and ideal for headless workflows. 📄 doi.org/10.1093/bioi... #bioinformatics #genomics #rust @johanneskoester.bsky.social

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Johannes Köster @johanneskoester.bsky.social · 28/11/2025

#Snakemake 9.14 is released. It integrates with yet another scripting language ( #hy, adding to the already existing #python, #r, #rust, #bash, and #julia support). Further it offers a massively improved local storage footprint. Many thanks to our awesome community! snakemake.github.io

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Felix Wiegand @fxwiegand.bsky.social · 23/11/2025

The official Datavzrd documentation now includes an AI (trained on docs, code and our paper) to answer all your questions: datavzrd.github.io/docs/index.h... Huge thanks to @gurubase.bsky.social for supporting Open-Source software and making this possible! @johanneskoester.bsky.social

datavzrd.github.io

Datavzrd: A low-code interactive reporting tool for tabular datasets | Datavzrd v2.61.10 documentation

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Felix Wiegand @fxwiegand.bsky.social · 13/11/2025

Check out our demo hosted on GitHub pages: alignoth.github.io/alignoth-exa... Props to my colleague Felix who worked with me on this over the last few weeks in the @johanneskoester.bsky.social lab.

alignoth.github.io

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Felix Wiegand @fxwiegand.bsky.social · 13/11/2025

We’ve added a new Snakemake meta-wrapper for creating standalone variant reports: 🔗 snakemake-wrappers.readthedocs.io/en/stable/me... It combines Datavzrd for an interactive overview table with Alignoth for read pileup plots — all linked together in one portable HTML report.

snakemake-wrappers.readthedocs.io

ALIGNOTH_REPORT | Snakemake wrappers

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Felix Wiegand @fxwiegand.bsky.social · 20/10/2025

Super happy to announce a major update of our portable and interactive alignment viewer #alignoth written in #rust. The new version provides improved highlighting of specific genomic sites or regions via VCF or BED inputs and also updates the coverage plot with variants! @johanneskoester.bsky.social

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Johannes Köster @johanneskoester.bsky.social · 19/10/2025

The #Snakemake wrapper repository and #Snakedeploy have received a major update: each wrapper now reports the latest version with changes, and #Snakedeploy can automatically upgrade all wrappers in your workflow to those versions. snakemake-wrappers.readthedocs.io

snakemake-wrappers.readthedocs.io

The Snakemake Wrappers repository | Snakemake wrappers

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Johannes Köster @johanneskoester.bsky.social · 19/10/2025

#Snakemake has a novel feature for generalizing rules and modules: pathvars! snakemake.readthedocs.io/en/stable/sn... Pathvars are particularly useful to make modules parameterizable and more generic. Further, they reduce boilerplate code commonly used for defining output folders.

snakemake.readthedocs.io

Snakefiles and Rules | Snakemake 9.13.3 documentation

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